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

Author: Grafiati

Published: 5 June 2025

Last updated: 1 August 2025

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1

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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2

Khattak, Saadullah, Mohd Ahmar Rauf, Qamar Zaman, et al. "Genome-Wide Analysis of Codon Usage Patterns of SARS-CoV-2 Virus Reveals Global Heterogeneity of COVID-19." Biomolecules 11, no. 6 (2021): 912. http://dx.doi.org/10.3390/biom11060912.

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The ongoing outbreak of coronavirus disease COVID-19 is significantly implicated by global heterogeneity in the genome organization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The causative agents of global heterogeneity in the whole genome of SARS-CoV-2 are not well characterized due to the lack of comparative study of a large enough sample size from around the globe to reduce the standard deviation to the acceptable margin of error. To better understand the SARS-CoV-2 genome architecture, we have performed a comprehensive analysis of codon usage bias of sixty (60) strain

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3

Vasilarou, Maria, Nikolaos Alachiotis, Joanna Garefalaki, Apostolos Beloukas, and Pavlos Pavlidis. "Population Genomics Insights into the First Wave of COVID-19." Life 11, no. 2 (2021): 129. http://dx.doi.org/10.3390/life11020129.

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Full-genome-sequence computational analyses of the SARS-coronavirus (CoV)-2 genomes allow us to understand the evolutionary events and adaptability mechanisms. We used population genetics analyses on human SARS-CoV-2 genomes available on 2 April 2020 to infer the mutation rate and plausible recombination events between the Betacoronavirus genomes in nonhuman hosts that may have contributed to the evolution of SARS-CoV-2. Furthermore, we localized the targets of recent and strong, positive selection during the first pandemic wave. The genomic regions that appear to be under positive selection a

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4

Gültekin, Visam, and Jens Allmer. "Novel perspectives for SARS-CoV-2 genome browsing." Journal of Integrative Bioinformatics 18, no. 1 (2021): 19–26. http://dx.doi.org/10.1515/jib-2021-0001.

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Abstract SARS-CoV-2 has spread worldwide and caused social, economic, and health turmoil. The first genome assembly of SARS-CoV-2 was produced in Wuhan, and it is widely used as a reference. Subsequently, more than a hundred additional SARS-CoV-2 genomes have been sequenced. While the genomes appear to be mostly identical, there are variations. Therefore, an alignment of all available genomes and the derived consensus sequence could be used as a reference, better serving the science community. Variations are significant, but representing them in a genome browser can become, especially if their

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5

Rouchka, Eric C., Julia H. Chariker, and Donghoon Chung. "Variant analysis of 1,040 SARS-CoV-2 genomes." PLOS ONE 15, no. 11 (2020): e0241535. http://dx.doi.org/10.1371/journal.pone.0241535.

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The severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) viral genome is an RNA virus consisting of approximately 30,000 bases. As part of testing efforts, whole genome sequencing of human isolates has resulted in over 1,600 complete genomes publicly available from GenBank. We have performed a comparative analysis of the sequences, in order to detect common mutations within the population. Analysis of variants occurring within the assembled genomes yields 417 variants occurring in at least 1% of the completed genomes, including 229 within the 5’ untranslated region (UTR), 152 within th

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6

Gunadi, Hendra Wibawa, Marcellus, et al. "Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia." PeerJ 8 (December 21, 2020): e10575. http://dx.doi.org/10.7717/peerj.10575.

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Background Recently, SARS-CoV-2 virus with the D614G mutation has become a public concern due to rapid dissemination of this variant across many countries. Our study aims were (1) to report full-length genome sequences of SARS-CoV-2 collected from four COVID-19 patients in the Special Region of Yogyakarta and Central Java provinces, Indonesia; (2) to compare the clade distribution of full-length genome sequences from Indonesia (n = 60) from March to September 2020 and (3) to perform phylogenetic analysis of SARS-CoV-2 complete genomes from different countries, including Indonesia. Methods Whol

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7

Parlikar, Arohi, Kishan Kalia, Shruti Sinha, et al. "Understanding genomic diversity, pan-genome, and evolution of SARS-CoV-2." PeerJ 8 (July 17, 2020): e9576. http://dx.doi.org/10.7717/peerj.9576.

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Coronovirus disease 2019 (COVID-19) infection, which originated from Wuhan, China, has seized the whole world in its grasp and created a huge pandemic situation before humanity. Since December 2019, genomes of numerous isolates have been sequenced and analyzed for testing confirmation, epidemiology, and evolutionary studies. In the first half of this article, we provide a detailed review of the history and origin of COVID-19, followed by the taxonomy, nomenclature and genome organization of its causative agent Severe Acute Respiratory Syndrome-related Coronavirus-2 (SARS-CoV-2). In the latter

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8

ŞAHİNGİL, Mehmet Cihan, and Yakup OZKAZANC. "Comparison of SARS-CoV-2 Virus Variant Genomes Detected in China and the USA." Genetics & Applications 4, no. 2 (2020): 10. http://dx.doi.org/10.31383/ga.vol4iss2pp10-26.

