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Journal articles on the topic 'SARS-CoV-2 sequencing'

Author: Grafiati

Published: 14 March 2023

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1

Nazario-Toole, Ashley, Holly M. Nguyen, Hui Xia, Dianne N. Frankel, John W. Kieffer, and Thomas F. Gibbons. "Sequencing SARS-CoV-2 from antigen tests." PLOS ONE 17, no. 2 (2022): e0263794. http://dx.doi.org/10.1371/journal.pone.0263794.

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Genomic surveillance empowers agile responses to SARS-CoV-2 by enabling scientists and public health analysts to issue recommendations aimed at slowing transmission, prioritizing contact tracing, and building a robust genomic sequencing surveillance strategy. Since the start of the pandemic, real time RT-PCR diagnostic testing from upper respiratory specimens, such as nasopharyngeal (NP) swabs, has been the standard. Moreover, respiratory samples in viral transport media are the ideal specimen for SARS-CoV-2 whole-genome sequencing (WGS). In early 2021, many clinicians transitioned to antigen-

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Mugnier, Nathalie, Aurélien Griffon, Bruno Simon, et al. "Evaluation of EPISEQ SARS-CoV-2 and a Fully Integrated Application to Identify SARS-CoV-2 Variants from Several Next-Generation Sequencing Approaches." Viruses 14, no. 8 (2022): 1674. http://dx.doi.org/10.3390/v14081674.

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Whole-genome sequencing has become an essential tool for real-time genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) worldwide. The handling of raw next-generation sequencing (NGS) data is a major challenge for sequencing laboratories. We developed an easy-to-use web-based application (EPISEQ SARS-CoV-2) to analyse SARS-CoV-2 NGS data generated on common sequencing platforms using a variety of commercially available reagents. This application performs in one click a quality check, a reference-based genome assembly, and the analysis of the generated consensus

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Turakhia, Yatish, Nicola De Maio, Bryan Thornlow, et al. "Stability of SARS-CoV-2 phylogenies." PLOS Genetics 16, no. 11 (2020): e1009175. http://dx.doi.org/10.1371/journal.pgen.1009175.

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The SARS-CoV-2 pandemic has led to unprecedented, nearly real-time genetic tracing due to the rapid community sequencing response. Researchers immediately leveraged these data to infer the evolutionary relationships among viral samples and to study key biological questions, including whether host viral genome editing and recombination are features of SARS-CoV-2 evolution. This global sequencing effort is inherently decentralized and must rely on data collected by many labs using a wide variety of molecular and bioinformatic techniques. There is thus a strong possibility that systematic errors

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Sekulic, Miroslav, Holly Harper, Behtash G. Nezami, et al. "Molecular Detection of SARS-CoV-2 Infection in FFPE Samples and Histopathologic Findings in Fatal SARS-CoV-2 Cases." American Journal of Clinical Pathology 154, no. 2 (2020): 190–200. http://dx.doi.org/10.1093/ajcp/aqaa091.

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Abstract Objectives To report methods and findings of 2 autopsies with molecular evaluation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive individuals. Methods Postmortem examination was completed following Centers for Disease Control and Prevention public guidelines. Numerous formalin-fixed paraffin-embedded (FFPE) tissue types from each case were surveyed for SARS-CoV-2 RNA by quantitative reverse transcription polymerase chain reaction (qRT-PCR). SARS-CoV-2 viral genome was sequenced by next-generation sequencing (NGS) from FFPE lung tissue blocks. Results Postmort

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Xiaoli, Lingzi, Jill V. Hagey, Daniel J. Park, et al. "Benchmark datasets for SARS-CoV-2 surveillance bioinformatics." PeerJ 10 (September 5, 2022): e13821. http://dx.doi.org/10.7717/peerj.13821.

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Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), has spread globally and is being surveilled with an international genome sequencing effort. Surveillance consists of sample acquisition, library preparation, and whole genome sequencing. This has necessitated a classification scheme detailing Variants of Concern (VOC) and Variants of Interest (VOI), and the rapid expansion of bioinformatics tools for sequence analysis. These bioinformatic tools are means for major actionable results: maintaining quality assurance and check

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Mavzyutov, A. R., R. R. Garafutdinov, E. Yu Khalikova, et al. "The enigmas of the new coronavirus SARS-CoV-2." Biomics 13, no. 1 (2021): 75–99. http://dx.doi.org/10.31301/2221-6197.bmcs.2021-7.

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The emergence of the new SARS-CoV-2 coronavirus has given rise to many enigmas, to which there are no answers yet. However, the degree of threat to humanity, due to the fact that by the beginning of February 2021, more than 100 million people were ill in the world, of which 2 million died, led to the fact that the efforts of many researchers were aimed at combating this disease, including massive sequencing of the complete genomes of SARS-CoV-2, as this is necessary for diagnostics and prediction of the epidemiological situation, including in the long term. Currently, a fairly high level of co

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Petersen, J. M., and D. Jhala. "Sequencing for COVID-19 in the Pandemic Era: What Does it Mean?" American Journal of Clinical Pathology 156, Supplement_1 (2021): S140—S141. http://dx.doi.org/10.1093/ajcp/aqab191.300.

