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1
Fuss, Franz Konstantin, Yehuda Weizman, and Adin Ming Tan. "The Difference in Wave Dynamics between SARS-CoV-2 Pre-Omicron and Omicron Variant Waves." COVID 3, no. 1 (2022): 28–50. http://dx.doi.org/10.3390/covid3010002.
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Compared to previous SARS-CoV-2 variants, the Omicron variant exhibited different epidemiological features. The purpose of this study was to assess the wave dynamics of pre-Omicron and Omicron waves in terms of differences and similarities. We investigated the COVID-19 waves since the beginning of the pandemic up to 28 August 2022, 1000 waves in total, as to their effectiveness for flattening the curve, calculated from the first and second time derivative of the daily case data. The average number of Omicron waves per month (42.78) was greater than the one of pre-Omicron waves per month (25.62). Omicron waves steepen and flatten the curve significantly faster, more effectively and with sharper peaks. Omicron waves generated more daily case data than pre-Omicron waves; the pre-Omicron trend showed increasing numbers over time, whereas the Omicron trend showed decreasing numbers. In denser populated countries, pre-Omicron waves were managed more effectively, in contrast to Omicron waves which were managed less effectively (but more effectively in less densely populated countries). This study provides the evidence for a different behaviour of Omicron waves in terms of wave dynamics, and thereby confirms that the Omicron variant is not only genetically different but even more so in terms of epidemiological dynamics.
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Shervani, Zameer, Nudrat Jamal, Umair Yaqub Qazi, et al. "Prevalence and Pathogenicity of Omicron Varian." European Journal of Medical and Health Sciences 4, no. 5 (2022): 125–32. http://dx.doi.org/10.24018/ejmed.2022.4.5.1511.
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The surge of the Omicron variant has been studied in overall India, Delhi and Mumbai. The increase in the percentage share of the Omicron strain in total registered cases resulted in a surge of daily new infections. The pathogenicity of Original, Delta, and Omicron variants has been compared using the data collected at the Max Healthcare network in India. The Omicron wave was the least severe of all three waves. The third Omicron wave did not cause much damage due to hybrid immunity generated in the population as a result of vaccination and previous SARS-CoV-2 infection. The low pathogenic nature of the Omicron virus is also the reason for the less severe illnesses the variant caused. Hospitalization during the Omicron wave was just 10% of the Delta wave. The percentage of patients who needed oxygen support was the least during the Omicron wave (23.4%) followed by the Original (63%) and the Delta variant (74%). The less severe nature of the Omicron wave gave the hope of recovering from the deadly devastating COVID-19 pandemic. The symptoms of “long COVID” patients have been compared during all three waves. Nearly the same number of the patients at 5.3% and 5.16% had health issues during Original and Omicron waves, respectively whereas during the Delta surge 5.9% of patients with “long COVID” had symptoms.
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Postans, Mark, Nicole Pacchiarini, Jiao Song, et al. "Evaluating the risk of SARS-CoV-2 reinfection with the Omicron or Delta variant in Wales, UK." PLOS ONE 19, no. 9 (2024): e0309645. http://dx.doi.org/10.1371/journal.pone.0309645.
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Recent studies suggest an increased risk of reinfection with the SARS-CoV-2 Omicron variant compared with previous variants, potentially due to an increased ability to escape immunity specific to older variants, high antigenic divergence of Omicron from earlier virus variants as well as its altered cell entry pathway. The present study sought to investigate epidemiological evidence for differential SARS-CoV-2 reinfection intervals and incidence rates for the Delta versus Omicron variants within Wales. Reinfections in Wales up to February 2022 were defined using genotyping and whole genome sequencing. The median inter-infection intervals for Delta and Omicron were 226 and 192 days, respectively. An incidence rate ratio of 2.17 for reinfection with Omicron compared to Delta was estimated using a conditional Poisson model, which accounted for several factors including sample collection date, age group, area of residence, vaccination and travel status. These findings are consistent with an increased risk of reinfection with the Omicron variant, and highlight the value of monitoring emerging variants that have the potential for causing further waves of cases.
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Kenney, Patrick O., Arthur J. Chang, Lorna Krabill, and Mark D. Hicar. "Decreased Clinical Severity of Pediatric Acute COVID-19 and MIS-C and Increase of Incidental Cases during the Omicron Wave in Comparison to the Delta Wave." Viruses 15, no. 1 (2023): 180. http://dx.doi.org/10.3390/v15010180.
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This study describes differences in clinical presentation in hospitalized children with acute COVID-19 and MIS-C between the Delta and Omicron (BA.1.1) waves in a tertiary children’s hospital. This retrospective cohort study with case adjudication of hospitalized children with SARS-CoV-2-positive testing or MIS-C diagnosis occurred during the Delta and Omicron waves, from August 2021 until February 2022. There were no differences noted by race, but both waves disproportionally affected black children (24% and 25%). Assigned by a three-person expert panel, incidental diagnoses were higher in the Omicron wave (34% versus 19%). Hospitalization rates of non-incidental cases were higher during Omicron (3.8 versus 5.9 per 1000 PCR-positive community cases). Respiratory-related admissions were prominent during Delta, while Omicron clinical presentations varied, including a high number of cases of croup and seizures. Length of stay and ICU use during Omicron was significantly less than Delta for MIS-C and acute cases. Estimation of vaccination efficacy for preventing hospital admissions was 85.1–91.7% in the early Omicron period. Our estimates suggest that a protective role for vaccination continues into the Omicron wave. The high rate of incidental cases during the Omicron wave should be considered when reviewing more cursory summative data sets. This study emphasizes the need for continued clinical suspicion of COVID-19 even when lower respiratory symptoms are not dominant.
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Shukla, Surabhi, and Peetam Singh. "A comparison of Delta and Omicron waves of COVID-19 pandemic: An observation from a tertiary care center from North India." Medicine India 2 (November 2, 2023): 16. http://dx.doi.org/10.25259/medindia_24_2023.
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Objectives: The impact of the Omicron variant (B.1.1.529) was very low as compared to the Delta variant (B.1.617.2) in North India. Very few studies are there highlighting the clinical parameters associated with disease outcomes among coronavirus disease-2019 (COVID-19) patients during the Delta and Omicron waves of the pandemic. This study was conducted to observe various clinical parameters associated with disease outcomes among COVID-19 patients during Delta and Omicron waves. Materials and Methods: This retrospective observational study was conducted during the Delta wave (March 2021 to June 2021) and Omicron wave (December 2021 to March 2022) on patients with positive reverse transcriptase–polymerase chain reaction (RT-PCR) admitted during the study period. The patient characteristics and outcome measures including demographic, baseline clinical, disease severity, intensive care unit admissions, and hospital mortality were recorded. Results: Out of total of 1731 patients who tested positive for severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) by RT-PCR, 16 patients were admitted during the omicron wave and 878 were admitted during the Delta wave. The majority of admitted patients during the Delta wave were in the age groups of 21–40 and 41–60 years, with significantly less number of admissions in the age group of <20 years during the Omicron wave. The admissions were significantly lower during the Omicron wave (P < 0.001). Patients without a previous history of COVID-19 and unvaccinated status were having significantly higher admissions (P < 0.001). During Delta and Omicron waves 71.4% and 18.75% of the patients, respectively, were having no comorbidities. Conclusion: Hospital admissions were higher during the Delta wave in comparison to the Omicron wave. During the Delta wave, the degree of severity and number of deaths were also very high.
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Savulescu, Camelia, Albert Prats-Uribe, Kim Brolin, et al. "Incidence of SARS-CoV-2 Infection Among European Healthcare Workers and Effectiveness of the First Booster COVID-19 Vaccine, VEBIS HCW Observational Cohort Study, May 2021–May 2023." Vaccines 12, no. 11 (2024): 1295. http://dx.doi.org/10.3390/vaccines12111295.
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Background: European countries have included healthcare workers (HCWs) among priority groups for COVID-19 vaccination. We established a multi-country hospital network to measure the SARS-CoV-2 incidence and effectiveness of COVID-19 vaccines among HCWs against laboratory-confirmed SARS-CoV-2 infection. Methods: HCWs from 19 hospitals in 10 countries participated in a dynamic prospective cohort study, providing samples for SARS-CoV-2 testing at enrolment and during weekly/fortnightly follow-up. We measured the incidence during pre-Delta (2 May–6 September 2021), Delta (7 September–14 December 2021), and Omicron (15 December 2021–2 May 2023) waves. Using Cox regression, we measured the relative vaccine effectiveness (rVE) of the first COVID-19 booster dose versus primary course alone during Delta and Omicron waves. Results: We included a total of 3015 HCWs. Participants were mostly female (2306; 79%), with a clinical role (2047; 68%), and had a median age of 44 years. The overall incidence of SARS-CoV-2 infection was 3.01/10,000 person-days during pre-Delta, 4.21/10,000 during Delta, and 23.20/10,000 during Omicron waves. rVE was 59% (95% CI: −25; 86) during Delta and 22% (1; 39) during Omicron waves. rVE was 51% (30; 65) 7–90 days after the first booster dose during the Omicron wave. Conclusions: The incidence of SARS-CoV-2 infection among HCWs was higher during the Omicron circulation period. The first COVID-19 vaccine booster provided additional protection against SARS-CoV-2 infection compared to primary course vaccination when recently vaccinated <90 days. This multi-country HCW cohort study addressing infection as the main outcome is crucial for informing public health interventions for HCWs.
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Lakman, I. A., D. F. Gareeva, L. F. Sadikova, et al. "Long-term mortality in different COVID-19 variants: 18-month follow-up." Russian Journal of Cardiology 28, no. 12 (2023): 5672. http://dx.doi.org/10.15829/1560-4071-2023-5672.
