New framework for recombination and adaptive evolution analysis with application to the novel coronavirus SARS-CoV-2

Wang, Yinghan; Zeng, Jinfeng; Zhang, Chi; Qiu, Zekai; Pang, Jiali; Xu, Yutian; Dong, Zhi-Qi; Song, Yanxin; Liu, Weiying; Dong, Peipei; Sun, Litao; Chen, Yao-Qing; Shu, Yuelong; Du, Xiangjun

doi:10.1093/bib/bbab107

Cited by 8 publications

(9 citation statements)

References 47 publications

(49 reference statements)

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“…Thereafter, we compared the growth rate between the 203K/484K/501Y variant and the R203/484K/501Y variant at different geographical levels. We did not consider D614G in this comparison because this mutation has been fixed in virus genomes around the world (Fig 1L) since July 2020 23,28 . In line with the results of the comparison results between the Gamma and Beta variants, the growth rate of the 203K/484K/501Y variant was consistently higher than that of the R203/484K/501Y variant (Figs.…”

Section: Resultsmentioning

confidence: 99%

Nucleocapsid 203 mutations enhance SARS-CoV-2 immune evasion

Lin

Xue

Zhang

et al. 2021

Preprint

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Previous work indicated that the nucleocapsid 203 mutation increase the virulence and transmission of the SARS-CoV-2 Alpha variant. However, Delta later outcompeted Alpha and other lineages, promoting a new wave of infections. Delta also possesses a nucleocapsid 203 mutation, R203M. Large-scale epidemiological analyses suggest a synergistic effect of the 203 mutation and the spike L452R mutation, associated with Delta expansion. Viral competition experiments demonstrate the synergistic effect in fitness and infectivity. More importantly, we found that the combination of R203M and L452R brings in a 3.2-fold decrease in neutralizing titers to the neutralizing serum relative to L452R-only virus. R203M/L452R show an increased fitness after the initiation of global vaccination programmes, possibly associated with the enhanced immune evasion. Another rapidly emerging variant Omicron also bears the 203 mutation. Thus, we proposed that nucleocapsid mutations play an essential role for the rise and predominance of variants in concern.

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Section: Resultsmentioning

confidence: 99%

Nucleocapsid 203 mutations enhance SARS-CoV-2 immune evasion

Lin

Xue

Zhang

et al. 2021

Preprint

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“…Genetic-recombinant network-analysis helps understanding complex genetic relationships and evolution including viruses ( 48 ). Network analysis showed clustering of IBV HH06 strain with Duck-CoV and Pheasant-CoV which indicated an evolutionary relationship between these two viruses.…”

Section: Discussionmentioning

confidence: 99%

Molecular Characterization of Infectious Bronchitis Virus Strain HH06 Isolated in a Poultry Farm in Northeastern China

et al. 2021

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Spike (S) glycoprotein is an important virulent factor for coronaviruses (CoVs), and variants of CoVs have been characterized based on S gene analysis. We present phylogenetic relationship of an isolated infectious bronchitis virus (IBV) strain with reference to the available genome and protein sequences based on network, multiple sequence, selection pressure, and evolutionary fingerprinting analysis in People's Republic of China. One hundred and elven strains of CoVs i.e., Alphacoronaviruses (Alpha-CoVs; n = 12), Betacoronaviruses (Beta-CoVs; n = 37), Gammacoronaviruses (Gamma-CoVs; n = 46), and Deltacoronaviruses (Delta-CoVs; n = 16) were selected for this purpose. Phylogenetically, SARS-CoV-2 and SARS-CoVs clustered together with Bat-CoVs and MERS-CoV of Beta-CoVs (C). The IBV HH06 of Avian-CoVs was closely related to Duck-CoV and partridge S14, LDT3 (teal and chicken host). Beluga whale-CoV (SW1) and Bottlenose dolphin-CoVs of mammalian origin branched distantly from other animal origin viruses, however, making group with Avian-CoVs altogether into Gamma-CoVs. The motif analysis indicated well-conserved domains on S protein, which were similar within the same phylogenetic class and but variable at different domains of different origins. Recombination network tree indicated SARS-CoV-2, SARS-CoV, and Bat-CoVs, although branched differently, shared common clades. The MERS-CoVs of camel and human origin spread branched into a different clade, however, was closely associated closely with SARS-CoV-2, SARS-CoV, and Bat-CoVs. Whereas, HCoV-OC43 has human origin and branched together with bovine CoVs with but significant distant from other CoVs like SARS CoV-2 and SARS-CoV of human origin. These findings explain that CoVs' constant genetic recombination and evolutionary process that might maintain them as a potential veterinary and human epidemic threat.

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“…Based on the foregoing questions, it is important to explore the synonymous evolutionary rate (SER) in the open reading frames (ORFs) of the SARS-CoV-2 genome, the factors that influence the SER, and what rules can be drawn through comparison of fixed-characteristic amino acid mutations with different lineages. To answer these questions, using a mutation network approach (Zhang C. et al, 2020 ; Wang Y. et al, 2021 ), we described the distribution of the SER across the SARS-CoV-2 genome along with its influential factors and explored the conserved motifs based on the SER and the motifs' potential functional relationships with the host by performing enrichment analyses. We also assessed the potentially important and functional amino acid mutations based on the SER for identifying future dominant variants to better control the pandemic.…”

Section: Introductionmentioning

confidence: 99%

Variation in synonymous evolutionary rates in the SARS-CoV-2 genome

et al. 2023

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IntroductionCoronavirus disease 2019 is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Influential variants and mutants of this virus continue to emerge, and more effective virus-related information is urgently required for identifying and predicting new mutants. According to earlier reports, synonymous substitutions were considered phenotypically silent; thus, such mutations were frequently ignored in studies of viral mutations because they did not directly cause amino acid changes. However, recent studies have shown that synonymous substitutions are not completely silent, and their patterns and potential functional correlations should thus be delineated for better control of the pandemic.MethodsIn this study, we estimated the synonymous evolutionary rate (SER) across the SARS-CoV-2 genome and used it to infer the relationship between the viral RNA and host protein. We also assessed the patterns of characteristic mutations found in different viral lineages.ResultsWe found that the SER varies across the genome and that the variation is primarily influenced by codon-related factors. Moreover, the conserved motifs identified based on the SER were found to be related to host RNA transport and regulation. Importantly, the majority of the existing fixed-characteristic mutations for five important virus lineages (Alpha, Beta, Gamma, Delta, and Omicron) were significantly enriched in partially constrained regions.DiscussionTaken together, our results provide unique information on the evolutionary and functional dynamics of SARS-CoV-2 based on synonymous mutations and offer potentially useful information for better control of the SARS-CoV-2 pandemic.

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New framework for recombination and adaptive evolution analysis with application to the novel coronavirus SARS-CoV-2

Cited by 8 publications

References 47 publications

Nucleocapsid 203 mutations enhance SARS-CoV-2 immune evasion

Nucleocapsid 203 mutations enhance SARS-CoV-2 immune evasion

Molecular Characterization of Infectious Bronchitis Virus Strain HH06 Isolated in a Poultry Farm in Northeastern China

Variation in synonymous evolutionary rates in the SARS-CoV-2 genome

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