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In the spreading period of the SARS-CoV-2 virus which is the cause of COVID-19 in the world, it is seen that the genome of the virus mutates and this mutation processes create new SARS-CoV-2 variants. In this study, we examined two variant genome groups. The first group includes the genomes of variants detected in China, while the second includes those detected in the USA. We applied the multiple sequence alignment process on these publicly available SARS-CoV-2 virus genomes and reported the obtained results. There are 87 genomes for China variants and 200 for USA variants in the used data. Th

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9

Shrestha, R., N. Katuwal, N. Adhikari, et al. "Whole Genome Sequence Analysis to Identify SARS-CoV-2 Variant in Nepal." Kathmandu University Medical Journal 19, no. 2 (2021): 237–42. http://dx.doi.org/10.3126/kumj.v19i2.49653.

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Background The spread of SARS-CoV-2 has become a global public health crisis. Nepal is facing the second wave of COVID-19 pandemic but, there is still a limited data on the genomic sequence of SARS-CoV-2 variants circulating in Nepal. Objective The objective of this study is to sequence the whole genome of SARS-CoV-2 in Nepal to detect possible mutation profiles and phylogenetic lineages of circulating SARSCoV- 2 variants. Method In this study, swab samples tested positive for SARS-CoV-2 were investigated. After RNA extraction, the investigation was performed through real-time PCR

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10

Xia, Xuhua. "Dating the Common Ancestor from an NCBI Tree of 83688 High-Quality and Full-Length SARS-CoV-2 Genomes." Viruses 13, no. 9 (2021): 1790. http://dx.doi.org/10.3390/v13091790.

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All dating studies involving SARS-CoV-2 are problematic. Previous studies have dated the most recent common ancestor (MRCA) between SARS-CoV-2 and its close relatives from bats and pangolins. However, the evolutionary rate thus derived is expected to differ from the rate estimated from sequence divergence of SARS-CoV-2 lineages. Here, I present dating results for the first time from a large phylogenetic tree with 86,582 high-quality full-length SARS-CoV-2 genomes. The tree contains 83,688 genomes with full specification of collection time. Such a large tree spanning a period of about 1.5 years

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11

Handrick, Susann, Malena Bestehorn-Willmann, Simone Eckstein, et al. "Whole genome sequencing and phylogenetic classification of Tunisian SARS-CoV-2 strains from patients of the Military Hospital in Tunis." Virus Genes 56, no. 6 (2020): 767–71. http://dx.doi.org/10.1007/s11262-020-01795-9.

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AbstractIn the present work, two complete genome sequences of SARS-CoV-2 were obtained from nasal swab samples of Tunisian SARS-CoV-2 PCR-positive patients using nanopore sequencing. The virus genomes of two of the patients examined, a Tunisian soldier returning from a mission in Morocco and a member of another Tunisian family, showed significant differences in analyses of the total genome and single nucleotide polymorphisms (SNPs). Phylogenetic relationships with known SARS-CoV-2 genomes in the African region, some European and Middle Eastern countries and initial epidemiological conclusions

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12

Yuen, K. Y., S. K. P. Lau, and P. C. Y. Woo. "Wild animal surveillance for coronavirus HKU1 and potential variants of other coronaviruses." Hong Kong Medical Journal = Xianggang Yi Xue Za Zhi 18 Suppl 2 (June 12, 2012): 25–26. https://doi.org/10.5281/zenodo.13532165.

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(Uploaded by Plazi for the Bat Literature Project) 1. Although CoV-HKU1 was not identified in any of the studied animals, a coronavirus closely related to SARS-CoV (bat-SARS-CoV) was identified in 23 (19%) of 118 wild Chinese horseshoe bats by reverse transcriptase polymerase chain reaction (RT-PCR). 2. Complete genome sequencing and phylogenetic analysis showed that bat-SARS-CoV formed a distinct cluster with SARS-CoV as group 2b coronaviruses, distantly related to known group 2 coronaviruses. 3. Most differences between the bat-SARS-CoV and SARS-CoV genomes were observed in the spike gene. T

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13

Yuen, K. Y., S. K. P. Lau, and P. C. Y. Woo. "Wild animal surveillance for coronavirus HKU1 and potential variants of other coronaviruses." Hong Kong Medical Journal = Xianggang Yi Xue Za Zhi 18 Suppl 2 (June 7, 2012): 25–26. https://doi.org/10.5281/zenodo.13532165.

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(Uploaded by Plazi for the Bat Literature Project) 1. Although CoV-HKU1 was not identified in any of the studied animals, a coronavirus closely related to SARS-CoV (bat-SARS-CoV) was identified in 23 (19%) of 118 wild Chinese horseshoe bats by reverse transcriptase polymerase chain reaction (RT-PCR). 2. Complete genome sequencing and phylogenetic analysis showed that bat-SARS-CoV formed a distinct cluster with SARS-CoV as group 2b coronaviruses, distantly related to known group 2 coronaviruses. 3. Most differences between the bat-SARS-CoV and SARS-CoV genomes were observed in the spike gene. T

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14

Tang, Tao, and Jinyan Li. "Comparative studies on the high-performance compression of SARS-CoV-2 genome collections." Briefings in Functional Genomics 21, no. 2 (2021): 103–12. http://dx.doi.org/10.1093/bfgp/elab041.