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The viral infection and pandemic of coronavirus infection 2019 (COVID-19) was characterized not only by high morbidity and in-hospital mortality, but also by an increase in the mortality of patients after hospital discharge. At the same time, differences were noted in hospitalization rate, the number of complications and mortality of patients, and mortality rate between different pandemic waves from 2020 to 2023.Aim. To compare the 18-month post-hospital mortality rate of patients between three COVID-19 variants (Alpha, Delta and Omicron).Material and methods. In this prospective, single-center, non-randomized continuous study, 2400 medical records of patients with the Alpha variant (2020), 1826 with the Delta variant (2021) and 997 with the Omicron variant (2022) were analyzed. The end point was all-cause mortality during the follow-up period.Results. There were following differences in clinical and demographic characteristics in the context of COVID-19 strains: more women were hospitalized in the Delta and Omicron waves; in the Omicron wave, patients were older. Also, comorbid patients were more common with the Delta and Omicron variants than with the Alpha (in chronic obstructive pulmonary disease, hypertension and heart failure), but chronic kidney disease was more common with the Alpha and Omicron variants. The groups differed significantly in mortality, with the maximum being with Delta and the minimum with Omicron, and the maximum mortality with Delta was observed in the first 90 days after discharge. Between 12 and 18 months, survival estimates decreased most for patients hospitalized in the Delta wave, which is determined by the risk of long-term cardiovascular consequences.Conclusion. Clinical and demographic differences between patients with different COVID-19 variants, as well as a significant difference in the mortality rate of patients of different waves, emphasize the importance of a personalized approach to treatment and long-term post-hospital monitoring.
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Newcomb, Ken, Shakir Bilal, and Edwin Michael. "Combining predictive models with future change scenarios can produce credible forecasts of COVID-19 futures." PLOS ONE 17, no. 11 (2022): e0277521. http://dx.doi.org/10.1371/journal.pone.0277521.
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The advent and distribution of vaccines against SARS-CoV-2 in late 2020 was thought to represent an effective means to control the ongoing COVID-19 pandemic. This optimistic expectation was dashed by the omicron waves that emerged over the winter of 2021/2020 even in countries that had managed to vaccinate a large fraction of their populations, raising questions about whether it is possible to use scientific knowledge along with predictive models to anticipate changes and design management measures for the pandemic. Here, we used an extended SEIR model for SARS-CoV-2 transmission sequentially calibrated to data on cases and interventions implemented in Florida until Sept. 24th 2021, and coupled to scenarios of plausible changes in key drivers of viral transmission, to evaluate the capacity of such a tool for exploring the future of the pandemic in the state. We show that while the introduction of vaccinations could have led to the permanent, albeit drawn-out, ending of the pandemic if immunity acts over the long-term, additional futures marked by complicated repeat waves of infection become possible if this immunity wanes over time. We demonstrate that the most recent omicron wave could have been predicted by this hybrid system, but only if timely information on the timing of variant emergence and its epidemiological features were made available. Simulations for the introduction of a new variant exhibiting higher transmissibility than omicron indicated that while this will result in repeat waves, forecasted peaks are unlikely to reach that observed for the omicron wave owing to levels of immunity established over time in the population. These results highlight that while limitations of models calibrated to past data for precisely forecasting the futures of epidemics must be recognized, insightful predictions of pandemic futures are still possible if uncertainties about changes in key drivers are captured appropriately through plausible scenarios.
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Kayali, Zeina, Gustavo Garcia, Karen Hamad, Wilhelmine Wiese-Rometsch, and Ke Ning. "Differential Host Response Contributing to Incidence of Arterial and Venous Thromboembolism at Index Hospitalization for Sars-Cov-2 Infection across Wuhan, Delta, Omicron and Omicron BA.x Variants." Blood 142, Supplement 1 (2023): 2654. http://dx.doi.org/10.1182/blood-2023-187791.
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Introduction SARS-CoV-2 induced coagulopathy has been associated with increased risk of arterial and venous thromboembolism. Literature demonstrates that incidence of thromboembolism has varied widely throughout the COVID-19 pandemic, with many reports preceding emergence of Delta and Omicron variants. This study aimed to characterize the incidence of arterial and venous thromboembolic events among patients hospitalized with acute SARS-CoV-2 infection during Wuhan, Delta, Omicron, or Omicron BA.x waves. To our knowledge, this study debuts variant specific analyses to shed some light on reported substantive differences pooled across SARS-CoV-2 variants regarding host response, clinical course, and outcomes. Intensity of pathophysiologic anomalies may have been associated with macro- and micro-circulatory clotting. Therefore, we hypothesized variant idiosyncratic host responses would be evoked and aimed to link our patient's demographics and comorbidity patterns with risk of thromboembolism. Methods This is a retrospective study including patients with laboratory confirmed SARS-CoV-2 infection who underwent index hospitalization during Wuhan (March 14, 2020- June 18, 2021), Delta (June 19, 2021- December 18, 2021), Omicron (December 19-March 30, 2022) or Omicron BA.x (March 31, 2022 - April 14, 2023) variant waves at an 820-bed academic public health trust hospital in Florida. Demographics, laboratory at presentation, ICD-10-CM-based comorbidity, SARS-CoV-2 directed treatment and administrative data were extracted under IRB exemption from electronic medical records. Generalized regression with adaptive LASSO identified variables associated with embolism in at least one variant wave controlling for extant dysrhythmia, chronic anticoagulation therapy, and COVID-19 directed treatment. Prespecified 2-way ANOVA examined interactions between intra- vs. inter-variant waves but was ruled out due to strong imbalances in variation. Thus, only within-variant contrasts were performed. Continuous data summarized with mean [±SD] were compared using an ANOVA test adjusting p-value for parametric vs. non-parametric distribution. Discrete data summarized as proportions were compared with chi-squared test. A p&lt;.05 was considered significant. Results We studied 6490 patients consecutively discharged across Wuhan (n=2249), Delta (n=1196), Omicron (n=953) and Omicron BA.x (n=2092) variants with respective embolic event(s) of 3%, 2%, 2%, and 4%. Table 1 summarizes demographics, anthropometric, comorbidities and laboratory biomarkers obtained within 24h of hospitalization across variants. Table 2 presents clinical course and outcomes. Discussion Incidence of embolic events was isomorphically distributed among waves tending to affect older males harboring hypertension, neurologic disease, and/or heart failure. D-dimer levels at presentation significantly distinguished risk of thromboembolism with Wuhan, Delta, or Omicron, but not Omicron BA.x variant infection. Indeed, Omicron BA.x infection was associated with numerically lower ICU visits, mechanical ventilation requirement, hospital LOS and mortality. Elevated D-dimer consistently has been associated with excess risk of progression to severe illness and mortality (Milenkovic M et al., 2022), mostly via pooled results across SARS-CoV variant waves. Some have suggested that D-dimer guided anticoagulation management improves outcomes in patients with COVID-19 (Ronderos Botero DM et al., 2023). Deeper phenotyping of patients infected with Omicron BA.x variants may reveal unique prothrombotic features driving what appears to be a less severe hypercoagulable state.
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Ali, Sobur, Marta Giovanetti, Catherine Johnston, Verónica Urdaneta-Páez, Taj Azarian, and Eleonora Cella. "From Emergence to Evolution: Dynamics of the SARS-CoV-2 Omicron Variant in Florida." Pathogens 13, no. 12 (2024): 1095. https://doi.org/10.3390/pathogens13121095.
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The continual evolution of SARS-CoV-2 has significantly influenced the global response to the COVID-19 pandemic, with the emergence of highly transmissible and immune-evasive variants posing persistent challenges. The Omicron variant, first identified in November 2021, rapidly replaced the Delta variant, becoming the predominant strain worldwide. In Florida, Omicron was first detected in December 2021, leading to an unprecedented surge in cases that surpassed all prior waves, despite extensive vaccination efforts. This study investigates the molecular evolution and transmission dynamics of the Omicron lineages during Florida’s Omicron waves, supported by a robust dataset of over 1000 sequenced genomes. Through phylogenetic and phylodynamic analyses, we capture the rapid diversification of the Omicron lineages, identifying significant importation events, predominantly from California, Texas, and New York, and exportation to North America, Europe, and South America. Variants such as BA.1, BA.2, BA.4, and BA.5 exhibited distinct transmission patterns, with BA.2 showing the ability to reinfect individuals previously infected with BA.1. Despite the high transmissibility and immune evasion of the Omicron sub-lineages, the plateauing of cases by late 2022 suggests increasing population immunity from prior infection and vaccination. Our findings underscore the importance of continuous genomic surveillance in identifying variant introductions, mapping transmission pathways, and guiding public health interventions to mitigate current and future pandemic risks.
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Tamrakar, Dipesh, Nishan Katuwal, Navin Adhikari, Surendra Kumar Madhup, Meghnath Dhimal, and Rajeev Shrestha. "Genomic analysis of SARS-CoV-2 Circulating during Second and Third Wave of COVID-19 in Nepal." Journal of Nepal Health Research Council 21, no. 1 (2023): 57–62. http://dx.doi.org/10.33314/jnhrc.v21i1.4489.
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Background: In Nepal, since the first detection of COVID-19 case in January 2020, the total cases have rose to almost a million with more than 12,000 deaths. Till now, WHO has classified 5 variants of SARS-Cov2 as variant of concerns at different time points causing many waves in different countries and regions at different time points. Nepal had also faced three distinct waves of COVID-19 caused by different variant of COVID 19. The objective of this study was to perform whole-genome sequencing of SARS-CoV-2 circulating in different waves of COVID-19 in Nepal and investigate its variant or lineage.Methods: In this study, samples from 49 SARS-CoV-2 infected subjects from May 2021 to January 2022, were investigated. The methodology followed RNA extraction, real-time PCR for confirmation and whole-genome sequencing. The consensus genomes were interpreted with appropriate bioinformatics tools and databases.Results: Sequence analysis of 49 genomes revealed to be of Delta (n=27) and Omicron Variant (n=22). The mutations in the consensus genomes contained the defining mutations of the respective lineages/variants. There were 20 genomes of Omicron sub-lineage BA.2, 1 of BA.1.1 and 1 of B.1.1.529.Conclusions: This study provides concise genomic evidence of presence of Delta and Omicron variant of COVID-19 in Nepal. Delta and Omicron variants were driving the second wave and the third wave of COVID-19 respectively in Nepal. Therefore, the genomic surveillance must be increased to clearly map out the pandemic and strategize vaccination approaches in the country.Keywords: COVID-19; delta, omicron; Nepal;SARS-CoV-2; whole-genome sequencing
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Tian, Dandan, Wenjian Nie, Yanhong Sun, and Qing Ye. "The Epidemiological Features of the SARS-CoV-2 Omicron Subvariant BA.5 and Its Evasion of the Neutralizing Activity of Vaccination and Prior Infection." Vaccines 10, no. 10 (2022): 1699. http://dx.doi.org/10.3390/vaccines10101699.
