Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations

Yang, Hsin Chou; Chen, Chun-Houh; Wang, Jen Hung; Liao, Hsiao Chi; Yang, Chorng-Horng; Chen, Chia Wei; Lin, Yin; Kao, Chiun How; Lu, Mei-Yeh Jade; Liao, James C.

doi:10.1073/pnas.2007840117

Cited by 75 publications

(78 citation statements)

References 18 publications

(13 reference statements)

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“…Viruses with 3037T-14408T-23403G have a fitness gain, which was reported by Yang et al. in their latest discovery [ 31 ]. A23403G were deemed as important mutations in spike protein.…”

Section: Discussionmentioning

confidence: 75%

Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2

Liang

Han

Zhu

et al. 2021

Briefings in Bioinformatics

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Since the first report of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019, the COVID-19 pandemic has spread rapidly worldwide. Due to the limited virus strains, few key mutations that would be very important with the evolutionary trends of virus genome were observed in early studies. Here, we downloaded 1809 sequence data of SARS-CoV-2 strains from GISAID before April 2020 to identify mutations and functional alterations caused by these mutations. Totally, we identified 1017 nonsynonymous and 512 synonymous mutations with alignment to reference genome NC_045512, none of which were observed in the receptor-binding domain (RBD) of the spike protein. On average, each of the strains could have about 1.75 new mutations each month. The current mutations may have few impacts on antibodies. Although it shows the purifying selection in whole-genome, ORF3a, ORF8 and ORF10 were under positive selection. Only 36 mutations occurred in 1% and more virus strains were further analyzed to reveal linkage disequilibrium (LD) variants and dominant mutations. As a result, we observed five dominant mutations involving three nonsynonymous mutations C28144T, C14408T and A23403G and two synonymous mutations T8782C, and C3037T. These five mutations occurred in almost all strains in April 2020. Besides, we also observed two potential dominant nonsynonymous mutations C1059T and G25563T, which occurred in most of the strains in April 2020. Further functional analysis shows that these mutations decreased protein stability largely, which could lead to a significant reduction of virus virulence. In addition, the A23403G mutation increases the spike-ACE2 interaction and finally leads to the enhancement of its infectivity. All of these proved that the evolution of SARS-CoV-2 is toward the enhancement of infectivity and reduction of virulence.

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“…Viruses with 3037T-14408T-23403G have a fitness gain, which was reported by Yang et al. in their latest discovery [ 31 ]. A23403G were deemed as important mutations in spike protein.…”

Section: Discussionmentioning

confidence: 75%

Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2

Liang

Han

Zhu

et al. 2021

Briefings in Bioinformatics

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“…The other three SNVs, 3037T-14408T-23403G characterising the increasing frequency of the type VI, in majority of samples from various regions indicate a possible fitness gain for the virus. Further, it has been noted that the variants missing one or two of these signature SNVs fail to persist or wiped out by other evolutionary more fit variants [16]. Taking a note of the major mutations, their lineages and effects on disease transmissibility is important to understand the changing face of the pandemic (Table 1).…”

Section: Mutations and Variation In Sars-cov-2mentioning

confidence: 99%

Evolving Patterns in COVID-19: The Virus, its Variants and Infectivity-cum-Virulence

Nikhra

2021

BJSTR

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The Virus, Variants and Pandemic: COVID-19 as a disease and SARS-CoV-2 as its causative organism, continue to remain an enigma. The pandemic continues to persist over a year with outbreaks and re-emergence involving newer regions and population groups. While we continue to explore the agent factors, disease transmission dynamics, pathogenesis and clinical spectrum of the disease, and therapeutic and vaccine modalities, the grievous nature of the disease is evolving with the genomic mutations and pathophysiological alterations. The Emerging SARS-Cov-2 Variants: Understanding the nucleotide variations in the virus genome provides a useful insight for the changing face of the disease and propagation of the pandemic. The emerging mutations can be interpreted as a strategy through natural selection to facilitate extensive spread of the viral infection. Of late, there is recurrent emergence, accumulation, and onward transmission of various mutations. Among the current major SARS-CoV-2 lineages A, B, B.1, B.1.1, and B.1.177, the lineage -B.1.1.7 is of present concern. Challenges Posed by the Mutations: In general, the D614G mutation leads to open conformations, increases density of the S protein and disease infectivity by facilitating the viral entry into the host cells. Another variant, named VUI-202012/01 or B.1.1.7identified in the UK, harbours multiple mutations which have been correlated with a significantly increased infection transmission rate during recent months. A new entrant, the South African variant carries a high infectivity and accompanied by probable high disease severity. There are salient potential consequences of emerging variants including rapid transmission, enhanced disease severity, and diagnostic failure as the variants may evade detection through certain diagnostic tests. Further, they may decrease susceptibility to antiviral drugs and monoclonal antibodies and evade natural or vaccineinduced immunity. Conclusion: Dealing with the Variants:The WHO is working with various countries to amplify and adapt the current surveillance systems to evaluate potential virus variations through ongoing systematic clinical and epidemiologic surveillance. There is need to establish genomic sequencing capacity and access to the sequencing services. Simultaneously, the disease control measures, and intensive public health response are needed to be strengthened to curtail the increased transmissibility associated with the emerging SARS-CoV-2 variants.

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“…Also, within viral populations variants can be traced due to the quasi-species nature of the SARS-CoV-2 virus ( Jary et al, 2020 ). For SARS-CoV-2 thousands of Single Nucleotide Polymorphisms (SNPs) have already been identified, several of which have become fixed in the more recent, geographically defined viral populations at large ( Saha et al, 2020 ; Sapoval et al, 2020 ; Kaushal et al, 2020 ; Yang et al, 2020 ). Rapid regional spread of SARS-CoV-2 may lead to increased allelic variability during periods of extended transmission ( Gudbjartsson et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Different SARS-CoV-2 haplotypes associate with geographic origin and case fatality rates of COVID-19 patients

Goyal

Bruyne²,

Belkum

et al. 2021

Infection, Genetics and Evolution

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Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations

Cited by 75 publications

References 18 publications

Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2

Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2

Evolving Patterns in COVID-19: The Virus, its Variants and Infectivity-cum-Virulence

Different SARS-CoV-2 haplotypes associate with geographic origin and case fatality rates of COVID-19 patients

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