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Abstract The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is fast mutating worldwide. The mutated strains have been timely sequenced by worldwide labs, accumulating a huge amount of viral genome sequences open to public for biomedicine research such as mRNA vaccine design and drug recommendation. It is inefficient to transmit the millions of genome sequences without compression. In this study, we benchmark the performance of reference-free and reference-based compression algorithms on SARS-CoV-2 genome collections extracted from NCBI. Experimental results show that reference-ba

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15

Wei, Yulong, Jordan R. Silke, Parisa Aris, and Xuhua Xia. "Coronavirus genomes carry the signatures of their habitats." PLOS ONE 15, no. 12 (2020): e0244025. http://dx.doi.org/10.1371/journal.pone.0244025.

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Coronaviruses such as SARS-CoV-2 regularly infect host tissues that express antiviral proteins (AVPs) in abundance. Understanding how they evolve to adapt or evade host immune responses is important in the effort to control the spread of infection. Two AVPs that may shape viral genomes are the zinc finger antiviral protein (ZAP) and the apolipoprotein B mRNA editing enzyme-catalytic polypeptide-like 3 (APOBEC3). The former binds to CpG dinucleotides to facilitate the degradation of viral transcripts while the latter frequently deaminates C into U residues which could generate notable viral seq

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16

Alisoltani, Arghavan, Lukasz Jaroszewski, Adam Godzik, et al. "ViralVar: A Web Tool for Multilevel Visualization of SARS-CoV-2 Genomes." Viruses 14, no. 12 (2022): 2714. http://dx.doi.org/10.3390/v14122714.

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The unprecedented growth of publicly available SARS-CoV-2 genome sequence data has increased the demand for effective and accessible SARS-CoV-2 data analysis and visualization tools. The majority of the currently available tools either require computational expertise to deploy them or limit user input to preselected subsets of SARS-CoV-2 genomes. To address these limitations, we developed ViralVar, a publicly available, point-and-click webtool that gives users the freedom to investigate and visualize user-selected subsets of SARS-CoV-2 genomes obtained from the GISAID public database. ViralVar

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17

Mohanta, Tapan Kumar. "Corona virus (CoVid19) genome: genomic and biochemical analysis revealed its possible synthetic origin." Journal of Applied Biotechnology & Bioengineering 7, no. 5 (2020): 200–213. http://dx.doi.org/10.15406/jabb.2020.07.00235.

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The Severe acute respiratory syndrome (SARS) corona virus 2 SARS-CoV-2 mediated epidemic is a global pandemic. It has evolved as a curse to the human civilization and at the present situation, where most of the cities in the world are on lockdown. The first genome sequence data of SARS-CoV-2 (CoVid19) and their reports that followed concluded that it was a member of the genus Betacoronavirus and has a bat reservoir. To understand its origin and evolution, we conducted a deep comparative study by comparing the genomes of bat SARS CoV and other SARS CoVs (including human SARS CoV of German isola

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18

Azgari, Cem, Zeynep Kilinc, Berk Turhan, Defne Circi, and Ogun Adebali. "The Mutation Profile of SARS-CoV-2 Is Primarily Shaped by the Host Antiviral Defense." Viruses 13, no. 3 (2021): 394. http://dx.doi.org/10.3390/v13030394.

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Understanding SARS-CoV-2 evolution is a fundamental effort in coping with the COVID-19 pandemic. The virus genomes have been broadly evolving due to the high number of infected hosts world-wide. Mutagenesis and selection are two inter-dependent mechanisms of virus diversification. However, which mechanisms contribute to the mutation profiles of SARS-CoV-2 remain under-explored. Here, we delineate the contribution of mutagenesis and selection to the genome diversity of SARS-CoV-2 isolates. We generated a comprehensive phylogenetic tree with representative genomes. Instead of counting mutations

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19

Lau, Susanna K. P., Patrick C. Y. Woo, Kenneth S. M. Li, et al. "Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats." Proceedings of the National Academy of Sciences 102, no. 39 (2005): 14040——14045. https://doi.org/10.1073/pnas.0506735102.

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Although the finding of severe acute respiratory syndrome coronavirus (SARS-CoV) in caged palm civets from live animal markets in China has provided evidence for interspecies transmission in the genesis of the SARS epidemic, subsequent studies suggested that the civet may have served only as an amplification host for SARS-CoV. In a surveillance study for CoV in noncaged animals from the wild areas of the Hong Kong Special Administration Region, we identified a CoV closely related to SARS-CoV (bat-SARS-CoV) from 23 (39\%) of 59 anal swabs of wild Chinese horseshoe bats (Rhinolophus sinicus) by

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20

Colson, Philippe, and Didier Raoult. "Global Discrepancies between Numbers of Available SARS-CoV-2 Genomes and Human Development Indexes at Country Scales." Viruses 13, no. 5 (2021): 775. http://dx.doi.org/10.3390/v13050775.