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Abstract Introduction/Objective SARS-CoV-2 has been developing mutations over the course of the pandemic, leading to the rise of variants. The sequencing of these variants, however, has an unclear role for the medical center providing patient treatment. Methods/Case Report Patient specimens that were positive for the presence of SARS-CoV-2 with a cycle threshold &lt;30 by reverse transcriptase polymerase chain reaction (RT-PCR) were sent for sequencing at the Veterans Health Administration Public Health Reference Laboratory (PHRL). Testing for SARS-CoV-2 was by RT-PCR was initially done by

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8

Nasir, Jalees A., Robert A. Kozak, Patryk Aftanas, et al. "A Comparison of Whole Genome Sequencing of SARS-CoV-2 Using Amplicon-Based Sequencing, Random Hexamers, and Bait Capture." Viruses 12, no. 8 (2020): 895. http://dx.doi.org/10.3390/v12080895.

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Genome sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is increasingly important to monitor the transmission and adaptive evolution of the virus. The accessibility of high-throughput methods and polymerase chain reaction (PCR) has facilitated a growing ecosystem of protocols. Two differing protocols are tiling multiplex PCR and bait capture enrichment. Each method has advantages and disadvantages but a direct comparison with different viral RNA concentrations has not been performed to assess the performance of these approaches. Here we compare Liverpool amplification

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Crawford, Dana C., and Scott M. Williams. "Global variation in sequencing impedes SARS-CoV-2 surveillance." PLOS Genetics 17, no. 7 (2021): e1009620. http://dx.doi.org/10.1371/journal.pgen.1009620.

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Avetyan, Diana, Siras Hakobyan, Maria Nikoghosyan, et al. "Molecular Analysis of SARS-CoV-2 Lineages in Armenia." Viruses 14, no. 5 (2022): 1074. http://dx.doi.org/10.3390/v14051074.

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The sequencing of SARS-CoV-2 provides essential information on viral evolution, transmission, and epidemiology. In this paper, we performed the whole-genome sequencing of SARS-CoV-2 using nanopore and Illumina sequencing to describe the circulation of the virus lineages in Armenia. The analysis of 145 full genomes identified six clades (19A, 20A, 20B, 20I, 21J, and 21K) and considerable intra-clade PANGO lineage diversity. Phylodynamic and transmission analysis allowed to attribute specific clades as well as infer their importation routes. Thus, the first two waves of positive case increase we

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Babiker, Ahmed, Heath L. Bradley, Victoria D. Stittleburg, et al. "Metagenomic Sequencing To Detect Respiratory Viruses in Persons under Investigation for COVID-19." Journal of Clinical Microbiology 59, no. 1 (2020): e02142-20. http://dx.doi.org/10.1128/jcm.02142-20.

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ABSTRACTBroad testing for respiratory viruses among persons under investigation (PUIs) for SARS-CoV-2 has been performed inconsistently, limiting our understanding of alternative viral infections and coinfections in these patients. RNA metagenomic next-generation sequencing (mNGS) offers an agnostic tool for the detection of both SARS-CoV-2 and other RNA respiratory viruses in PUIs. Here, we used RNA mNGS to assess the frequencies of alternative viral infections in SARS-CoV-2 RT-PCR-negative PUIs (n = 30) and viral coinfections in SARS-CoV-2 RT-PCR-positive PUIs (n = 45). mNGS identified all v

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De Salazar, A., A. Fuentes-López, L. Viñuela, et al. "SARS-CoV-2 genome sequencing in Andalusia, methodology and study of variants." ACTUALIDAD MEDICA 106, no. 106(814) (2022): 291–300. http://dx.doi.org/10.15568/am.2021.814.rev03.

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The incorporation of genomic sequencing techniques through next-generation sequencing has revolutionized clinical microbiology, innovating and improving the clinical diagnosis of infectious diseases. Today, whole genome sequencing in infectious diseases has many applications in virology, bacteriology, antibiotic resistance, epidemiology, and public health. With the appearance of SARS-CoV-2, the importance of the analysis and study of genetic sequences has been underlined. Since the initial identification of SARS-CoV-2, to date, more than 414,575 complete genomic sequences have been shared worl

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Chen, Zhiyuan, Andrew S. Azman, Xinhua Chen, et al. "Global landscape of SARS-CoV-2 genomic surveillance and data sharing." Nature Genetics 54, no. 4 (2022): 499–507. http://dx.doi.org/10.1038/s41588-022-01033-y.