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From December 2021 to May 2022, the Omicron BA.1 and BA.2 subvariants successively became the most dominant strains in many countries around the world. Subsequently, Omicron subvariants have emerged, and Omicron has been classified into five main lineages, including BA.1, BA.2, BA.3, BA.4, BA.5, and some sublineages (BA.1.1, BA.2.12.1, BA.2.11, BA.2.75, BA.4.6, BA.5.1, and BA.5.2) . The recent emergence of several Omicron subvariants has generated new concerns about further escape from immunity induced by prior infection and vaccination and the creation of new COVID-19 waves globally. In particular, BA.5 (first found in southern Africa, February 2022) displays a higher transmissibility than other Omicron subvariants and is replacing the previously circulating BA.1 and BA.2 in several countries.
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Desheva, Yulia A., Tamara N. Shvedova, Olga S. Kopteva, et al. "The Clinical and Laboratory Landscape of COVID-19 During the Initial Period of the Pandemic and at the Beginning of the Omicron Era." Viruses 17, no. 4 (2025): 481. https://doi.org/10.3390/v17040481.
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Introduction: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underwent significant mutations, resulting in the Omicron variant. Methods: In this study, we analyzed blood samples from 98 patients with acute coronavirus disease 19 (COVID-19) hospitalized during the initial SARS-CoV-2 wave and the onset of Omicron in 2021. High-resolution melting (HRM) analysis of PCR products was used to analyze RNA extracted from clinical samples collected in July and November 2021 from patients infected with SARS-CoV-2. Results: HRM analysis revealed a characteristic deletion in the N protein RNA of the virus isolated in November 2021, associated with the Omicron variant. Elevated levels of inflammatory markers and interleukin-6 (IL-6) were observed in both waves of COVID-19. Complement levels and IgG and IgM antibodies to SARS-CoV-2 were detected more often during the second wave. An increase in hemagglutinin-inhibiting (HI) antibodies against influenza viruses was observed in paired blood specimens from moderate to severe COVID-19 patients during both outbreaks. Conclusions: Patients admitted during both waves of COVID-19 showed a significant rise in inflammatory markers, suggesting that Omicron triggers inflammatory responses. The rapid formation of IgM and IgG in Omicron may indicate a faster immune response. Seasonal flu may negatively impact the clinical course of coronavirus infections.
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Päll, Taavi, Aare Abroi, Radko Avi, et al. "SARS-CoV-2 clade dynamics and their associations with hospitalisations during the first two years of the COVID-19 pandemic." PLOS ONE 19, no. 5 (2024): e0303176. http://dx.doi.org/10.1371/journal.pone.0303176.
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Background The COVID-19 pandemic was characterised by rapid waves of disease, carried by the emergence of new and more infectious SARS-CoV-2 virus variants. How the pandemic unfolded in various locations during its first two years has yet to be sufficiently covered. To this end, here we are looking at the circulating SARS-CoV-2 variants, their diversity, and hospitalisation rates in Estonia in the period from March 2000 to March 2022. Methods We sequenced a total of 27,550 SARS-CoV-2 samples in Estonia between March 2020 and March 2022. High-quality sequences were genotyped and assigned to Nextstrain clades and Pango lineages. We used regression analysis to determine the dynamics of lineage diversity and the probability of clade-specific hospitalisation stratified by age and sex. Results We successfully sequenced a total of 25,375 SARS-CoV-2 genomes (or 92%), identifying 19 Nextstrain clades and 199 Pango lineages. In 2020 the most prevalent clades were 20B and 20A. The various subsequent waves of infection were driven by 20I (Alpha), 21J (Delta) and Omicron clades 21K and 21L. Lineage diversity via the Shannon index was at its highest during the Delta wave. About 3% of sequenced SARS-CoV-2 samples came from hospitalised individuals. Hospitalisation increased markedly with age in the over-forties, and was negligible in the under-forties. Vaccination decreased the odds of hospitalisation in over-forties. The effect of vaccination on hospitalisation rates was strongly dependent upon age but was clade-independent. People who were infected with Omicron clades had a lower hospitalisation likelihood in age groups of forty and over than was the case with pre-Omicron clades regardless of vaccination status. Conclusions COVID-19 disease waves in Estonia were driven by the Alpha, Delta, and Omicron clades. Omicron clades were associated with a substantially lower hospitalisation probability than pre-Omicron clades. The protective effect of vaccination in reducing hospitalisation likelihood was independent of the involved clade.
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Cheng, Daryl R., Silja Schrader, Alissa McMinn, et al. "Paediatric admissions with SARS-CoV-2 during the Delta and Omicron waves: an Australian single-centre retrospective study." BMJ Paediatrics Open 7, no. 1 (2023): e001874. http://dx.doi.org/10.1136/bmjpo-2023-001874.
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BackgroundThe clinical course of Australian children admitted to hospital with COVID-19 infection is not well understood, particularly over the Omicron period.MethodsThis study describes paediatric admissions to a single tertiary paediatric institution through the Delta and Omicron variant waves. All children admitted from 1 June 2021 to 30 September 2022 with a diagnosis of COVID-19 infection were included for analysis.Results117 patients were admitted during the Delta wave compared with 737 during the Omicron wave. The median length of stay was 3.3 days (IQR 1.7–6.75.1) during Delta, compared with 2.1 days (IQR 1.1–4.53.4) during Omicron (p<0.01). 83 patients (9.7%) required intensive care unit (ICU) admission, a greater proportion during Delta (20, 17.1%) than Omicron (63, 8.6%, p<0.01). Patients admitted to the ICU were less likely to have received a dose of COVID-19 vaccination prior to admission than patients admitted to the ward (8, 24.2% vs 154, 45.8%, p=0.028).ConclusionThe Omicron wave resulted in an absolute increase in the number of children compared with Delta, but cases had lower severity, demonstrated by shorter length of stay and a smaller proportion of patients requiring intensive care. This is consistent with US and UK data describing a similar pattern.
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Viana, Raquel, Sikhulile Moyo, Daniel G. Amoako, et al. "Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa." Nature 603, no. 7902 (2022): 679–86. http://dx.doi.org/10.1038/s41586-022-04411-y.
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AbstractThe SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, while the second and third waves were driven by the Beta (B.1.351) and Delta (B.1.617.2) variants, respectively1–3. In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron, B.1.1.529) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, which are predicted to influence antibody neutralization and spike function4. Here we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.
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Doll, Margaret K., Alpana Waghmare, Antje Heit, et al. "Acute and Postacute COVID-19 Outcomes Among Immunologically Naive Adults During Delta vs Omicron Waves." JAMA Network Open 6, no. 2 (2023): e231181. http://dx.doi.org/10.1001/jamanetworkopen.2023.1181.
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ImportanceThe US arrival of the Omicron variant led to a rapid increase in SARS-CoV-2 infections. While numerous studies report characteristics of Omicron infections among vaccinated individuals or persons with previous infection, comprehensive data describing infections among adults who are immunologically naive are lacking.ObjectivesTo examine COVID-19 acute and postacute clinical outcomes among a well-characterized cohort of unvaccinated and previously uninfected adults who contracted SARS-CoV-2 during the Omicron (BA.1/BA.2) surge, and to compare outcomes with infections that occurred during the Delta wave.Design, Setting, and ParticipantsThis prospective multisite cohort study included community-dwelling adults undergoing high-resolution symptom and virologic monitoring in 8 US states between June 2021 and September 2022. Unvaccinated adults aged 30 to less than 65 years without an immunological history of SARS-CoV-2 who were at high risk of infection were recruited. Participants were followed for up to 48 weeks, submitting regular COVID-19 symptom surveys and nasal swabs for SARS-CoV-2 polymerase chain reaction (PCR) testing. Data were analyzed from May to October 2022.ExposuresOmicron (BA.1/BA.2 lineages) vs Delta SARS-CoV-2 infection, defined as a positive PCR test result that occurred during a period when the variant represented at least 50% of circulating SARS-CoV-2 variants in the participant’s geographic region.Main Outcomes and Measure(s)The main outcomes examined were the prevalence and severity of acute (≤28 days after onset) and postacute (≥5 weeks after onset) symptoms.ResultsAmong 274 participants who were immunologically naive (mean [SD] age, 49 [9.7] years; 186 [68%] female; 19 [7%] Hispanic participants; 242 [88%] White participants), 166 (61%) contracted SARS-CoV-2. Of these, 137 infections (83%) occurred during the Omicron-predominant period and 29 infections (17%) occurred during the Delta-predominant period. Asymptomatic infections occurred among 7% (95% CI, 3%-12%) of Omicron-wave infections and 0% (95% CI, 0%-12%) of Delta-wave infections. Health care use among individuals with Omicron-wave infections was 79% (95% CI, 43%-92%) lower relative to individuals with Delta-wave infections (P = .001). Compared with individuals infected during the Delta wave, individuals infected during the Omicron wave also experienced a 56% (95% CI, 26%-74%, P = .004) relative reduction in the risk of postacute symptoms and a 79% (95% CI, 54%-91%, P &amp;lt; .001) relative reduction in the rate of postacute symptoms.Conclusions and RelevanceThese findings suggest that among adults who were previously immunologically naive, few Omicron-wave (BA.1/BA.2) and Delta-wave infections were asymptomatic. Compared with individuals with Delta-wave infections, individuals with Omicron-wave infections were less likely to seek health care and experience postacute symptoms.
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Elssaig, Elmutuz H., Tarig M. S. Alnour, Mohammad Fahad Ullah, and Eltayib H. Ahmed-Abakur. "Omicron SARS-CoV-2 Variants in an In Silico Genomic Comparison Study with the Original Wuhan Strain and WHO-Recognized Variants of Concern." Polish Journal of Microbiology 71, no. 4 (2022): 577–87. http://dx.doi.org/10.33073/pjm-2022-053.
