Genetic analysis of SARS-CoV-2 isolates collected from Bangladesh: Insights into the origin, mutational spectrum and possible pathomechanism

Parvez, Sorwer Alam; Rahman, Mohammad Mahfujur; Morshed, Md. Niaz; Rahman, Dolilur; Anwar, Saeed

doi:10.1016/j.compbiolchem.2020.107413

Cited by 17 publications

(18 citation statements)

References 44 publications

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“…Analysis of 198 high-quality complete genome of SARS-CoV-2 from Bangladesh revealed that the circulating strains are of many sub-lineages harboring the same ancestry as Wuhan virus, although their direct evolution from the reference Wuhan virus was not found. Two previous reports by Parvez et al [ 30 ] and Hasan et al [ 31 ] were consistent with our findings that the contributory strains in the SARS-CoV-2 outbreak in Bangladesh might be arising from the different regions of the world other than China. Besides, that majority of the Bangladeshi isolates were found to fall within the clade B belonging to L type (Supplementary Table ST2).…”

Section: Discussionsupporting

confidence: 94%

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: 94%

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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“…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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“…McCarthy et al [ 26 ] highlight the importance of deletions in immune evasion on the evolutionary trajectory of SARS-CoV-2 to an endemic virus. According to Parvez et al [ 27 ] and Rahman et al [ 28 ], deletions in ORF7, ORF8, and ORF10 found in Bangladesh were associated with reduced virulence. According to Liu et al [ 29 ], isolates containing deletions in or near the furin polybasic site of the spike protein have been associated with mild or asymptomatic outcome.…”

Section: Evolution Of the Virusmentioning

confidence: 99%

Evolution of SARS-CoV-2: Review of Mutations, Role of the Host Immune System

Banoun

2021

Nephron

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Since the reporting of the first cases of coronavirus in China and the publication of the first sequence of SARS-CoV-2 in December 2019, the virus has undergone numerous mutations. In Europe, the spring outbreak (March–April) was followed by a drop in the number of cases and deaths. The disease may have evolved into a milder form. The increase in PCR-positive cases in late summer 2020 did not lead to the expected increase in hospitalizations, ICU admissions, and deaths, based on the severity of the disease in the spring. This difference in disease severity could be due to factors independent of the virus or to the evolution of the virus. This review attempts to identify the mutations that have appeared since the beginning of the pandemic and their role in the temporal evolution of the pandemic. There are a cell and humoral type cross-reactivity in a large part of the population to common cold coronaviruses (HCoVs) and SARS-CoV-2. Evolutionarily important mutations and deletions have emerged in the SARS-CoV-2 genes encoding proteins that interact with the host immune system. In addition, one of the major mutations (in viral polymerase) is logically associated with a higher frequency of mutations throughout the genome. This frequency fluctuates over time and shows a peak at the time when the epidemic was most active. The rate of mutations in proteins involved in the relationship to the immune system continues to increase after the first outbreak. The cross-reactivity on the 1 hand and the viral mutations observed on the other hand could explain the evolution of the pandemic until the summer of 2020, partly due to the evolution of the virus in relation to the host immune system. The immunization campaign began in December 2020: concerns are emerging about a possible escape of the circulating variants vaccines in early 2021. These variants could also escape immunity acquired through infection with the 2020 strains.

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Genetic analysis of SARS-CoV-2 isolates collected from Bangladesh: Insights into the origin, mutational spectrum and possible pathomechanism

Abstract: Graphical abstract

Cited by 17 publications

References 44 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

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

Evolution of SARS-CoV-2: Review of Mutations, Role of the Host Immune System

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