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AbstractGenomic surveillance has shaped our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. We performed a global landscape analysis on SARS-CoV-2 genomic surveillance and genomic data using a collection of country-specific data. Here, we characterize increasing circulation of the Alpha variant in early 2021, subsequently replaced by the Delta variant around May 2021. SARS-CoV-2 genomic surveillance and sequencing availability varied markedly across countries, with 45 countries performing a high level of routine genomic surveillance and 96 countries with

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Pembaur, Anton, Erwan Sallard, Patrick Philipp Weil, Jennifer Ortelt, Parviz Ahmad-Nejad, and Jan Postberg. "Simplified Point-of-Care Full SARS-CoV-2 Genome Sequencing Using Nanopore Technology." Microorganisms 9, no. 12 (2021): 2598. http://dx.doi.org/10.3390/microorganisms9122598.

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The scale of the ongoing SARS-CoV-2 pandemic warrants the urgent establishment of a global decentralized surveillance system to recognize local outbreaks and the emergence of novel variants of concern. Among available deep-sequencing technologies, nanopore-sequencing could be an important cornerstone, as it is mobile, scalable, and cost-effective. Therefore, streamlined nanopore-sequencing protocols need to be developed and optimized for SARS-CoV-2 variants identification. We adapted and simplified existing workflows using the ‘midnight’ 1200 bp amplicon split primer sets for PCR, which produc

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Shin, Yeun-Kyung, Oh-Kyu Kwon, Jinhwa Heo, et al. "Whole Genome Sequencing of SARS-CoV-2 in Cats and Dogs in South Korea in 2021." Veterinary Sciences 10, no. 1 (2022): 6. http://dx.doi.org/10.3390/vetsci10010006.

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SARS-CoV-2 infections have caused unprecedented damage worldwide by affecting humans and various animals. The first reported animal infection was observed in a pet dog in Hong Kong in March 2020. 36 countries reported 692 SARS-CoV-2 infections in 25 different animal species by 31 August 2022. Most outbreaks were caused by contact with SARS-CoV-2 infected humans. In South Korea, the first SARS-CoV-2 infection in an animal was reported in a cat in February 2021. As of 31 December 2021, 74 dogs and 42 cats have been confirmed to have SARS-CoV-2 in South Korea. Here, we identified various SARS-CoV

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Bahouq, Hanane, Madiha Bahouq, and Abdelmajid Soulaymani. "Overview of genomic surveillance related to Severe Acute Respiratory Syndrom Coronavirus 2 (SARS- CoV-2)." E3S Web of Conferences 319 (2021): 01043. http://dx.doi.org/10.1051/e3sconf/202131901043.

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Since the start of the Severe Acute Respiratory Syndrom Coronavirus 2 (SARS-CoV-2) pandemic, several thousand of variants circulated and others are emerging. Therefore, genomic surveillance is crucial, which aims to detect the emergence of new variants, in particular Variants of Concern (VOC) and to assess the impact of priority mutations on the transmissibility and lethality of the virus, the performance of viral diagnostic methods and vaccine efficiency. An overview of available papers was performed to understand conduct, tools and utility of genomic sequencing and surveillance related to Co

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Harilal, Divinlal, Sathishkumar Ramaswamy, Tom Loney, et al. "SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission." Clinical Chemistry 66, no. 11 (2020): 1450–58. http://dx.doi.org/10.1093/clinchem/hvaa187.

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Abstract Background With the gradual reopening of economies and resumption of social life, robust surveillance mechanisms should be implemented to control the ongoing COVID-19 pandemic. Unlike RT-qPCR, SARS-CoV-2 whole genome sequencing (cWGS) has the added advantage of identifying cryptic origins of the virus, and the extent of community-based transmissions versus new viral introductions, which can in turn influence public health policy decisions. However, the practical and cost considerations of cWGS should be addressed before it is widely implemented. Methods We performed shotgun transcript

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Alessandrini, Federica, Sara Caucci, Valerio Onofri, et al. "Evaluation of the Ion AmpliSeq SARS-CoV-2 Research Panel by Massive Parallel Sequencing." Genes 11, no. 8 (2020): 929. http://dx.doi.org/10.3390/genes11080929.

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Deep knowledge of the genetic features of SARS-CoV-2 is essential to track the ongoing pandemic through different geographical areas and to design and develop early diagnostic procedures, therapeutic strategies, public health interventions, and vaccines. We describe protocols and first results of the Ion AmpliSeq™ SARS-CoV-2 Research Panel by a massively parallel sequencing (MPS) assay. The panel allows for targeted sequencing by overlapping amplicons, thereby providing specific, accurate, and high throughput analysis. A modified reverse transcription reaction, which consists of the use of a S

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Bhoyar, Rahul C., Abhinav Jain, Paras Sehgal, et al. "High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing." PLOS ONE 16, no. 2 (2021): e0247115. http://dx.doi.org/10.1371/journal.pone.0247115.