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It has now been over a year since SARS-CoV-2 first emerged in China, in December 2019, and it has spread rapidly around the world. Some variants are currently considered of great concern. We aimed to analyze the numbers of SARS-CoV-2 genome sequences obtained in different countries worldwide until January 2021. On 28 January 2021, we downloaded the deposited genome sequence origin from the GISAID database, and from the “Our world in data” website we downloaded numbers of SARS-CoV-2-diagnosed cases, numbers of SARS-CoV-2-associated deaths, population size, life expectancy, gross domestic produc

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21

Lau, Susanna K. P., Patrick C. Y. Woo, Kenneth S. M. Li, et al. "Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats." Proceedings of the National Academy of Sciences of the United States of America 102, no. 39 (2005): 14040–45. https://doi.org/10.5281/zenodo.13504940.

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(Uploaded by Plazi for the Bat Literature Project) Although the finding of severe acute respiratory syndrome coronavirus (SARS-CoV) in caged palm civets from live animal markets in China has provided evidence for interspecies transmission in the genesis of the SARS epidemic, subsequent studies suggested that the civet may have served only as an amplification host for SARS-CoV. In a surveillance study for CoV in noncaged animals from the wild areas of the Hong Kong Special Administration Region, we identified a CoV closely related to SARS-CoV (bat-SARS-CoV) from 23 (39%) of 59 anal swabs of wil

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22

Lau, Susanna K. P., Patrick C. Y. Woo, Kenneth S. M. Li, et al. "Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats." Proceedings of the National Academy of Sciences of the United States of America 102, no. 39 (2005): 14040–45. https://doi.org/10.5281/zenodo.13504940.

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(Uploaded by Plazi for the Bat Literature Project) Although the finding of severe acute respiratory syndrome coronavirus (SARS-CoV) in caged palm civets from live animal markets in China has provided evidence for interspecies transmission in the genesis of the SARS epidemic, subsequent studies suggested that the civet may have served only as an amplification host for SARS-CoV. In a surveillance study for CoV in noncaged animals from the wild areas of the Hong Kong Special Administration Region, we identified a CoV closely related to SARS-CoV (bat-SARS-CoV) from 23 (39%) of 59 anal swabs of wil

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23

Lau, Susanna K. P., Patrick C. Y. Woo, Kenneth S. M. Li, et al. "Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats." Proceedings of the National Academy of Sciences of the United States of America 102, no. 39 (2005): 14040–45. https://doi.org/10.5281/zenodo.13504940.

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(Uploaded by Plazi for the Bat Literature Project) Although the finding of severe acute respiratory syndrome coronavirus (SARS-CoV) in caged palm civets from live animal markets in China has provided evidence for interspecies transmission in the genesis of the SARS epidemic, subsequent studies suggested that the civet may have served only as an amplification host for SARS-CoV. In a surveillance study for CoV in noncaged animals from the wild areas of the Hong Kong Special Administration Region, we identified a CoV closely related to SARS-CoV (bat-SARS-CoV) from 23 (39%) of 59 anal swabs of wil

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24

Lau, Susanna K. P., Patrick C. Y. Woo, Kenneth S. M. Li, et al. "Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats." Proceedings of the National Academy of Sciences of the United States of America 102, no. 39 (2005): 14040–45. https://doi.org/10.5281/zenodo.13504940.

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(Uploaded by Plazi for the Bat Literature Project) Although the finding of severe acute respiratory syndrome coronavirus (SARS-CoV) in caged palm civets from live animal markets in China has provided evidence for interspecies transmission in the genesis of the SARS epidemic, subsequent studies suggested that the civet may have served only as an amplification host for SARS-CoV. In a surveillance study for CoV in noncaged animals from the wild areas of the Hong Kong Special Administration Region, we identified a CoV closely related to SARS-CoV (bat-SARS-CoV) from 23 (39%) of 59 anal swabs of wil

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25

Weber, Stefanie, Christina M. Ramirez, and Walter Doerfler. "Ubiquitous Micro-Modular Homologies among Genomes from Viruses to Bacteria to Human Mitochondrial DNA: Platforms for Recombination during Evolution?" Viruses 14, no. 5 (2022): 885. http://dx.doi.org/10.3390/v14050885.

