In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh

Shishir, Tushar Ahmed; Naser, Iftekhar Bin; Faruque, Shah M.

doi:10.1371/journal.pone.0245584

Cited by 29 publications

(33 citation statements)

References 34 publications

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“…Notably, few other previous studies although suggest the involvement of the diseases severity with the specific mutation (D614, P323L) in the SARS-CoV-2 genome [ 45 ]. Most interestingly, in two studies by Shishir et al and Garvin et al suggested the involvement of the higher mortality rate in Bangladesh due to the mutation in NSP2, NSP13, and spike protein in the circulating SARS-COV-2 genome in our country, which is in accordance of our study [ 46 , 47 ].…”

Section: Discussionsupporting

confidence: 92%

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Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh

et al. 2021

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Along with intrinsic evolution, adaptation to selective pressure in new environments might have resulted in the circulatory SARS-CoV-2 strains in response to the geoenvironmental conditions of a country and the demographic profile of its population. With this target, the current study traced the evolutionary route and mutational frequency of 198 Bangladesh-originated SARS-CoV-2 genomic sequences available in the GISAID platform over a period of 13 weeks as of 14 July 2020. The analyses were performed using MEGA X, Swiss Model Repository, Virus Pathogen Resource and Jalview visualization. Our analysis identified that majority of the circulating strains strikingly differ from both the reference genome and the first sequenced genome from Bangladesh. Mutations in nonspecific proteins (NSP2-3, NSP-12(RdRp), NSP-13(Helicase)), S-Spike, ORF3a, and N-Nucleocapsid protein were common in the circulating strains with varying degrees and the most unique mutations (UM) were found in NSP3 (UM-18). But no or limited changes were observed in NSP9, NSP11, Envelope protein (E) and accessory factors (NSP7a, ORF 6, ORF7b) suggesting the possible conserved functions of those proteins in SARS-CoV-2 propagation. However, along with D614G mutation, more than 20 different mutations in the Spike protein were detected basically in the S2 domain. Besides, mutations in SR-rich region of N protein and P323L in RDRP were also present. However, the mutation accumulation showed a significant association ( p = 0.003) with sex and age of the COVID-19-positive cases. So, identification of these mutational accumulation patterns may greatly facilitate vaccine development deciphering the age and the sex-dependent differential susceptibility to COVID-19. Supplementary Information The online version contains supplementary material available at 10.1007/s11262-021-01860-x.

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Section: Discussionsupporting

confidence: 92%

“…Interestingly, the infection and mortality rates were also disproportionately higher in males than females of Bangladesh. In terms of mortality, it was 79.24% for males and 20.76% for females [ 46 ]. Similar phenomena have also been [ 49 ].…”

Section: Discussionmentioning

confidence: 99%

Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh

et al. 2021

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“…For example, the D614 virus persisted for a longer time in the Delhi region 17 , 19 and also in the South of India, 17 , 20 , 21 , 24 , 27 − 30 while the G614 virus dominated early in the West of India (Gujarat, Maharashtra), 17 , 19 , 25 , 31 and also in the Eastern and Central Indian states, 28 as well as in Bangladesh. 14 , 26 , 32 , 33 Pakistan and Sri Lanka had different waves of virus spread, with an early D614 dominance, but becoming all G614 in June and July 2020. 34 − 36 Importantly, the predominance of the G614 virus was delayed in South India until mid May to June of 2020.…”

Section: Resultsmentioning

confidence: 99%

The D614G Virus Mutation Enhances Anosmia in COVID-19 Patients: Evidence from a Systematic Review and Meta-analysis of Studies from South Asia

Bartheld

Hagen

Butowt

2021

ACS Chem. Neurosci.

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The prevalence of chemosensory dysfunction in patients with COVID-19 varies greatly between populations. It is unclear whether such differences are due to factors at the level of the human host, or at the level of the coronavirus, or both. At the host level, the entry proteins which allow virus binding and entry have variants with distinct properties, and the frequency of such variants differs between ethnicities. At the level of the virus, the D614G mutation enhances virus entry to the host cell. Since the two virus strains (D614 and G614) coexisted in the first six months of the pandemic in most populations, it has been difficult to distinguish between contributions of the virus and contributions of the host for anosmia. To answer this question, we conducted a systematic review and meta-analysis of studies in South Asian populations when either the D614 or the G614 virus was dominant. We show that populations infected predominantly with the G614 virus had a much higher prevalence of anosmia (pooled prevalence of 31.8%) compared with the same ethnic populations infected mostly with the D614 virus strain (pooled anosmia prevalence of 5.3%). We conclude that the D614G mutation is a major contributing factor that increases the prevalence of anosmia in COVID-19, and that this enhanced effect on olfaction constitutes a previously unrecognized phenotype of the D614G mutation. The new virus strains that have additional mutations on the background of the D614G mutation can be expected to cause a similarly increased prevalence of chemosensory dysfunctions.

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“…In this study, we comprehensively analyzed 791 SARS-CoV-2 complete genome sequences from Bangladesh. Limited molecular analysis of Bangladeshi SARS-CoV-2 was reported previously [ 27 , 28 , 29 ]. We used different bioinformatics approaches to systemically identify the evolutionary matrix, major clades, and lineage designation among the circulated viruses.…”

Section: Discussionmentioning

confidence: 99%

Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations

et al. 2021

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Virus evolution and mutation analyses are crucial for tracing virus transmission, the potential variants, and other pathogenic determinants. Despite continuing circulation of the SARS-CoV-2, very limited studies have been conducted on genetic evolutionary analysis of the virus in Bangladesh. In this study, a total of 791 complete genome sequences of SARS-CoV-2 from Bangladesh deposited in the GISAID database during March 2020 to January 2021 were analyzed. Phylogenetic analysis revealed circulation of seven GISAID clades G, GH, GR, GRY, L, O, and S or five Nextstrain clades 20A, 20B, 20C, 19A, and 19B in the country during the study period. The GISAID clade GR or the Nextstrain clade 20B or lineage B.1.1.25 is predominant in Bangladesh and closely related to the sequences from India, USA, Canada, UK, and Italy. The GR clade or B.1.1.25 lineage is likely to be responsible for the widespread community transmission of SARS-CoV-2 in the country during the first wave of infection. Significant amino acid diversity was observed among Bangladeshi SARS-CoV-2 isolates, where a total of 1023 mutations were detected. In particular, the D614G mutation in the spike protein (S_D614G) was found in 97% of the sequences. However, the introduction of lineage B.1.1.7 (UK variant/S_N501Y) and S_E484K mutation in lineage B.1.1.25 in a few sequences reported in late December 2020 is of particular concern. The wide genomic diversity indicated multiple introductions of SARS-CoV-2 into Bangladesh through various routes. Therefore, a continuous and extensive genome sequence analysis would be necessary to understand the genomic epidemiology of SARS-CoV-2 in Bangladesh.

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In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh

Cited by 29 publications

References 34 publications

Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh

Temporal landscape of mutational frequencies in SARS-CoV-2 genomes of Bangladesh: possible implications from the ongoing outbreak in Bangladesh

The D614G Virus Mutation Enhances Anosmia in COVID-19 Patients: Evidence from a Systematic Review and Meta-analysis of Studies from South Asia

Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations

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