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The rapid emergence of coronavirus disease 2019 (COVID-19) as a global pandemic affecting millions of individuals globally has necessitated sensitive and high-throughput approaches for the diagnosis, surveillance, and determining the genetic epidemiology of SARS-CoV-2. In the present study, we used the COVIDSeq protocol, which involves multiplex-PCR, barcoding, and sequencing of samples for high-throughput detection and deciphering the genetic epidemiology of SARS-CoV-2. We used the approach on 752 clinical samples in duplicates, amounting to a total of 1536 samples which could be sequenced on

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Zouaki, Amal, Hakima Kabbaj, Ghizlane El Amin, et al. "Evaluation of the MAScIR SARS-CoV-2 M Kit 2.0 on the SARS-CoV-2 Infection." Advances in Virology 2023 (February 7, 2023): 1–13. http://dx.doi.org/10.1155/2023/9313666.

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SARS-CoV-2 is a major public health problem worldwide. Since its emergence, several diagnostic kits have been developed to ensure rapid patient management. The aim of our study is to check the performance of the new Moroccan SARS-CoV-2 detection kit: MAScIR SARS-CoV-2 M 2.0. The following parameters were studied: repeatability, reproducibility, analytical specificity, analytical sensitivity, and comparison with the GeneFinder™ COVID-19 Plus RealAmp Kit. In addition, an external quality evaluation comprising five specimens was carried out as part of an international program for the external qua

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Petrillo, Mauro, Maddalena Querci, Carlo Brogna, et al. "Evidence of SARS-CoV-2 bacteriophage potential in human gut microbiota." F1000Research 11 (March 9, 2022): 292. http://dx.doi.org/10.12688/f1000research.109236.1.

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Background: In previous studies we have shown that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replicates in vitro in bacterial growth medium, that the viral replication follows bacterial growth, and it is influenced by the administration of specific antibiotics. These observations are compatible with a ‘bacteriophage-like’ behaviour of SARS-CoV-2. Methods: We have further elaborated on these unusual findings and here we present the results of three different supplementary experiments: (1) an electron-microscope analysis of samples of bacteria obtained from a faecal sample of

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Unselt, Desiree, Katherine Knudsen, Christopher Rounds, et al. "Abstract 437: Characterization of SARS-CoV-2 using the Ion AmpliSeq SARS-CoV-2 research panel." Cancer Research 82, no. 12_Supplement (2022): 437. http://dx.doi.org/10.1158/1538-7445.am2022-437.

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Abstract Background: The rapid spread of COVID-19 has resulted in an urgent need for effective diagnostic and therapeutic strategies against SARS-CoV-2. Next-generation sequencing (NGS) is a powerful tool in the identification and characterization of this pathogen and genomic information may aid in understanding the mechanisms of therapeutic resistance, vaccine escape, virulence, and pathogenicity. The Ion AmpliSeq SARS-CoV-2 Research Panel is a targeted NGS solution that facilitates sequence analysis of the SARS-CoV-2 genome. Paired with a bioinformatics assembly and variant calling pipelines

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Khateeb, Dina, Tslil Gabrieli, Bar Sofer, et al. "SARS-CoV-2 variants with reduced infectivity and varied sensitivity to the BNT162b2 vaccine are developed during the course of infection." PLOS Pathogens 18, no. 1 (2022): e1010242. http://dx.doi.org/10.1371/journal.ppat.1010242.

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In-depth analysis of SARS-CoV-2 quasispecies is pivotal for a thorough understating of its evolution during infection. The recent deployment of COVID-19 vaccines, which elicit protective anti-spike neutralizing antibodies, has stressed the importance of uncovering and characterizing SARS-CoV-2 variants with mutated spike proteins. Sequencing databases have allowed to follow the spread of SARS-CoV-2 variants that are circulating in the human population, and several experimental platforms were developed to study these variants. However, less is known about the SARS-CoV-2 variants that are develo

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Bačenková, Darina, Marianna Trebuňová, Tatiana Špakovská, Marek Schnitzer, Lucia Bednarčíková, and Jozef Živčák. "Comparison of Selected Characteristics of SARS-CoV-2, SARS-CoV, and HCoV-NL63." Applied Sciences 11, no. 4 (2021): 1497. http://dx.doi.org/10.3390/app11041497.

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The global pandemic known as coronavirus disease 2019 (COVID-19) was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This review article presents the taxonomy of SARS-CoV-2 coronaviruses, which have been classified as the seventh known human pathogenic coronavirus. The etiology of COVID-19 is also briefly discussed. Selected characteristics of SARS-CoV-2, SARS-CoV, and HCoV-NL63 are compared in the article. The angiotensin converting enzyme-2 (ACE-2) has been identified as the receptor for the SARS-CoV-2 viral entry. ACE2 is well-known as a counter-regulator of the reni

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Eichmeier, Ales, Tomas Kiss, Maria Kocanova, et al. "Conserved MicroRNAs in Human Nasopharynx Tissue Samples from Swabs Are Differentially Expressed in Response to SARS-CoV-2." Genes 13, no. 2 (2022): 348. http://dx.doi.org/10.3390/genes13020348.