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Abstract This study aimed to determine the genetic alterations in the Omicron variants compared to other variants of concern (VOCs) to trace the evolutionary genetics of the SARS-CoV-2 variants responsible for the multiple COVID-19 waves globally. The present study is an in silico analysis determining the evolution of selected 11 VOCs compared to the original Wuhan strain. The variants included six Omicrons and one variant of Alpha, Beta, Delta, Gamma, and Mu. The pairwise alignment with the local alignment search tool of NCBI Nucleotide-BLAST and NCBI Protein-BLAST were used to determine the nucleotide base changes and corresponding amino acid changes in proteins, respectively. The genomic analysis revealed 210 nucleotide changes; most of these changes (127/210, 60.5%) were non-synonymous mutations that occurred mainly in the S gene (52/127, 40.1%). The remaining 10.5% (22/210) and 1.9% (4/210) of the mutations were frameshift deletions and frameshift insertions, respectively. The frameshift insertion (Ins22194T T22195G) led to frameshift deletion (Δ211N). Only four mutations (C241T, C3037T, C14408T, and A23403G) were shared among all the VOCs. The nucleotide changes among Omicron variants resulted in 61 amino acid changes, while the nucleotide changes in other VOCs showed 11 amino acid changes. The present study showed that most mutations (38/61, 62.3%) among Omicron variants occurred in the S gene; and 34.2% of them (13/38) occurred in the receptor-binding domain. The present study confirmed that most of mutations developed by Omicron variants occurred in the vaccine target gene (S gene).
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Nikam, Chaitali, Wilson Suraweera, Sze Hang (Hana) Fu, Patrick E. Brown, Nico Nagelkerke, and Prabhat Jha. "PCR Test Positivity and Viral Loads during Three SARS-CoV-2 Viral Waves in Mumbai, India." Biomedicines 11, no. 7 (2023): 1939. http://dx.doi.org/10.3390/biomedicines11071939.
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SARS-CoV-2 polymerase chain reaction (PCR) tests generally report only binary (positive or negative) outcomes. Quantitative PCR tests can provide epidemiological information on viral transmission patterns in populations. SARS-CoV-2 transmission patterns during India’s SARS-CoV-2 viral waves remain largely undocumented. We analyzed 2.7 million real-time PCR testing records collected in Mumbai, a bellwether for other Indian cities. We used the inverse of cycle threshold (Ct) values to determine the community-level viral load. We quantified wave-specific differences by age, sex, and slum population density. Overall, PCR positivity was 3.4% during non-outbreak periods, rising to 23.2% and 42.8% during the original (June–November 2020) and Omicron waves (January 2022), respectively, but was a surprisingly low 9.9% during the Delta wave (March–June 2021; which had the largest increase in COVID deaths). The community-level median Ct values fell and rose ~7–14 days prior to PCR positivity rates. Viral loads were four-fold higher during the Delta and Omicron waves than during non-outbreak months. The Delta wave had high viral loads at older ages, in women, and in areas of higher slum density. During the Omicron wave, differences in viral load by sex and slum density had disappeared, but older adults continued to show a higher viral load. Mumbai’s viral waves had markedly high viral loads representing an early signal of the pandemic trajectory. Ct values are practicable monitoring tools.
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Walmsley, Sharon, Majid Nabipoor, Leif Erik Lovblom, et al. "Predictors of Breakthrough SARS-CoV-2 Infection after Vaccination." Vaccines 12, no. 1 (2023): 36. http://dx.doi.org/10.3390/vaccines12010036.
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The initial two-dose vaccine series and subsequent booster vaccine doses have been effective in modulating SARS-CoV-2 disease severity and death but do not completely prevent infection. The correlates of infection despite vaccination continue to be under investigation. In this prospective decentralized study (n = 1286) comparing antibody responses in an older- (≥70 years) to a younger-aged cohort (aged 30–50 years), we explored the correlates of breakthrough infection in 983 eligible subjects. Participants self-reported data on initial vaccine series, subsequent booster doses and COVID-19 infections in an online portal and provided self-collected dried blood spots for antibody testing by ELISA. Multivariable survival analysis explored the correlates of breakthrough infection. An association between higher antibody levels and protection from breakthrough infection observed during the Delta and Omicron BA.1/2 waves of infection no longer existed during the Omicron BA.4/5 wave. The older-aged cohort was less likely to have a breakthrough infection at all time-points. Receipt of an original/Omicron vaccine and the presence of hybrid immunity were associated with protection of infection during the later Omicron BA.4/5 and XBB waves. We were unable to determine a threshold antibody to define protection from infection or to guide vaccine booster schedules.
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Seyler, Lucie, Els Van Nedervelde, Diederik De Cock, et al. "Surfing the Waves: Differences in Hospitalised COVID-19 Patients across 4 Variant Waves in a Belgian University Hospital." Viruses 15, no. 3 (2023): 618. http://dx.doi.org/10.3390/v15030618.
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The unprecedented COVID-19 pandemic took the form of successive variant waves, spreading across the globe. We wanted to investigate any shift in hospitalised patients’ profiles throughout the pandemic. For this study, we used a registry that collected data automatically from electronic patient health records. We compared clinical data and severity scores, using the National Institute of Health (NIH) severity scores, from all patients admitted for COVID-19 during four SARS-CoV-2 variant waves. Our study concluded that patients hospitalised for COVID-19 showed very different profiles across the four variant waves in Belgium. Patients were younger during the Alpha and Delta waves and frailer during the Omicron period. ‘Critical’ patients according to the NIH criteria formed the largest fraction among the Alpha wave patients (47.7%), while ‘severe’ patients formed the largest fraction among Omicron patients (61.6%). We discussed host factors, vaccination status, and other confounders to put this into perspective. High-quality real-life data remain crucial to inform stakeholders and policymakers that shifts in patients’ clinical profiles have an impact on clinical practice.
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Rubi, Ghazala. "COVID-19 Waves with Associated Variants & Scenario in Pakistan." Open Access Journal of Pulmonary & Respiratory Sciences 7, no. 1 (2023): 1–12. http://dx.doi.org/10.23880/oajprs-16000155.
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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped RNA beta-coronavirus virus that is coronaviridae-related. It originated in Wuhan, China in December 2019 and is known to cause COVID-19 illness. SARS-CoV-2 posed a major threat to the world in concern of health along with trade and medical facilities. COVID-19 patients experience comorbid conditions like severe fever, typhoid, myocarditis, and a fatal black fungus attack. World Health Organization declared COVID-19 as an emergency on 30th January 2020 and a pandemic on 11th March. As of right now, COVID-19 has been verified to have infected over 100 million people across 210 nations, and 2 million of those infections have resulted in death. RT-qPCR (Reverse transcriptase qualitative PCR) test is performed if any symptoms exist, and isolation is necessary for three to five days after the confirmation. In Pakistan, it was reported firstly on 26th February 2020 by the Pakistan government when two persons were found infected with the disease. SARS-CoV-2 changes its genome constantly and results in the emergence of different variants in different waves. Pakistan has faced 6 sequential waves since 2020 to date, each associated with different variants and overlapping variants. The first wave was associated with B.1, B.1.471, B.1.36, second with B.1.36.31, B.1.247, B.1.1.1, B.1.160, B.1.471, B.1.562, B.1.1.7, B.1.1.250, B.1.261, B.1.351, P.1, third with B.1.1.7, B.1.351, P.1, B.1.617.2, B.1.36, B.1.468, B.1.1.413, A.27, fourth with P.1, B.1.617.2, fifth with Omicron (B.1.1.529) and sixth with new subvariants of Omicron (BA.4 & BA.5). In terms of severity and infectivity, Omicron and its subvariants differ from Delta and other SARS-CoV-2 variants. In this review, we have discussed SARS-CoV-2 spike mutations, its variants along with their origin & association to wave(s), and its scenario in Pakistan.
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Yu, Yangyang, Yuan Liu, Shi Zhao, and Daihai He. "A simple model to estimate the transmissibility of the Beta, Delta, and Omicron variants of SARS-COV-2 in South Africa." Mathematical Biosciences and Engineering 19, no. 10 (2022): 10361–73. http://dx.doi.org/10.3934/mbe.2022485.
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<abstract> <p>The COVID-19 pandemic caused multiple waves of mortality in South Africa, where three genetic variants of SARS-COV-2 and their ancestral strain dominated consecutively. State-of-the-art mathematical modeling approach was used to estimate the time-varying transmissibility of SARS-COV-2 and the relative transmissibility of Beta, Delta, and Omicron variants. The transmissibility of the three variants were about 73%, 87%, and 276% higher than their preceding variants. To the best of our knowledge, our model is the first simple model that can simulate multiple mortality waves and three variants' replacements in South Africa. The transmissibility of the Omicron variant is substantially higher than that of previous variants.</p> </abstract>
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Vogel, Gretchen. "New Omicron strains may portend big COVID-19 waves." Science 377, no. 6614 (2022): 1479. http://dx.doi.org/10.1126/science.adf0777.
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Dhama, Kuldeep, Deepak Chandran, Hitesh Chopra, et al. "SARS-CoV-2 emerging Omicron subvariants with a special focus on BF.7 and XBB.1.5 recently posing fears of rising cases amid ongoing COVID-19 pandemic." Journal of Experimental Biology and Agricultural Sciences 10, no. 6 (2022): 1215–21. http://dx.doi.org/10.18006/2022.10(6).1215.1221.
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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron versions have been the sole one circulating for quite some time. Subvariants BA.1, BA.2, BA.3, BA.4, and BA.5 of the Omicron emerged over time and through mutation, with BA.1 responsible for the most severe global pandemic between December 2021 and January 2022. Other Omicron subvariants such as BQ.1, BQ.1.1, BA.4.6, BF.7, BA.2.75.2, XBB.1 appeared recently and could cause a new wave of increased cases amid the ongoing COVID-19 pandemic. There is evidence that certain Omicron subvariants have increased transmissibility, extra spike mutations, and ability to overcome protective effects of COVID-19 neutralizing antibodies through immunological evasion. In recent months, the Omicron BF.7 subvariant has been in the news due to its spread in China and a small number of other countries, raising concerns about a possible rebound in COVID-19 cases. More recently, the Omicron XBB.1.5 subvariant has captured international attention due to an increase in cases in the United States. As a highly transmissible sublineage of Omicron BA.5, as well as having a shorter incubation time and the potential to reinfect or infect immune population, BF.7 has stronger infection ability. It appears that the regional immunological landscape is affected by the amount and timing of previous Omicron waves, as well as the COVID-19 vaccination coverage, which in turn determines whether the increased immune escape of BF.7 and XBB.1.5 subvariants is sufficient to drive new infection waves. Expanding our understanding of the transmission and efficacy of vaccines, immunotherapeutics, and antiviral drugs against newly emerging Omicron subvariants and lineages, as well as bolstering genomic facilities for tracking their spread and maintaining a constant vigilance, and shedding more light on their evolution and mutational events, would help in the development of effective mitigation strategies. Importantly, reducing the occurrence of mutations and recombination in the virus can be aided by bolstering One health approach and emphasizing its significance in combating zoonosis and reversal zoonosis linked with COVID-19. This article provides a brief overview on Omicron variant, its recently emerging lineages and subvairants with a special focus on BF.7 and XBB.1.5 as much more infectious and highly transmissible variations that may once again threaten a sharp increase in COVID-19 cases globally amid the currently ongoing pandemic, along with presenting salient mitigation measures.