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The emerging Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) and its variants have raised tantalizing questions about evolutionary mechanisms that continue to shape biology today. We have compared the nucleotide sequence of SARS-CoV-2 RNA to that of genomes of many different viruses, of endosymbiotic proteobacterial and bacterial DNAs, and of human mitochondrial DNA. The entire 4,641,652 nt DNA sequence of Escherichia coli K12 has been computer-matched to SARS-CoV-2 RNA. Numerous, very similar micro-modular clusters of 3 to 13 nucleotides lengths were detected with sequence identi

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26

Weber, Stefanie, Christina M. Ramirez, and Walter Doerfler. "Ubiquitous Micro-Modular Homologies among Genomes from Viruses to Bacteria to Human Mitochondrial DNA: Platforms for Recombination during Evolution?" Viruses 14, no. 5 (2022): 885. http://dx.doi.org/10.3390/v14050885.

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The emerging Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) and its variants have raised tantalizing questions about evolutionary mechanisms that continue to shape biology today. We have compared the nucleotide sequence of SARS-CoV-2 RNA to that of genomes of many different viruses, of endosymbiotic proteobacterial and bacterial DNAs, and of human mitochondrial DNA. The entire 4,641,652 nt DNA sequence of Escherichia coli K12 has been computer-matched to SARS-CoV-2 RNA. Numerous, very similar micro-modular clusters of 3 to 13 nucleotides lengths were detected with sequence identi

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27

Koyama, Takahiko, Daniel Platt, and Laxmi Parida. "Variant analysis of SARS-CoV-2 genomes." Bulletin of the World Health Organization 98, no. 7 (2020): 495–504. http://dx.doi.org/10.2471/blt.20.253591.

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28

Gand, Mathieu, Kevin Vanneste, Isabelle Thomas, et al. "Use of Whole Genome Sequencing Data for a First in Silico Specificity Evaluation of the RT-qPCR Assays Used for SARS-CoV-2 Detection." International Journal of Molecular Sciences 21, no. 15 (2020): 5585. http://dx.doi.org/10.3390/ijms21155585.

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The current COronaVIrus Disease 2019 (COVID-19) pandemic started in December 2019. COVID-19 cases are confirmed by the detection of SARS-CoV-2 RNA in biological samples by RT-qPCR. However, limited numbers of SARS-CoV-2 genomes were available when the first RT-qPCR methods were developed in January 2020 for initial in silico specificity evaluation and to verify whether the targeted loci are highly conserved. Now that more whole genome data have become available, we used the bioinformatics tool SCREENED and a total of 4755 publicly available SARS-CoV-2 genomes, downloaded at two different time

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29

Khalid, Mohammad, Anas Alshishani, and Yousef Al-ebini. "Genome Similarities between Human-Derived and Mink-Derived SARS-CoV-2 Make Mink a Potential Reservoir of the Virus." Vaccines 10, no. 8 (2022): 1352. http://dx.doi.org/10.3390/vaccines10081352.

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SARS-CoV-2 has RNA as the genome, which makes the virus more prone to mutations. Occasionally, mutations help a virus to cross the species barrier. SARS-CoV-2 infections in humans and minks (Neovison vison) are examples of zoonotic spillover. Many studies on the mutational analysis of human-derived SARS-CoV-2 have been published, but insight into the mink-derived SARS-CoV-2 genome of mutations is still required. Here, we performed a mutation analysis of the mink-derived SARS-CoV-2 genome sequences. We analyzed all available full-length mink-derived SARS-CoV-2 genome sequences on GISAID (214 ge

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Matyášek, Roman, and Aleš Kovařík. "Mutation Patterns of Human SARS-CoV-2 and Bat RaTG13 Coronavirus Genomes Are Strongly Biased Towards C>U Transitions, Indicating Rapid Evolution in Their Hosts." Genes 11, no. 7 (2020): 761. http://dx.doi.org/10.3390/genes11070761.

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The pandemic caused by the spread of SARS-CoV-2 has led to considerable interest in its evolutionary origin and genome structure. Here, we analyzed mutation patterns in 34 human SARS-CoV-2 isolates and a closely related RaTG13 isolated from Rhinolophus affinis (a horseshoe bat). We also evaluated the CpG dinucleotide contents in SARS-CoV-2 and other human and animal coronavirus genomes. Out of 1136 single nucleotide variations (~4% divergence) between human SARS-CoV-2 and bat RaTG13, 682 (60%) can be attributed to C>U and U>C substitutions, far exceeding other types of substitutions. An

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31

Hakmaoui, Abdelmalek, Faisal Khan, Abdelhamid Liacini, et al. "Relevant SARS-CoV-2 Genome Variation through Six Months of Worldwide Monitoring." BioMed Research International 2021 (June 29, 2021): 1–10. http://dx.doi.org/10.1155/2021/5553173.

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Real-time genome monitoring of the SARS-CoV-2 pandemic outbreak is of utmost importance for designing diagnostic tools, guiding antiviral treatment and vaccination strategies. In this study, we present an accurate method for temporal and geographical comparison of mutational events based on GISAID database genome sequencing. Among 42523 SARS-CoV-2 genomes analyzed, we found 23202 variants compared to the reference genome. The Ti/Tv (transition/transversion) ratio was used to filter out possible false-positive errors. Transition mutations generally occurred more frequently than transversions. O

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32

Pan, Bohu, Zuowei Ji, Sugunadevi Sakkiah, et al. "Identification of Epidemiological Traits by Analysis of SARS−CoV−2 Sequences." Viruses 13, no. 5 (2021): 764. http://dx.doi.org/10.3390/v13050764.