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The use of high-throughput small RNA sequencing is well established as a technique to unveil the miRNAs in various tissues. The miRNA profiles are different between infected and non-infected tissues. We compare the SARS-CoV-2 positive and SARS-CoV-2 negative RNA samples extracted from human nasopharynx tissue samples to show different miRNA profiles. We explored differentially expressed miRNAs in response to SARS-CoV-2 in the RNA extracted from nasopharynx tissues of 10 SARS-CoV-2-positive and 10 SARS-CoV-2-negative patients. miRNAs were identified by small RNA sequencing, and the expression l

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Pećar, Dino, Ivana Čeko, Lana Salihefendić, and Rijad Konjhodžić. "Assessment of Ion S5 NGS protocol for SARS-CoV-2 genome sequencing." Genetics & Applications 5, no. 2 (2021): 24. http://dx.doi.org/10.31383/ga.vol5iss2pp24-30.

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Monitoring of the lineages SARS-CoV-2 is equally important in a fight against COVID-19 epidemics, as is regular RT - PCR testing. Ion AmpliSeq Library kit plus is a robust and validated protocol for library preparation, but certain optimizations for better sequencing results were required. Clinical SARS-CoV-2 samples were transported in three different viral transport mediums (VTM), on arrival at the testing lab, samples were stored on -20OC. Viral RNA isolation was done on an automatic extractor using a magnetic beads-based protocol. Screening for positive SARS-CoV-2 samples was performed on

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Kockelbergh, Hannah, Shelley Evans, Tong Deng, et al. "Utility of Bulk T-Cell Receptor Repertoire Sequencing Analysis in Understanding Immune Responses to COVID-19." Diagnostics 12, no. 5 (2022): 1222. http://dx.doi.org/10.3390/diagnostics12051222.

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Measuring immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 19 (COVID-19), can rely on antibodies, reactive T cells and other factors, with T-cell-mediated responses appearing to have greater sensitivity and longevity. Because each T cell carries an essentially unique nucleic acid sequence for its T-cell receptor (TCR), we can interrogate sequence data derived from DNA or RNA to assess aspects of the immune response. This review deals with the utility of bulk, rather than single-cell, sequencing of TCR repertoires, considering

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Salles, Tiago Souza, Andrea Cony Cavalcanti, Fábio Burack da Costa, et al. "Genomic surveillance of SARS-CoV-2 Spike gene by sanger sequencing." PLOS ONE 17, no. 1 (2022): e0262170. http://dx.doi.org/10.1371/journal.pone.0262170.

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The SARS-CoV-2 responsible for the ongoing COVID pandemic reveals particular evolutionary dynamics and an extensive polymorphism, mainly in Spike gene. Monitoring the S gene mutations is crucial for successful controlling measures and detecting variants that can evade vaccine immunity. Even after the costs reduction resulting from the pandemic, the new generation sequencing methodologies remain unavailable to a large number of scientific groups. Therefore, to support the urgent surveillance of SARS-CoV-2 S gene, this work describes a new feasible protocol for complete nucleotide sequencing of

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Parker, Matthew D., Benjamin B. Lindsey, Shay Leary, et al. "Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data." Genome Research 31, no. 4 (2021): 645–58. http://dx.doi.org/10.1101/gr.268110.120.

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González-Recio, Oscar, Mónica Gutiérrez-Rivas, Ramón Peiró-Pastor, et al. "Sequencing of SARS-CoV-2 genome using different nanopore chemistries." Applied Microbiology and Biotechnology 105, no. 8 (2021): 3225–34. http://dx.doi.org/10.1007/s00253-021-11250-w.

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Gladkikh, Anna, Ekaterina Klyuchnikova, Polina Pavlova, et al. "Comparative Analysis of Library Preparation Approaches for SARS-CoV-2 Genome Sequencing on the Illumina MiSeq Platform." International Journal of Molecular Sciences 24, no. 3 (2023): 2374. http://dx.doi.org/10.3390/ijms24032374.

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been responsible for over two years of the COVID-19 pandemic and a global health emergency. Genomic surveillance plays a key role in overcoming the ongoing COVID-19 pandemic despite its relative successive waves and the continuous emergence of new variants. Many technological approaches are currently applied for the whole genome sequencing (WGS) of SARS-CoV-2. They differ in key stages of the process, and they feature some differences in genomic coverage, sequencing depth, and in the accuracy of variant-calling options. In this s

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Deminco, Felice, Sara N. Vaz, Daniele S. Santana, et al. "A Simplified Sanger Sequencing Method for Detection of Relevant SARS-CoV-2 Variants." Diagnostics 12, no. 11 (2022): 2609. http://dx.doi.org/10.3390/diagnostics12112609.