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Jachman-Kapułka, Justyna, Aleksander Zińczuk, Wojciech Szymański, Krzysztof Simon, and Marta Rorat. "Complexity and Diversity of the Neurological Spectrum of SARS-CoV-2 over Three Waves of COVID-19." Journal of Clinical Medicine 13, no. 12 (2024): 3477. http://dx.doi.org/10.3390/jcm13123477.
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Background/Objectives: SARS-CoV-2 continually mutates, with five identified variants. Many neurological manifestations were observed during the COVID-19 pandemic, with differences between virus variants. The aim of this study is to assess the frequency and characteristics of neurological manifestations during COVID-19 in hospitalized patients over three waves in Poland with comparison and analysis correlation with the course of infection. Methods: This retrospective single-center study included 600 consecutive adults with confirmed COVID-19, hospitalized during 3 waves (pre-Delta, Delta and Omicron) in Poland. Demographic and clinical information and neurological manifestations were collected and compared across three periods. Results: The median age of the study group was 68, lower during the Delta wave. In the Omicron period, the disease severity at admission and inflammatory markers concentration were the lowest. Neurological manifestations were observed in 49%. The most common were altered mentation, headache, myalgia, mood disorder, ischemic stroke and encephalopathy. Smell and taste disturbances (STDs) were less frequent in the Omicron period. Neurological complications were predominant in the pre-Delta and Omicron periods. Ischemic stroke was observed more often in pre-Delta period. Altered mentation was related to higher severity at admission, worse lab test results, higher admission to ICU and mortality, while headache reduced mortality. Pre-existing dementia was related to higher mortality. Conclusions: Neurological manifestations of COVID-19 are frequent, with a lower rate of STDs in the Omicron period and more often cerebrovascular diseases in the pre-Delta period. Headache improves the course of COVID-19, while altered mentation, stroke and neurological comorbidities increase severity and mortality.
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Bingham, Jeremy, Stefano Tempia, Harry Moultrie, et al. "Estimating the time-varying reproduction number for COVID-19 in South Africa during the first four waves using multiple measures of incidence for public and private sectors across four waves." PLOS ONE 18, no. 9 (2023): e0287026. http://dx.doi.org/10.1371/journal.pone.0287026.
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Objectives The aim of this study was to quantify transmission trends in South Africa during the first four waves of the COVID-19 pandemic using estimates of the time-varying reproduction number (R) and to compare the robustness of R estimates based on three different data sources, and using data from public and private sector service providers. Methods R was estimated from March 2020 through April 2022, nationally and by province, based on time series of rt-PCR-confirmed cases, hospitalisations, and hospital-associated deaths, using a method that models daily incidence as a weighted sum of past incidence, as implemented in the R package EpiEstim. R was also estimated separately using public and private sector data. Results Nationally, the maximum case-based R following the introduction of lockdown measures was 1.55 (CI: 1.43–1.66), 1.56 (CI: 1.47–1.64), 1.46 (CI: 1.38–1.53) and 3.33 (CI: 2.84–3.97) during the first (Wuhan-Hu), second (Beta), third (Delta), and fourth (Omicron) waves, respectively. Estimates based on the three data sources (cases, hospitalisations, deaths) were generally similar during the first three waves, but higher during the fourth wave for case-based estimates. Public and private sector R estimates were generally similar except during the initial lockdowns and in case-based estimates during the fourth wave. Conclusion Agreement between R estimates using different data sources during the first three waves suggests that data from any of these sources could be used in the early stages of a future pandemic. The high R estimates for Omicron relative to earlier waves are interesting given a high level of exposure pre-Omicron. The agreement between public and private sector R estimates highlights that clients of the public and private sectors did not experience two separate epidemics, except perhaps to a limited extent during the strictest lockdowns in the first wave.
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Jombo, GTA. "Omicron Variant of Corona Virus' Covid-19 Pandemic Waves: Any Cause for Alarm?" West J Med & Biomed Sci 3, no. 1 (2022): xvii—xxi. https://doi.org/10.5281/zenodo.5905358.
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<strong>ABSTRACT</strong> This abstract looks at the present wave of Omicron B.1.1.529 variant of SARS-CoV-2 variant of concern (VOC) causing COVID-19 epidemic spikes across the world which was first reported in South Africa in November 2021. The viral variant has rapidly spread to all continents of the world and more than half of the countries of the world. So far while the virus is said to have a much higher transmissibility rate compared to the previous epidemic spikes caused by earlier variants, it is generally said to have a milder disease course and infects both the vaccinated and unvaccinated as well. Vaccines are said to prevent severe disease and hospitalizations in Omicron infections. If the generally milder clinical disease picture presented by Omicron continues and subsequent mutations all present a consistently milder clinical pictures, this might as well mark the beginning of the winding down of the present COVID-19 pandemic globally. Meanwhile both the non-pharmaceutical preventive measures and pharmaceutical ones (vaccines and drugs) should be sustained and intensified as we may not know the clinical disposition of the newer variants ahead.
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Nasir, Asghar, Uzma Bashir Aamir, Akbar Kanji, et al. "Tracking SARS-CoV-2 variants through pandemic waves using RT-PCR testing in low-resource settings." PLOS Global Public Health 3, no. 6 (2023): e0001896. http://dx.doi.org/10.1371/journal.pgph.0001896.
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COVID-19 resulted in extensive morbidity and mortality worldwide. SARS-CoV-2 evolved rapidly, with increasing transmission due to Variants of Concern (VOC). Identifying VOC became important but genome submissions from low-middle income countries (LMIC) remained low leading to gaps in genomic epidemiology. We demonstrate the use of a specific mutation RT-PCR based approach to identify VOC in SARS-CoV-2 positive samples through the pandemic in Pakistan. We selected 2150 SARS-CoV-2 PCR positive respiratory specimens tested between April 2021 and February 2022, at the Aga Khan University Hospital Clinical Laboratories, Karachi, Pakistan. Commercially available RT-PCR assays were used as required for mutations in Spike protein (N501Y, A570D, E484K, K417N, L452R, P681R and deletion69_70) to identify Alpha, Beta, Gamma, Delta, and Omicron variants respectively. Three pandemic waves associated with Alpha, Delta and Omicron occurred during the study period. Of the samples screened, VOC were identified in 81.7% of cases comprising mainly; Delta (37.2%), Alpha (29.8%) and Omicron (17.1%) variants. During 2021, Alpha variants were predominant in April and May; Beta and Gamma variants emerged in May and peaked in June; the Delta variant peaked in July and remained predominant until November. Omicron (BA.1) emerged in December 2021 and remained predominant until February 2022. The CT values of Alpha, Beta, Gamma and Delta were all significantly higher than that of Omicron variants (p<0.0001). We observed VOC through the pandemic waves using spike mutation specific RT-PCR assays. We show the spike mutation specific RT-PCR assay is a rapid, low-cost and adaptable for the identification of VOC as an adjunct approach to NGS to effectively inform the public health response. Further, by associating the VOC with CT values of its diagnostic PCR we gain information regarding the viral load of samples and therefore the level of transmission and disease severity in the population.
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Shervani, Zameer, Deepali Bhardwaj, Muhammad Jehanzeb Khan, et al. "COVID-19 Aftereffects (Long COVID) Associated with Wuhan, Delta, and Omicron Variants Reported in Japanese Hospitals." European Journal of Medical and Health Sciences 6, no. 2 (2024): 82–89. http://dx.doi.org/10.24018/ejmed.2024.6.2.1686.
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COVID-19 patients who visited hospitals in Japan reported aftereffects, also known as Long COVID or Post COVID symptoms. The studycompared the Long COVID symptoms caused by the original Wuhan, Delta, and Omicron variants. The analysis of COVID-19 lingering symptoms(Post COVID) conducted by researchers in Japan have been included. Symptoms may last from one month to one year, putting a strain on thehealth care system. According to a joint study done by Osaka University and Toyonaka City on patients mostly infected with Omicron, one in fivepatients experienced aftereffects one month after their recovery. The report indicated that the symptoms improved over time. A majority of the patients reported difficulties with their daily activities. About 14%of the patients experienced aftereffects even one year after being discharged from hospitals, according to data recorded during Delta and previous waves that were presented to the Japanese government. Patients hospitalized during the Delta and Wuhan waves for SARS-CoV-2 infection showed a 50% reduction in symptoms between three and six months, according to a longitudinal follow-up study of sequelae. According to a gender-wise study, symptoms improved more quickly in women than in men. Compared to older patients, younger patients recovered a little faster in the firsttwo months. Patients infected during the first four non-Delta waves recovered slower than those infected during the Omicron surge. Longitudinalstudies of persistent symptoms are needed to develop treatments and possibly the COVID-19-specific drugs.
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Keeton, Roanne, Marius B. Tincho, Amkele Ngomti, et al. "T cell responses to SARS-CoV-2 spike cross-recognize Omicron." Nature 603, no. 7901 (2022): 488–92. http://dx.doi.org/10.1038/s41586-022-04460-3.