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Severe acute respiratory syndrome coronavirus 2 (SARS−CoV−2) has caused the ongoing global COVID-19 pandemic that began in late December 2019. The rapid spread of SARS−CoV−2 is primarily due to person-to-person transmission. To understand the epidemiological traits of SARS−CoV−2 transmission, we conducted phylogenetic analysis on genome sequences from >54K SARS−CoV−2 cases obtained from two public databases. Hierarchical clustering analysis on geographic patterns in the resulting phylogenetic trees revealed a co-expansion tendency of the virus among neighboring countries with diverse source

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Bedford, Trevor, Alexander L. Greninger, Pavitra Roychoudhury, et al. "Cryptic transmission of SARS-CoV-2 in Washington state." Science 370, no. 6516 (2020): 571–75. http://dx.doi.org/10.1126/science.abc0523.

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After its emergence in Wuhan, China, in late November or early December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus rapidly spread globally. Genome sequencing of SARS-CoV-2 allows the reconstruction of its transmission history, although this is contingent on sampling. We analyzed 453 SARS-CoV-2 genomes collected between 20 February and 15 March 2020 from infected patients in Washington state in the United States. We find that most SARS-CoV-2 infections sampled during this time derive from a single introduction in late January or early February 2020, which subse

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Ryder, Rahil, Emily Smith, Deva Borthwick, et al. "Emergence of Recombinant SARS-CoV-2 Variants in California from 2020 to 2022." Viruses 16, no. 8 (2024): 1209. http://dx.doi.org/10.3390/v16081209.

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The detection, characterization, and monitoring of SARS-CoV-2 recombinant variants constitute a challenge for public health authorities worldwide. Recombinant variants, composed of two or more SARS-CoV-2 lineages, often have unknown impacts on transmission, immune escape, and virulence in the early stages of emergence. We examined 4213 SARS-CoV-2 recombinant SARS-CoV-2 genomes collected between 2020 and 2022 in California to describe regional and statewide trends in prevalence. Many of these recombinant genomes, such as those belonging to the XZ lineage or novel recombinant lineages, likely or

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35

Liu, Boxiang, Kaibo Liu, He Zhang, Liang Zhang, Yuchen Bian, and Liang Huang. "CoV-Seq, a New Tool for SARS-CoV-2 Genome Analysis and Visualization: Development and Usability Study." Journal of Medical Internet Research 22, no. 10 (2020): e22299. http://dx.doi.org/10.2196/22299.

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Background COVID-19 became a global pandemic not long after its identification in late 2019. The genomes of SARS-CoV-2 are being rapidly sequenced and shared on public repositories. To keep up with these updates, scientists need to frequently refresh and reclean data sets, which is an ad hoc and labor-intensive process. Further, scientists with limited bioinformatics or programming knowledge may find it difficult to analyze SARS-CoV-2 genomes. Objective To address these challenges, we developed CoV-Seq, an integrated web server that enables simple and rapid analysis of SARS-CoV-2 genomes. Meth

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Warren, René L., and Inanc Birol. "Interactive SARS-CoV-2 mutation timemaps." F1000Research 10 (February 3, 2021): 68. http://dx.doi.org/10.12688/f1000research.50857.1.

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As the year 2020 came to a close, several new strains have been reported of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the agent responsible for the coronavirus disease 2019 (COVID-19) pandemic that has afflicted us all this past year. However, it is difficult to comprehend the scale, in sequence space, geographical location and time, at which SARS-CoV-2 mutates and evolves in its human hosts. To get an appreciation for the rapid evolution of the coronavirus, we built interactive scalable vector graphics maps that show daily nucleotide variations in genomes from the six

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Warren, René L., and Inanc Birol. "Interactive SARS-CoV-2 mutation timemaps." F1000Research 10 (June 3, 2021): 68. http://dx.doi.org/10.12688/f1000research.50857.2.

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As the year 2020 came to a close, several new strains have been reported of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the agent responsible for the coronavirus disease 2019 (COVID-19) pandemic that has afflicted us all this past year. However, it is difficult to comprehend the scale, in sequence space, geographical location and time, at which SARS-CoV-2 mutates and evolves in its human hosts. To get an appreciation for the rapid evolution of the coronavirus, we built interactive scalable vector graphics maps that show daily nucleotide variations in genomes from the six

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Bader, Wahiba, Jeremy Delerce, Sarah Aherfi, Bernard La Scola, and Philippe Colson. "Quasispecies Analysis of SARS-CoV-2 of 15 Different Lineages during the First Year of the Pandemic Prompts Scratching under the Surface of Consensus Genome Sequences." International Journal of Molecular Sciences 23, no. 24 (2022): 15658. http://dx.doi.org/10.3390/ijms232415658.