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Molecular surveillance of the new coronavirus through new genomic sequencing technologies revealed the circulation of important variants of SARS-CoV-2. Sanger sequencing has been useful in identifying important variants of SARS-CoV-2 without the need for whole-genome sequencing. A sequencing protocol was constructed to cover a region of 1000 base pairs, from a 1120 bp product generated after a two-step RT-PCR assay in samples positive for SARS-CoV-2. Consensus sequence construction and mutation identification were performed. Of all 103 samples sequenced, 69 contained relevant variants represen

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Alasia, Datonye Dennis, Omosivie Maduka, Kennedy Wariso, Temitayo Awopeju, and Faith Emuh. "SARS-CoV-2 recurrence and probable reinfection: outcome of a descriptive surveillance in a Nigerian tertiary hospital." International Journal of Research in Medical Sciences 9, no. 6 (2021): 1498. http://dx.doi.org/10.18203/2320-6012.ijrms20211912.

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Background: The reports of SARS-CoV-2 reinfection have increased. This stimulates the need for surveillance in diverse populations to establish the extent of reinfections and the challenges to diagnosis.Methods: A retrospective descriptive survey aimed at identifying probable SARS-CoV-2 reinfections using established criteria and proposed definitions was performed at a tertiary hospital in South-South, Nigeria.Results: The study found two cases for evaluation of reinfection. One case was identified as probable reinfection, pending the outcome of gene sequencing, while the second case was categ

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Umair, Massab, Aamer Ikram, Muhammad Salman, et al. "Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan." PLOS ONE 16, no. 3 (2021): e0248371. http://dx.doi.org/10.1371/journal.pone.0248371.

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Since its emergence in China, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide including Pakistan. During the pandemic, whole genome sequencing has played an important role in understanding the evolution and genomic diversity of SARS-CoV-2. Although an unprecedented number of SARS-CoV-2 full genomes have been submitted in GISAID and NCBI, data from Pakistan is scarce. We report the sequencing, genomic characterization, and phylogenetic analysis of five SARS-CoV-2 strains isolated from patients in Pakistan. The oropharyngeal swabs of patients that were confirmed

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Peddu, Vikas, Ryan C. Shean, Hong Xie, et al. "Metagenomic Analysis Reveals Clinical SARS-CoV-2 Infection and Bacterial or Viral Superinfection and Colonization." Clinical Chemistry 66, no. 7 (2020): 966–72. http://dx.doi.org/10.1093/clinchem/hvaa106.

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Abstract Background More than 2 months separated the initial description of SARS-CoV-2 and discovery of its widespread dissemination in the United States. Despite this lengthy interval, implementation of specific quantitative reverse transcription (qRT)-PCR-based SARS-CoV-2 tests in the US has been slow, and testing is still not widely available. Metagenomic sequencing offers the promise of unbiased detection of emerging pathogens, without requiring prior knowledge of the identity of the responsible agent or its genomic sequence. Methods To evaluate metagenomic approaches in the context of the

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Hernandez, Sarah, Phuong-Vi Nguyen, Taz Azmain, Anne Piantadosi, and Jesse J. Waggoner. "SARS-CoV-2 genotyping and sequencing following a simple and economical RNA extraction and storage protocol." PLOS ONE 18, no. 1 (2023): e0280577. http://dx.doi.org/10.1371/journal.pone.0280577.

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Since the beginning of the SARS-CoV-2 pandemic, supply chain shortages have caused major disruptions in sourcing the materials needed for laboratory-based molecular assays. With increasing demand for molecular testing, these disruptions have limited testing capacity and hindered efforts to mitigate spread of the virus and new variants. Here we evaluate an economical and reliable protocol for the extraction and short-term ambient temperature storage of SARS-CoV-2 RNA. Additional objectives of the study were to evaluate RNA from this protocol for 1) detection of single nucleotide polymorphisms (

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Babiker, Ahmed, Heath L. Bradley, Victoria D. Stittleburg, et al. "64. Metagenomic Sequencing to Identify Alternative Infections and Co-infections in Persons Under Investigation for covid-19." Open Forum Infectious Diseases 7, Supplement_1 (2020): S163—S164. http://dx.doi.org/10.1093/ofid/ofaa439.374.

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Abstract Background Broad testing for respiratory viruses among persons under investigation (PUI) for SARS-CoV-2 is performed inconsistently, limiting our understanding of alternative infections and co-infections in these patients. Here, we used unbiased metagenomic next-generation sequencing (mNGS) to assess the frequencies of 1) alternative viral infections in SARS-CoV-2 RT-PCR negative PUIs and 2) viral co-infections in SARS-CoV-2 RT-PCR positive PUIs. Methods A convenience sample set was selected from PUIs who were tested for SARS-CoV-2 in the Emory Healthcare system during the first 2 mon

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Rueca, Martina, Emanuela Giombini, Francesco Messina, et al. "The Easy-to-Use SARS-CoV-2 Assembler for Genome Sequencing: Development Study." JMIR Bioinformatics and Biotechnology 3, no. 1 (2022): e31536. http://dx.doi.org/10.2196/31536.