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AbstractThe SARS-CoV-2 Omicron variant (B.1.1.529) has multiple spike protein mutations1,2 that contribute to viral escape from antibody neutralization3–6 and reduce vaccine protection from infection7,8. The extent to which other components of the adaptive response such as T cells may still target Omicron and contribute to protection from severe outcomes is unknown. Here we assessed the ability of T cells to react to Omicron spike protein in participants who were vaccinated with Ad26.CoV2.S or BNT162b2, or unvaccinated convalescent COVID-19 patients (n = 70). Between 70% and 80% of the CD4+ and CD8+ T cell response to spike was maintained across study groups. Moreover, the magnitude of Omicron cross-reactive T cells was similar for Beta (B.1.351) and Delta (B.1.617.2) variants, despite Omicron harbouring considerably more mutations. In patients who were hospitalized with Omicron infections (n = 19), there were comparable T cell responses to ancestral spike, nucleocapsid and membrane proteins to those in patients hospitalized in previous waves dominated by the ancestral, Beta or Delta variants (n = 49). Thus, despite extensive mutations and reduced susceptibility to neutralizing antibodies of Omicron, the majority of T cell responses induced by vaccination or infection cross-recognize the variant. It remains to be determined whether well-preserved T cell immunity to Omicron contributes to protection from severe COVID-19 and is linked to early clinical observations from South Africa and elsewhere9–12.
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González-Parra, Gilberto, and Abraham J. Arenas. "Mathematical Modeling of SARS-CoV-2 Omicron Wave under Vaccination Effects." Computation 11, no. 2 (2023): 36. http://dx.doi.org/10.3390/computation11020036.
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Over the course of the COVID-19 pandemic millions of deaths and hospitalizations have been reported. Different SARS-CoV-2 variants of concern have been recognized during this pandemic and some of these variants of concern have caused uncertainty and changes in the dynamics. The Omicron variant has caused a large amount of infected cases in the US and worldwide. The average number of deaths during the Omicron wave toll increased in comparison with previous SARS-CoV-2 waves. We studied the Omicron wave by using a highly nonlinear mathematical model for the COVID-19 pandemic. The novel model includes individuals who are vaccinated and asymptomatic, which influences the dynamics of SARS-CoV-2. Moreover, the model considers the waning of the immunity and efficacy of the vaccine against the Omicron strain. This study uses the facts that the Omicron strain has a higher transmissibility than the previous circulating SARS-CoV-2 strain but is less deadly. Preliminary studies have found that Omicron has a lower case fatality rate compared to previous circulating SARS-CoV-2 strains. The simulation results show that even if the Omicron strain is less deadly it might cause more deaths, hospitalizations and infections. We provide a variety of scenarios that help to obtain insight about the Omicron wave and its consequences. The proposed mathematical model, in conjunction with the simulations, provides an explanation for a large Omicron wave under various conditions related to vaccines and transmissibility. These results provide an awareness that new SARS-CoV-2 variants can cause more deaths even if their fatality rate is lower..
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Moros, Zoila C., José Luis Zambrano, Yoneira Sulbaran, et al. "Dissemination of the Omicron Variant and Its Sub-Lineages among Residents and Travelers in Its First Year of Emergence in Venezuela." Viruses 15, no. 7 (2023): 1460. http://dx.doi.org/10.3390/v15071460.
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The emergence of the SARS-CoV-2 Variant of Concern (VOC), Omicron, has been characterized by an explosive number of cases in almost every part of the world. The dissemination of different sub-lineages and recombinant genomes also led to several posterior waves in many countries. The circulation of this VOC and its major sub-lineages (BA.1 to BA.5) was monitored in community cases and in international travelers returning to Venezuela by a rapid partial sequencing method. The specific sub-lineage assignment was performed by complete genome sequencing. Epidemic waves of SARS-CoV-2 cases were observed among international travelers during 2022, a situation not seen before December 2021. The succession of the Omicron VOC sub-lineages BA.1 to BA.5 occurred sequentially, except for BA.3, which was almost not detected. However, the sub-lineages generally circulated two months earlier in international travelers than in community cases. The diversity of Omicron sub-lineages found in international travelers was related to the one found in the USA, consistent with the most frequent destination of international travel from Venezuela this year. These differences are compatible with the delay observed sometimes in Latin American countries in the circulation of the different lineages of the Omicron VOC. Once the sub-lineages were introduced in the country, community transmission was responsible for generating a characteristic distribution of them, with a predominance of sub-lineages not necessarily similar to the one observed in travelers or neighboring countries.
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Chia, Travis Ren Teen, Barnaby Edward Young, and Po Ying Chia. "The Omicron-transformer: Rise of the subvariants in the age of vaccines." Annals of the Academy of Medicine, Singapore 51, no. 11 (2022): 712–29. http://dx.doi.org/10.47102/annals-acadmedsg.2022294.
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Introduction: Omicron is the latest SARS-CoV-2 variant of concern, the pathogen that causes COVID-19. Since its emergence in late 2021, Omicron has displaced other circulating variants and caused successive waves of infection worldwide throughout 2022. Omicron is characterised by the rapid emergence of many subvariants and high rates of infection in people with vaccine- and/or infection-induced immunity. This review article will consolidate current knowledge regarding Omicron subvariants, the role of boosters, and future vaccine development. Method: This narrative review is based on a literature search using PubMed. Search terms related to Omicron were used and priority was given to published peer-reviewed articles over pre-prints. Results: Studies indicate that vaccinations and boosters are important to reduce disease severity, hospitalisation and death from Omicron. A variety of factors, such as differing host factors, circulating variants, and forces of infection, can influence the benefit of repeated booster administration. Next-generation bivalent vaccines have now been approved in some countries including Singapore and have demonstrated the ability to induce broad variant protection. Future third-generation vaccines involving mucosal vaccines and/or pan-sarbecovirus vaccines may provide broader and longer-lasting protection. Conclusion: Due to current high levels of vaccine- and infection-induced immunity, it is likely that rates of severe illness, hospitalisation, and death due to Omicron will continue to moderate. Nevertheless, the virus is ever-changing, and public health policies, especially those related to vaccinations, will also have to continually evolve and adapt as COVID-19 transitions to endemicity. Keywords: Booster, COVID-19, infectious diseases, Omicron, vaccine
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Parikh, Bijal, Rakasa Pattanaik, Eliane Shinder, et al. "Wild type through omicron: obstetric outcomes across COVID-19 waves." American Journal of Obstetrics and Gynecology 228, no. 1 (2023): S443. http://dx.doi.org/10.1016/j.ajog.2022.11.766.
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Parikh, Bijal, Eliane Shinder, Rakasa Pattanaik, et al. "Wild type through Omicron: Maternal outcomes across COVID-19 waves." American Journal of Obstetrics and Gynecology 228, no. 1 (2023): S100—S101. http://dx.doi.org/10.1016/j.ajog.2022.11.212.
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Fahma, Siskalil, Hirowati Ali, and Andani Eka Putra. "Genetic Variations of SARS-COV-2: Distribution of Variants and Mutations in the N Gene." International Journal of Research and Review 11, no. 9 (2024): 9–18. http://dx.doi.org/10.52403/ijrr.20240902.
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The SARS-CoV-2 nucleocapsid (N) gene is the most frequently mutated gene after the spike gene. This research aims to analyze the distribution of SARS-CoV-2 and nucleotide variations of the N gene in the SARS-CoV-2 variant found in West Sumatra. We analyzed 268 genome sequences of SARS-COV-2 at the start of the pandemic from April 2020 to March 2022 and compared them with NC45512. The range consists of three waves: the first, second, and third waves, all of which are dominated by the B.1.466.2 lineage. Distribution lineage found 20 lineages, with the majority being B.1.466.2 (31.72%), a local variant. The delta variant is 19.20% divided into two lineages, AY.23 and AY24, and the Omicron variant is 14.18%. In this study, we found unique mutations in the N gene where the B.1.466.2 variant can be seen with the T205I amino acid change and Delta with the D64G, R203M, and G215C amino acid changes; omicron variant with amino acid changes P13L, DEL 31/33, R203K, and G204R. Conclusion: We conclude that there are nucleotide variations in the West Sumatra SARS-CoV-2 N gene. Keywords: SARS CoV-2, nucleocapsid gene, mutation variant B.1.466.2, delta, omicron
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Bulată-Pop, Irina, Angela Cozma, Violeta Tincuța Briciu, Mihaela Sorina Lupșe, and Lia-Monica Junie. "Severity, outcomes, and vaccination status in hospitalized children who tested positive for SARS-CoV-2 during two pandemic waves." Medicine and Pharmacy Reports 98, no. 1 (2025): 54–59. https://doi.org/10.15386/mpr-2850.
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Background. The infection with SARS-CoV-2 in children usually manifests as a mild respiratory tract infection. The aim of this study was to evaluate the severity, outcome and vaccination status in children hospitalized for COVID-19 in a single center during two pandemic waves determined by different SARS-CoV-2 variants of concern (VOCs). Methods. A retrospective study on 656 consecutive pediatric patients was performed from September 1, 2021, to April 30, 2023. The study interval was divided into waves, according to official data on the circulation of Delta and Omicron VOCs. Data collected included sex, age, comorbidities, date of diagnosis, duration of hospitalization, vaccination status, clinical outcome. Results. The Delta group consisted of 234 children with a mean age of approximately 9 years, while the Omicron group included 422 children with a mean age of around 2.5 years. Most cases were mild, although in the Omicron wave the hospitalization rate was higher and 41.7% of the cases were medium in severity. The presence of comorbidities was not linked to an increase in severity. Vaccination rates were low in both groups, with a mean of 4% for the total of eligible patients. Conclusion. This pioneering study highlights the nature of COVID-19 in children, focusing on both clinical aspects and public health issues.
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Karpova, L. S., A. B. Komissarov, K. A. Stolyarov, et al. "Features of the COVID-19 Epidemic Process in Each of the of the Five Waves of Morbidity in Russia." Epidemiology and Vaccinal Prevention 22, no. 2 (2023): 23–36. http://dx.doi.org/10.31631/2073-3046-2023-22-2-23-36.