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The tremendous majority of SARS-CoV-2 genomic data so far neglected intra-host genetic diversity. Here, we studied SARS-CoV-2 quasispecies based on data generated by next-generation sequencing (NGS) of complete genomes. SARS-CoV-2 raw NGS data had been generated for nasopharyngeal samples collected between March 2020 and February 2021 by the Illumina technology on a MiSeq instrument, without prior PCR amplification. To analyze viral quasispecies, we designed and implemented an in-house Excel file (“QuasiS”) that can characterize intra-sample nucleotide diversity along the genomes using data of

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Campos, João H. C., Juliana T. Maricato, Carla T. Braconi, Fernando Antoneli, Luiz Mario R. Janini, and Marcelo R. S. Briones. "Direct RNA Sequencing Reveals SARS-CoV-2 m6A Sites and Possible Differential DRACH Motif Methylation among Variants." Viruses 13, no. 11 (2021): 2108. http://dx.doi.org/10.3390/v13112108.

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The causative agent of COVID-19 pandemic, SARS-CoV-2, has a 29,903 bases positive-sense single-stranded RNA genome. RNAs exhibit about 150 modified bases that are essential for proper function. Among internal modified bases, the N6-methyladenosine, or m6A, is the most frequent, and is implicated in SARS-CoV-2 immune response evasion. Although the SARS-CoV-2 genome is RNA, almost all genomes sequenced thus far are, in fact, reverse transcribed complementary DNAs. This process reduces the true complexity of these viral genomes because the incorporation of dNTPs hides RNA base modifications. Here

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Panchin, Alexander Y., and Yuri V. Panchin. "Excessive G–U transversions in novel allele variants in SARS-CoV-2 genomes." PeerJ 8 (July 28, 2020): e9648. http://dx.doi.org/10.7717/peerj.9648.

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Background SARS-CoV-2 is a novel coronavirus that causes COVID-19 infection, with a closest known relative found in bats. For this virus, hundreds of genomes have been sequenced. This data provides insights into SARS-CoV-2 adaptations, determinants of pathogenicity and mutation patterns. A comparison between patterns of mutations that occurred before and after SARS-CoV-2 jumped to human hosts may reveal important evolutionary consequences of zoonotic transmission. Methods We used publically available complete genomes of SARS-CoV-2 to calculate relative frequencies of single nucleotide variatio

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Miroshnichenko, L. A., V. D. Gusev, and Yu P. Dzhioev. "Comparison of genomes of different species of coronaviruses using spectra of periodicities." Journal of Physics: Conference Series 2099, no. 1 (2021): 012038. http://dx.doi.org/10.1088/1742-6596/2099/1/012038.

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Abstract In the genomes of different organisms, there are periodicities, i.e. fragments of DNA (RNA)-sequences formed by tandem repetition of the basic monomer (period). The spectra of periodicities with lengths exceeding the ‘noise’ threshold are quite compact and visible even for complete genomes. This makes them an acceptable tool for differentiating closely related objects. The objects of analysis in this work are the periodicities at genomes of three species of coronavirus: MERS, SARS, and SARS-CoV-2. It has been shown that there are markers in the form of periodicities that make it possi

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Agarwal, Akshay, Kristen L. Beck, Sara Capponi, et al. "Predicting Epitope Candidates for SARS-CoV-2." Viruses 14, no. 8 (2022): 1837. http://dx.doi.org/10.3390/v14081837.

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Epitopes are short amino acid sequences that define the antigen signature to which an antibody or T cell receptor binds. In light of the current pandemic, epitope analysis and prediction are paramount to improving serological testing and developing vaccines. In this paper, known epitope sequences from SARS-CoV, SARS-CoV-2, and other Coronaviridae were leveraged to identify additional antigen regions in 62K SARS-CoV-2 genomes. Additionally, we present epitope distribution across SARS-CoV-2 genomes, locate the most commonly found epitopes, and discuss where epitopes are located on proteins and h

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Xia, Xuhua. "Extreme Genomic CpG Deficiency in SARS-CoV-2 and Evasion of Host Antiviral Defense." Molecular Biology and Evolution 37, no. 9 (2020): 2699–705. http://dx.doi.org/10.1093/molbev/msaa094.

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Abstract Wild mammalian species, including bats, constitute the natural reservoir of betacoronavirus (including SARS, MERS, and the deadly SARS-CoV-2). Different hosts or host tissues provide different cellular environments, especially different antiviral and RNA modification activities that can alter RNA modification signatures observed in the viral RNA genome. The zinc finger antiviral protein (ZAP) binds specifically to CpG dinucleotides and recruits other proteins to degrade a variety of viral RNA genomes. Many mammalian RNA viruses have evolved CpG deficiency. Increasing CpG dinucleotides

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Forster, Peter, Lucy Forster, Colin Renfrew, and Michael Forster. "Phylogenetic network analysis of SARS-CoV-2 genomes." Proceedings of the National Academy of Sciences 117, no. 17 (2020): 9241–43. http://dx.doi.org/10.1073/pnas.2004999117.