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Background Early sequencing and quick analysis of the SARS-CoV-2 genome have contributed to the understanding of the dynamics of COVID-19 epidemics and in designing countermeasures at a global level. Objective Amplicon-based next-generation sequencing (NGS) methods are widely used to sequence the SARS-CoV-2 genome and to identify novel variants that are emerging in rapid succession as well as harboring multiple deletions and amino acid–changing mutations. Methods To facilitate the analysis of NGS sequencing data obtained from amplicon-based sequencing methods, here, we propose an easy-to-use S

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Lim, Ho Jae, Min Young Park, Hye Soo Jung, et al. "Development of an efficient Sanger sequencing-based assay for detecting SARS-CoV-2 spike mutations." PLOS ONE 16, no. 12 (2021): e0260850. http://dx.doi.org/10.1371/journal.pone.0260850.

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Novel strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) harboring nucleotide changes (mutations) in the spike gene have emerged and are spreading rapidly. These mutations are associated with SARS-CoV-2 transmissibility, virulence, or resistance to some neutralizing antibodies. Thus, the accurate detection of spike mutants is crucial for controlling SARS-CoV-2 transmission and identifying neutralizing antibody-resistance caused by amino acid changes in the receptor-binding domain. Here, we developed five SARS-CoV-2 spike gene primer pairs (5-SSG primer assay; 69S, 144S, 41

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Loconsole, Daniela, Anna Sallustio, Marisa Accogli, et al. "Symptomatic SARS-CoV-2 Reinfection in a Healthy Healthcare Worker in Italy Confirmed by Whole-Genome Sequencing." Viruses 13, no. 5 (2021): 899. http://dx.doi.org/10.3390/v13050899.

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This study describes a case of SARS-CoV-2 reinfection confirmed by whole-genome sequencing in a healthy physician who had been working in a COVID-19 hospital in Italy since the beginning of the pandemic. Nasopharyngeal swabs were obtained from the patient at each presentation as part of routine surveillance. Nucleic acid amplification testing was performed on the two samples to confirm SARS-CoV-2 infection, and serological tests were used to detect SARS-CoV-2 IgG antibodies. Comparative genome analysis with whole-genome sequencing was performed on nasopharyngeal swabs collected during the two

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So, Min-Kyung, Sholhui Park, Kyunghoon Lee, Soo-Kyung Kim, Hae-Sun Chung, and Miae Lee. "Variant Prediction by Analyzing RdRp/S Gene Double or Low Amplification Pattern in Allplex SARS-CoV-2 Assay." Diagnostics 11, no. 10 (2021): 1854. http://dx.doi.org/10.3390/diagnostics11101854.

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The spread of delta variants (B.1.671.2) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a severe global threat. Multiplex real-time PCR is a common method for confirming SARS-CoV-2 infection, however, additional tests, such as whole genomic sequencing, are required to reveal the presence or type of viral mutation. Moreover, applying whole genomic sequencing to all SARS-CoV-2 positive samples is challenging due to time and cost constraints. Here, we report that the double or low amplification curve observed during RNA-dependent RNA polymerase (RdRp) gene/S gene amplification

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Vacca, Davide, Antonino Fiannaca, Fabio Tramuto, et al. "Direct RNA Nanopore Sequencing of SARS-CoV-2 Extracted from Critical Material from Swabs." Life 12, no. 1 (2022): 69. http://dx.doi.org/10.3390/life12010069.

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In consideration of the increasing prevalence of COVID-19 cases in several countries and the resulting demand for unbiased sequencing approaches, we performed a direct RNA sequencing (direct RNA seq.) experiment using critical oropharyngeal swab samples collected from Italian patients infected with SARS-CoV-2 from the Palermo region in Sicily. Here, we identified the sequences SARS-CoV-2 directly in RNA extracted from critical samples using the Oxford Nanopore MinION technology without prior cDNA retrotranscription. Using an appropriate bioinformatics pipeline, we could identify mutations in t

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Gregory, Devon A., Monica Trujillo, Clayton Rushford, et al. "Genetic diversity and evolutionary convergence of cryptic SARS- CoV-2 lineages detected via wastewater sequencing." PLOS Pathogens 18, no. 10 (2022): e1010636. http://dx.doi.org/10.1371/journal.ppat.1010636.

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Wastewater-based epidemiology (WBE) is an effective way of tracking the appearance and spread of SARS-COV-2 lineages through communities. Beginning in early 2021, we implemented a targeted approach to amplify and sequence the receptor binding domain (RBD) of SARS-COV-2 to characterize viral lineages present in sewersheds. Over the course of 2021, we reproducibly detected multiple SARS-COV-2 RBD lineages that have never been observed in patient samples in 9 sewersheds located in 3 states in the USA. These cryptic lineages contained between 4 to 24 amino acid substitutions in the RBD and were ob

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Wiegand, Tanner, Artem Nemudryi, Anna Nemudraia, et al. "The Rise and Fall of SARS-CoV-2 Variants and Ongoing Diversification of Omicron." Viruses 14, no. 9 (2022): 2009. http://dx.doi.org/10.3390/v14092009.