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Aim. To assess the intensity of the epidemic process in each of the five waves of COVID-19 in Russia.Materials and methods. The data on morbidity, hospitalization and deaths from COVID-19 of the population as a whole and by age groups from 48 (in the I rise) to 54 cities (in the V wave) and data from the website of the Russian consortium for sequencing coronavirus genomes were analyzed.Results. The nature of the course of the first 5 waves in the incidence of COVID-19 in Russia remains undulating. The waves in morbidity began in megacities, and the direction of spread across the FD differed in different waves of morbidity. The results of gene sequencing showed the participation of the main genovariants of the coronavirus in the etiology of diseases up to 3-4 waves. Some genovariants identified earlier received maximum distribution in the following wave. In Russia, the European descendants of the Wuhan strain (74.4%) were dominant in the I wave in morbidity, in the II wave – its daughter genovariants (68.5%), in the III – AY.122 (80.1%), in the IV – AY.122 (84.7%) and in the V wave – Omicron (76.7%).Conclusions. The features of each wave in the incidence of COVID-19 depended on the properties of the dominant genovariants: their ability to transmit from person to person and virulence. The rate of spread of the epidemic by FD, the susceptibility of all age groups and the intensity of epidemics were maximal during the period of the V wave in morbidity with the Omicron gene variant. Mortality was minimal in the I wave of morbidity, maximal in the IV with AY.122 strains and low in the V wave with Omicron genovariants. The influence of the season of the year was manifested in the summer season by an increase in the incidence of COVID-19 earlier in the Russian Federation as a whole (immediately after megacities) than in most federal districts, but with a lower incidence.
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Cantu, Rebecca M., Sara C. Sanders, Grace A. Turner, et al. "Younger and rural children are more likely to be hospitalized for SARS-CoV-2 infections." PLOS ONE 19, no. 10 (2024): e0308221. http://dx.doi.org/10.1371/journal.pone.0308221.
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Purpose To identify characteristics of SARS-CoV-2 infection that are associated with hospitalization in children initially evaluated in a Pediatric Emergency Department (ED). Methods We identified cases of SARS-CoV-2 positive patients seen in the Arkansas Children’s Hospital (ACH) ED or hospitalized between May 27, 2020, and April 28, 2022, using ICD-10 codes within the Pediatric Hospital Information System (PHIS) Database. We compared infection waves for differences in patient characteristics and used logistic regressions to examine which features led to a higher chance of hospitalization. Findings We included 681 pre-Delta cases, 673 Delta cases, and 970 Omicron cases. Almost 17% of patients were admitted to the hospital. Compared to Omicron-infected children, pre-Delta and Delta-infected children were twice as likely hospitalized (OR = 2.2 and 2.0, respectively; p<0.0001). Infants under one year were >3 times as likely to be hospitalized than children ages 5–14 years regardless of wave (OR = 3.42; 95%CI = 2.36–4.94). Rural children were almost three times as likely than urban children to be hospitalized across all waves (OR = 2.73; 95%CI = 1.97–3.78). Finally, those with a complex condition had nearly a 15-fold increase in odds of admission (OR = 14.6; 95%CI = 10.6–20.0). Conclusions Children diagnosed during the pre-Delta or Delta waves were more likely to be hospitalized than those diagnosed during the Omicron wave. Younger and rural patients were more likely to be hospitalized regardless of the wave. We suspect lower vaccination rates and larger distances from medical care influenced higher hospitalization rates.
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Almishaal, Ali A. "Comparative Study of Audiovestibular Symptoms between Early and Late Variants of COVID-19." Audiology Research 12, no. 6 (2022): 680–95. http://dx.doi.org/10.3390/audiolres12060065.
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Audiovestibular symptoms during the acute phase of the corona virus disease 2019 (COVID-19), have been reported for earlier waves of the pandemic, while no studies investigated nor compared audiovestibular manifestations during subsequent waves of COVID-19. In the current study, we aimed to compare the occurrence of audiovestibular symptoms associated with COVID-19 between the alpha/beta, delta, and omicron variants. An online questionnaire was distributed to individuals with confirmed test results for COVID-19. We asked participants to report whether they experienced audiovestibular symptoms during the acute phase of the disease. The study included 939 participants; 120 un-infected controls and infected participants during alpha/beta (n = 301), delta (n = 102), and omicron (n = 416) predominance periods. Self-reported audiovestibular symptoms were found to be statistically significantly different between un-infected controls and COVID-19 infected individuals in all analyzed variants. Furthermore, our results showed no significant differences in audiovestibular symptoms among individuals infected during alpha/beta, delta, and omicron waves. Although individuals infected during the delta variant predominance period reported higher percentages of audiovestibular symptoms (ranging from 11.8% to 26.5% for auditory symptoms and from 12.7% to 34.3% for vestibular symptoms) than for the alpha/beta (ranging from 6.3% to 18.9% for auditory symptoms and 8.3% to 29.9% for vestibular symptoms) and omicron (ranging from 9.6% to 21.2% for auditory and 12.5 to 29.1% for vestibular symptoms) variants, this did not achieve statistical significance. With regards to auditory symptoms, the most commonly reported symptoms were aural fullness followed by hearing loss and tinnitus. With regards to vestibular symptoms, dizziness was the most commonly reported symptom followed by vertigo and unsteadiness. Logistic regression revealed that experiencing auditory symptoms were associated with other neurological symptoms, back and joint pain, and chest pain as COVID-19 symptoms. Vestibular symptoms were associated with anemia, gender, fatigue, headache, and breathing difficulties. In conclusion, our study shows that audiovestibular symptoms are common during the acute phase of early and late COVID-19 variants with no significant differences between them.
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de León, Ugo Avila-Ponce, Angel G. C. Pérez, and Eric Avila-Vales. "Modeling the SARS-CoV-2 Omicron variant dynamics in the United States with booster dose vaccination and waning immunity." Mathematical Biosciences and Engineering 20, no. 6 (2023): 10909–53. http://dx.doi.org/10.3934/mbe.2023484.
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<abstract><p>We carried out a theoretical and numerical analysis for an epidemic model to analyze the dynamics of the SARS-CoV-2 Omicron variant and the impact of vaccination campaigns in the United States. The model proposed here includes asymptomatic and hospitalized compartments, vaccination with booster doses, and the waning of natural and vaccine-acquired immunity. We also consider the influence of face mask usage and efficiency. We found that enhancing booster doses and using N95 face masks are associated with a reduction in the number of new infections, hospitalizations and deaths. We highly recommend the use of surgical face masks as well, if usage of N95 is not a possibility due to the price range. Our simulations show that there might be two upcoming Omicron waves (in mid-2022 and late 2022), caused by natural and acquired immunity waning with respect to time. The magnitude of these waves will be 53% and 25% lower than the peak in January 2022, respectively. Hence, we recommend continuing to use face masks to decrease the peak of the upcoming COVID-19 waves.</p></abstract>
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Zambrano, José Luis, Rossana Jaspe, Mariana Hidalgo, et al. "Sub-lineages of the Omicron variant of SARS-CoV-2: characteristic mutations and their relation to epidemiological behavior." Investigación Clínica 63, no. 3 (2022): 262–74. http://dx.doi.org/10.54817/ic.v63n3a05.
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By the end of 2021, the Omicron variant of SARS-CoV-2, the coronavirus responsible for COVID-19, emerges, causing immediate concern, due to the explosive increase in cases in South Africa and a large number of mutations. This study describes the characteristic mutations of the Omicron variant in the Spike protein, and the behavior of the successive epidemic waves associated to the sub-lineages throughout the world. The mutations in the Spike protein described are related to the virus ability to evade the protec-tion elicited by current vaccines, as well as with possible reduced susceptibil-ity to host proteases for priming of the fusion process, and how this might be related to changes in tropism, a replication enhanced in nasal epithelial cells, and reduced in pulmonary tissue; traits probably associated with the apparent reduced severity of Omicron compared to other variants.
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Conceicao, Edwin Philip, Yingqi Xu, Sze Ling Chan, et al. "Incubation Periods of SARS-CoV-2 Wild-Type, Delta, and Omicron Variants–Dominant Periods in Singapore." COVID 4, no. 10 (2024): 1578–84. http://dx.doi.org/10.3390/covid4100109.
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This study in Singapore analysed the incubation periods of the following SARS-CoV-2 variants: Wuhan-Hu-1, Delta, and Omicron. Three pandemic waves were examined: Wuhan-Hu-1 (January 2020–March 2021), Delta (May–October 2021), and Omicron (January–June 2022). Data from the SingHealth COVID-19 registry, covering patients from 23 January 2020 to 10 June 2022, were used to calculate incubation periods during the three time periods. The study found median incubation periods of 11 days for Wuhan-Hu-1, 3 days for Delta, and 3 days for Omicron (p-value: <0.001). This study highlighted the impact of different containment measures and the importance of robust EMR systems for tracking and managing infectious diseases. Key challenges included accurate contact tracing and IT infrastructure capabilities. The findings support the use of EMR data for future infectious disease preparedness in Singapore.
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Jassat, Waasila, Salim S. Abdool Karim, Lovelyn Ozougwu, et al. "Trends in Cases, Hospitalization and Mortality Related to the Omicron BA.4/BA.5 Sub-Variants in South Africa." Clinical Infectious Diseases, December 1, 2022. http://dx.doi.org/10.1093/cid/ciac921.
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ABSTRACT Background This study compared admission incidence risk across waves, and the risk of mortality in the Omicron BA.4/BA.5 wave, to the Omicron BA.1/BA.2 and Delta waves. Methods Data from South Africa’s national hospital surveillance system, SARS-CoV-2 case linelist and Electronic Vaccine Data System were linked and analysed. Wave periods were defined when the country passed a weekly incidence of 30 cases/100,000 people. In-hospital case fatality ratios (CFR) in the Delta, Omicron BA.1/BA.2 and Omicron BA.4/BA.5 wave periods were compared by post-imputation random effect multivariable logistic regression models. Results The CFR was 25.9% (N = 37,538/144,778), 10.9% (N = 6,123/56,384) and 8.2% (N = 1,212/14,879) in the Delta, Omicron BA.1/BA.2, and Omicron BA.4/BA.5 waves respectively. After adjusting for age, sex, race, comorbidities, health sector and province, compared to the Omicron BA.4/BA.5 wave, patients had higher risk of mortality in the Omicron BA.1/BA.2 wave (adjusted odds ratio [aOR] 1.3; 95% confidence interval [CI] 1.2-1.4) and Delta (aOR 3.0; 95% CI 2.8-3.2) wave. Being partially vaccinated (aOR 0.9, CI 0.9-0.9), fully vaccinated (aOR 0.6, CI 0.6-0.7) and boosted (aOR 0.4, CI 0.4-0.5); and prior laboratory-confirmed infection (aOR 0.4, CI 0.3-0.4) were associated with reduced risks of mortality. Conclusion Overall, admission incidence risk and in-hospital mortality, which had increased progressively in South Africa’s first three waves, decreased in the fourth Omicron BA.1/BA.2 wave and declined even further in the fifth Omicron BA.4/BA.5 wave. Mortality risk was lower in those with natural infection and vaccination, declining further as the number of vaccine doses increased.