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In a phylogenetic network analysis of 160 complete human severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) genomes, we find three central variants distinguished by amino acid changes, which we have named A, B, and C, with A being the ancestral type according to the bat outgroup coronavirus. The A and C types are found in significant proportions outside East Asia, that is, in Europeans and Americans. In contrast, the B type is the most common type in East Asia, and its ancestral genome appears not to have spread outside East Asia without first mutating into derived B types, pointing

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Saavedra Camacho, Johnny Leandro, Sebastian Iglesias-Osores, Miguel Alcántara-Mimbela, and Lizbeth M. Córdova-Rojas. "Analysis Of SARS-CoV-2 Genomes Of Samples From Peru." Revista de la Facultad de Medicina Humana 21, no. 3 (2021): 475–85. http://dx.doi.org/10.25176/rfmh.v21i3.3712.

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A. Pater, Adrian, Michael S. Bosmeny, Adam A. White, et al. "High throughput nanopore sequencing of SARS-CoV-2 viral genomes from patient samples." Journal of Biological Methods 8, no. 4 (2021): 1. http://dx.doi.org/10.14440/jbm.2021.360.

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In late 2019, a novel coronavirus began spreading in Wuhan, China, causing a potentially lethal respiratory viral infection. By early 2020, the novel coronavirus, called SARS-CoV-2, had spread globally, causing the COVID-19 pandemic. The infection and mutation rates of SARS-CoV-2 make it amenable to tracking introduction, spread and evolution by viral genome sequencing. Efforts to develop effective public health policies, therapeutics, or vaccines to treat or prevent COVID-19 are also expected to benefit from tracking mutations of the SARS-CoV-2 virus. Here we describe a set of comprehensive w

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Jian, Ming-Jr, Hsing-Yi Chung, Chih-Kai Chang, et al. "Genomic analysis of early transmissibility assessment of the D614G mutant strain of SARS-CoV-2 in travelers returning to Taiwan from the United States of America." PeerJ 9 (September 2, 2021): e11991. http://dx.doi.org/10.7717/peerj.11991.

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Background There is a global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Information on viral genomics is crucial for understanding global dispersion and for providing insight into viral pathogenicity and transmission. Here, we characterized the SARS-CoV-2 genomes isolated from five travelers who returned to Taiwan from the United States of America (USA) between March and April 2020. Methods Haplotype network analysis was performed using genome-wide single-nucleotide variations to trace potential infection routes. To determine the genetic variations and evolutiona

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Qian, Zhaohui, Pei Li, Xiaolu Tang, and Jian Lu. "Evolutionary dynamics of the severe acute respiratory syndrome coronavirus 2 genomes." Medical Review 2, no. 1 (2022): 3–22. http://dx.doi.org/10.1515/mr-2021-0035.

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Abstract The coronavirus disease 2019 (COVID-19) pandemic has caused immense losses in human lives and the global economy and posed significant challenges for global public health. As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, has evolved, thousands of single nucleotide variants (SNVs) have been identified across the viral genome. The roles of individual SNVs in the zoonotic origin, evolution, and transmission of SARS-CoV-2 have become the focus of many studies. This review summarizes recent comparative genomic analyses of SARS-CoV-2 and rela

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Bartoszewski, Rafal, Michal Dabrowski, Bogdan Jakiela, et al. "SARS-CoV-2 may regulate cellular responses through depletion of specific host miRNAs." American Journal of Physiology-Lung Cellular and Molecular Physiology 319, no. 3 (2020): L444—L455. http://dx.doi.org/10.1152/ajplung.00252.2020.

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Cold viruses have generally been considered fairly innocuous until the appearance of the severe acute respiratory coronavirus 2 (SARS-CoV-2) in 2019, which caused the coronavirus disease 2019 (COVID-19) global pandemic. Two previous viruses foreshadowed that a coronavirus could potentially have devastating consequences in 2002 [severe acute respiratory coronavirus (SARS-CoV)] and in 2012 [Middle East respiratory syndrome coronavirus (MERS-CoV)]. The question that arises is why these viruses are so different from the relatively harmless cold viruses. On the basis of an analysis of the current l

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O'Murchu, Eamon, Sinead O'Neill, Paula Byrne, et al. "Comparative genomic analysis demonstrates that true reinfection following SARS-CoV-2 infection is possible." Journal of Clinical Virology Plus 1, no. 1 (2021): 100015. https://doi.org/10.1016/j.jcvp.2021.100015.

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Background: In recent months, multiple cases of confirmed SARS-CoV-2 reinfection have been reported. However, accurate epidemiological and virological data, including genomic analysis where possible, are required to differentiate cases of prolonged viral RNA shedding (i.e. intermittent detection) from true reinfection. The objective of this review was to systematically identify and summarise all cases of SARS-CoV-2 reinfection confirmed by comparative genomic analysis. Methods: A protocol based on Cochrane rapid review methodology was employed. Databases and pre-print servers were se

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