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In late December of 2019, high-throughput sequencing technologies enabled rapid identification of SARS-CoV-2 as the etiological agent of COVID-19, and global sequencing efforts are now a critical tool for monitoring the ongoing spread and evolution of this virus. Here, we provide a short retrospective analysis of SARS-CoV-2 variants by analyzing a subset (n = 97,437) of all publicly available SARS-CoV-2 genomes (n = ~11.9 million) that were randomly selected but equally distributed over the course of the pandemic. We plot the appearance of new variants of concern (VOCs) over time and show that

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Al-Ghazawy, Ola. "Egypt’s SARS-CoV-2 sequencing challenges." Nature Middle East, May 7, 2021. http://dx.doi.org/10.1038/nmiddleeast.2021.43.

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Alpert, Tara, Chantal B. F. Vogels, Mallery I. Breban, et al. "Sequencing SARS-CoV-2 Genomes from Saliva." Virus Evolution, January 3, 2022. http://dx.doi.org/10.1093/ve/veab098.

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Abstract Genomic sequencing is crucial to understanding the epidemiology and evolution of SARS-CoV-2. Often, genomic studies rely on remnant diagnostic material, typically nasopharyngeal swabs, as input into whole genome SARS-CoV-2 next-generation sequencing pipelines. Saliva has proven to be a safe and stable specimen for the detection of SARS-CoV-2 RNA via traditional diagnostic assays, however saliva is not commonly used for SARS-CoV-2 sequencing. Using the ARTIC Network amplicon-generation approach with sequencing on the Oxford Nanopore MinION, we demonstrate that sequencing SARS-CoV-2 fro

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Rachiglio, Anna Maria, Luca De Sabato, Cristin Roma, et al. "SARS-CoV-2 complete genome sequencing from the Italian Campania region using a highly automated next generation sequencing system." Journal of Translational Medicine 19, no. 1 (2021). http://dx.doi.org/10.1186/s12967-021-02912-4.

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Abstract Background Since the first complete genome sequencing of SARS-CoV-2 in December 2019, more than 550,000 genomes have been submitted into the GISAID database. Sequencing of the SARS-CoV-2 genome might allow identification of variants with increased contagiousness, different clinical patterns and/or different response to vaccines. A highly automated next generation sequencing (NGS)-based method might facilitate an active genomic surveillance of the virus. Methods RNA was extracted from 27 nasopharyngeal swabs obtained from citizens of the Italian Campania region in March–April 2020 who

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Bull, Rowena A., Thiruni N. Adikari, James M. Ferguson, et al. "Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis." Nature Communications 11, no. 1 (2020). http://dx.doi.org/10.1038/s41467-020-20075-6.

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AbstractViral whole-genome sequencing (WGS) provides critical insight into the transmission and evolution of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Long-read sequencing devices from Oxford Nanopore Technologies (ONT) promise significant improvements in turnaround time, portability and cost, compared to established short-read sequencing platforms for viral WGS (e.g., Illumina). However, adoption of ONT sequencing for SARS-CoV-2 surveillance has been limited due to common concerns around sequencing accuracy. To address this, here we perform viral WGS with ONT and Illumina

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Park, Changwoo, Kwan Woo Kim, Dongju Park, et al. "Rapid and sensitive amplicon-based genome sequencing of SARS-CoV-2." Frontiers in Microbiology 13 (August 17, 2022). http://dx.doi.org/10.3389/fmicb.2022.876085.

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As SARS-CoV-2 variants of concern emerged, the genome sequencing of SARS-CoV-2 strains became more important. In this study, SARS-CoV-2 was sequenced using amplicon-based genome sequencing with MinION. The primer panel used in this study consisted of only 11 primer panels and the size of the amplicons was approximately 3 kb. Full genome sequences were obtained with a hundred copies of the SARS-CoV-2 genome, and 92.33% and 75.39% of the genome sequences were obtained with 10 copies of the SARS-CoV-2 genome. The few differences in nucleotide sequences originated from mutations in laboratory cult

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Brito, Anderson F., Elizaveta Semenova, Gytis Dudas, et al. "Global disparities in SARS-CoV-2 genomic surveillance." Nature Communications 13, no. 1 (2022). http://dx.doi.org/10.1038/s41467-022-33713-y.

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AbstractGenomic sequencing is essential to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments, vaccines, and guide public health responses. To investigate the global SARS-CoV-2 genomic surveillance, we used sequences shared via GISAID to estimate the impact of sequencing intensity and turnaround times on variant detection in 189 countries. In the first two years of the pandemic, 78% of high-income countries sequenced >0.5% of their COVID-19 cases, while 42% of low- and middle-income countries reached that mark. Around 25% of the genomes from high income count

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