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Shin, Hye Won, Alecia James, Theresa Feng, Lillian Chow, and Robert Foronjy. "Comparing the demographics and laboratory biomarkers of the COVID-19 Omicron wave and the Alpha wave in a predominantly Afro-Caribbean patient population in New York City." Pneumonia 14, no. 1 (2022). http://dx.doi.org/10.1186/s41479-022-00099-w.
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Abstract Background There is a knowledge gap of specific characteristics linked to disease severity of the different COVID-19 waves, especially in underserved populations. We compared the demographic and clinical factors associated with SARS-CoV-2-infected patients admitted to the intensive care unit (ICU) during the Omicron and Alpha waves. Methods An observational study comparing two COVID-19 waves was conducted in Brooklyn, NY. Twenty-seven ICU admitted patients with a positive COVID-19 test result during the period of November 1, 2021, to January 31, 2022, (“Omicron wave”) were compared to 271 COVID-19 patients who received ICU consults during the Alpha wave, the period from March 28, 2020, to April 30, 2020. Results The Omicron wave had a 55.6% mortality rate compared to a 67.2% mortality rate in the Alpha wave. For the non-survivors, there were more females (66.7%) in the Omicron wave, while the trend was reversed in the Alpha wave (38.5%). Most of the patients seen were Black (> 85%) in both waves. A bivariate comparison of the two waves found that patients in the Omicron wave had overall significantly lower ALT levels (p = 0.03) and higher monocyte % (p = 0.005) compared to the patients in the Alpha wave. In the multivariate analysis, adjusting for age and sex, increasing levels of HCO3- were significantly associated with reduced mortality in the Omicron wave (OR: 0.698; 95% CI: 0.516 – 0.945; p = 0.02). Also, multivariable analyses using both waves combined found that neutrophil % was significantly associated with increased mortality (OR: 1.05; 95% CI: 1.02 – 1.09; p = 0.006) while lymphocyte % was significantly associated with reduced mortality (OR: 0.946; 95% CI: 0.904 – 0.990; p = 0.018). Conclusions The COVID-19-positive ICU patients in the Omicron wave experienced less severe outcomes than those of the Alpha wave. In contrast to the Alpha variant, the Omicron variant exhibited enhanced infectivity and disease severity in females.
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Pather, Shanti, Shabir A. Madhi, Benjamin J. Cowling, et al. "SARS-CoV-2 Omicron variants: burden of disease, impact on vaccine effectiveness and need for variant-adapted vaccines." Frontiers in Immunology 14 (May 23, 2023). http://dx.doi.org/10.3389/fimmu.2023.1130539.
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The highly transmissible Omicron (B.1.1.529) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first detected in late 2021. Initial Omicron waves were primarily made up of sub-lineages BA.1 and/or BA.2, BA.4, and BA.5 subsequently became dominant in mid-2022, and several descendants of these sub-lineages have since emerged. Omicron infections have generally caused less severe disease on average than those caused by earlier variants of concern in healthy adult populations, at least, in part, due to increased population immunity. Nevertheless, healthcare systems in many countries, particularly those with low population immunity, have been overwhelmed by unprecedented surges in disease prevalence during Omicron waves. Pediatric admissions were also higher during Omicron waves compared with waves of previous variants of concern. All Omicron sub-lineages exhibit partial escape from wild-type (Wuhan-Hu 1) spike-based vaccine-elicited neutralizing antibodies, with sub-lineages with more enhanced immuno-evasive properties emerging over time. Evaluating vaccine effectiveness (VE) against Omicron sub-lineages has become challenging against a complex background of varying vaccine coverage, vaccine platforms, prior infection rates, and hybrid immunity. Original messenger RNA vaccine booster doses substantially improved VE against BA.1 or BA.2 symptomatic disease. However, protection against symptomatic disease waned, with reductions detected from 2 months after booster administration. While original vaccine-elicited CD8+ and CD4+ T-cell responses cross-recognize Omicron sub-lineages, thereby retaining protection against severe outcomes, variant-adapted vaccines are required to expand the breadth of B-cell responses and improve durability of protection. Variant-adapted vaccines were rolled out in late 2022 to increase overall protection against symptomatic and severe infections caused by Omicron sub-lineages and antigenically aligned variants with enhanced immune escape mechanisms.
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Zhao, Xin‐Jing, Xiao‐Lin Liu, Yu‐Min Liang, et al. "Epidemiological characteristics and antibody kinetics of elderly population with booster vaccination following both Omicron BA.5 and XBB waves in China." Journal of Medical Virology 96, no. 5 (2024). http://dx.doi.org/10.1002/jmv.29640.
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AbstractAfter the termination of zero‐COVID‐19 policy, the populace in China has experienced both Omicron BA.5 and XBB waves. Considering the poor antibody responses and severe outcomes observed among the elderly following infection, we conducted a longitudinal investigation to examine the epidemiological characteristics and antibody kinetics among 107 boosted elderly participants following the Omicron BA.5 and XBB waves. We observed that 96 participants (89.7%) were infected with Omicron BA.5, while 59 (55.1%) participants were infected with Omicron XBB. Notably, 52 participants (48.6%) experienced dual infections of both Omicron BA.5 and XBB. The proportion of symptomatic cases appeared to decrease following the XBB wave (18.6%) compared to that after the BA.5 wave (59.3%). Omicron BA.5 breakthrough infection induced lower neutralizing antibody titers against XBB.1.5, BA.2.86, and JN.1, while reinfection with Omicron XBB broadened the antibody responses against all measured Omicron subvariants and may alleviate the wild type‐vaccination induced immune imprinting. Boosted vaccination type and comorbidities were the significant factors associated with antibody responses. Updated vaccines based on emerging severe acute respiratory syndrome coronavirus 2 variants are needed to control the Coronavirus Disease 2019 pandemic in the elderly.
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Chen, Boqiang, Yanji Zhao, Zhen Jin, Daihai He, and Huaichen Li. "Twice evasions of Omicron variants explain the temporal patterns in six Asian and Oceanic countries." BMC Infectious Diseases 23, no. 1 (2023). http://dx.doi.org/10.1186/s12879-023-07984-9.
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Abstract Background The ongoing coronavirus 2019 (COVID-19) pandemic has emerged and caused multiple pandemic waves in the following six countries: India, Indonesia, Nepal, Malaysia, Bangladesh and Myanmar. Some of the countries have been much less studied in this devastating pandemic. This study aims to assess the impact of the Omicron variant in these six countries and estimate the infection fatality rate (IFR) and the reproduction number $${R}_{0}$$ R 0 in these six South Asia, Southeast Asia and Oceania countries. Methods We propose a Susceptible-Vaccinated-Exposed-Infectious-Hospitalized-Death-Recovered model with a time-varying transmission rate $$\beta (t)$$ β ( t ) to fit the multiple waves of the COVID-19 pandemic and to estimate the IFR and $${R}_{0}(t)$$ R 0 ( t ) in the aforementioned six countries. The level of immune evasion and the intrinsic transmissibility advantage of the Omicron variant are also considered in this model. Results We fit our model to the reported deaths well. We estimate the IFR (in the range of 0.016 to 0.136%) and the reproduction number $${R}_{0}(t)$$ R 0 ( t ) (in the range of 0 to 9) in the six countries. Multiple pandemic waves in each country were observed in our simulation results. Conclusions The invasion of the Omicron variant caused the new pandemic waves in the six countries. The higher $${R}_{0}(t)$$ R 0 ( t ) suggests the intrinsic transmissibility advantage of the Omicron variant. Our model simulation forecast implies that the Omicron pandemic wave may be mitigated due to the increasing immunized population and vaccine coverage.
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Roser, Lynn P., Harideep Samanapally, T’shura Ali, et al. "Different clinical characteristics and outcomes of adult hospitalized SARS-CoV-2 pneumonia patients complicated by cardiovascular events during the first, delta and omicron waves of COVID-19." Frontiers in Epidemiology 4 (April 18, 2024). http://dx.doi.org/10.3389/fepid.2024.1342917.
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BackgroundThe effects of SARS-CoV-2 have varied between significant waves of hospitalization.Research questionAre cardiovascular complications different among the first, delta and omicron waves of hospitalized COVID-19 pneumonia patients?Study design and methodsThis was a multi-centre retrospective study of patients hospitalized with SARS-CoV-2 pneumonia: 632 were hospitalized during the first wave (March–July 2020), 1013 during the delta wave (September 2020–March 2021), and 323 during the omicron wave (January 2022–July 2022). Patients were stratified by wave and occurrence of cardiovascular events.ResultsAmong all hospitalized patients with cardiovascular events, patients in the omicron wave were younger (62.4 ± 14 years) than patients in the first wave (67.4 ± 7.8 years) and the delta wave (66.9 ± 12.6 years) and had a higher proportion of non-Hispanic White people than in the first wave (78.6% vs. 61.7%). For COVID-19 patients who suffered from cardiovascular events, the omicron wave patients had significantly higher neutrophil/lymphocyte ratio, white blood cell and platelet counts when compared to the first wave. Omicron wave patients had significantly lower albumin and B-type natriuretic peptide levels (only 5.8% of the first wave and 14.6% of the delta wave) when compared to either the first wave or delta wave patients. In COVID-19 patients who suffered cardiovascular events during hospitalization, mortality rate in the omicron wave (26.8%) was significantly lower than the first wave (48.3%), time to mortality for non-survivors of COVID-19 patients who suffered cardiovascular events was significantly longer in the omicron wave (median 16 days) than in the first wave (median 10 days).ConclusionsYounger and white patients were affected with cardiovascular complications more often by the omicron variant. Despite higher neutrophil/lymphocyte ratio and WBC counts, the omicron patients with cardiovascular events showed lower heart injuries, lower mortality and longer time to mortality for non-survivors when compared to the first and delta waves.