Characterizing genomic variants and mutations in SARS-CoV-2 proteins from Indian isolates

Das, Jayanta Kumar; Sengupta, A. K.; Choudhury, Pabitra Pal; Roy, Swarup

doi:10.1016/j.genrep.2021.101044

Cited by 26 publications

(36 citation statements)

References 55 publications

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“…SARS-CoV-2 genetic diversity within and between hosts understood, N T205I may increase stability of the N protein [33,34]. Despite the detection within-host and subsequent emergence of N205I globally, this iSNV was only detected in our dataset in one sample at low frequency.…”

Section: Plos Pathogensmentioning

confidence: 65%

“…C28887T encodes a threonine-to-isoleucine change at position 205 in the N protein, and is a clade-defining mutation for the B.1.351 lineage. Although the functional impact of this mutation is not completely understood, N T205I may increase stability of the N protein [ 33 , 34 ]. Despite the detection within-host and subsequent emergence of N205I globally, this iSNV was only detected in our dataset in one sample at low frequency.…”

Section: Resultsmentioning

confidence: 99%

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Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks

et al. 2021

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The emergence of divergent SARS-CoV-2 lineages has raised concern that novel variants eliciting immune escape or the ability to displace circulating lineages could emerge within individual hosts. Though growing evidence suggests that novel variants arise during prolonged infections, most infections are acute. Understanding how efficiently variants emerge and transmit among acutely-infected hosts is therefore critical for predicting the pace of long-term SARS-CoV-2 evolution. To characterize how within-host diversity is generated and propagated, we combine extensive laboratory and bioinformatic controls with metrics of within- and between-host diversity to 133 SARS-CoV-2 genomes from acutely-infected individuals. We find that within-host diversity is low and transmission bottlenecks are narrow, with very few viruses founding most infections. Within-host variants are rarely transmitted, even among individuals within the same household, and are rarely detected along phylogenetically linked infections in the broader community. These findings suggest that most variation generated within-host is lost during transmission.

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Section: Plos Pathogensmentioning

confidence: 65%

Section: Resultsmentioning

confidence: 99%

Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks

et al. 2021

View full text Add to dashboard Cite

show abstract

“…C28887T encodes a threonine-to-isoleucine change at position 205 in the N protein, and is a clade-defining mutation for the B.1.351 lineage. Although the functional impact of this mutation is not completely understood, N T205I may increase stability of the N protein (32,33). Despite the detection within-host and subsequent emergence of N205I globally, this iSNV was only detected in our dataset in one sample at low frequency.…”

Section: Most Within-host Variation Does Not Contribute To Consensus Diversitymentioning

confidence: 71%

Limited within-host diversity and tight transmission bottlenecks limit SARS-CoV-2 evolution in acutely infected individuals

Braun

Moreno

Wagner

et al. 2021

Preprint

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The recent emergence of divergent SARS-CoV-2 lineages has raised concerns about the role of selection within individual hosts in propagating novel variants. Of particular concern are variants associated with immune escape and/or enhanced transmissibility. Though growing evidence suggests that novel variants can arise during prolonged infections, most infections are acute. Understanding the extent to which variants emerge and transmit among acutely infected hosts is therefore critical for predicting the pace at which variants resistant to vaccines or conferring increased transmissibility might emerge in the majority of SARS-CoV-2 infections. To characterize how within-host diversity is generated and propagated, we combine extensive laboratory and bioinformatic controls with metrics of within- and between-host diversity to 133 SARS-CoV-2 genomes from acutely infected individuals. We find that within-host diversity during acute infection is low and transmission bottlenecks are narrow, with very few viruses founding most infections. Within-host variants are rarely transmitted, even among individuals within the same household. Accordingly, we also find that within-host variants are rarely detected along phylogenetically linked infections in the broader community. Together, these findings suggest that efficient selection and transmission of novel SARS-CoV-2 variants is unlikely during typical, acute infection.

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“…For instance, provoking a mutational meltdown phenomenon (population extinction) by giving a drug such as Favipiravir, which increases the accumulation rate of harmful mutations, subsequently inducing population collapse [ 53 ]. In parallel, three neutral amino acid replacements were identified among the Algerian sequences; this implies no changes in the protein function [ 54 ]. The E681D amino acid replacement in the protease gene ( NSP3 ) was first acknowledged in the Algerian genome EPI_ISL_766862 and occurring only in three samples worldwide demonstrated disease exportation from Algeria to Austria (EPI_ISL_853900) via the sample collection dates.…”

Section: Discussionmentioning

confidence: 99%

The Algerian Chapter of SARS-CoV-2 Pandemic: An Evolutionary, Genetic, and Epidemiological Prospect

Zeghbib

Somogyi

Zana

et al. 2021

Viruses

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To explore the SARS-CoV-2 pandemic in Algeria, a dataset comprising ninety-five genomes originating from SARS-CoV-2 sampled from Algeria and other countries worldwide, from 24 December 2019, through 4 March 2021, was thoroughly examined. While performing a multi-component analysis regarding the Algerian outbreak, the toolkit of phylogenetic, phylogeographic, haplotype, and genomic analysis were effectively implemented. We estimated the Time to the Most Recent Common Ancestor (TMRCA) in reference to the Algerian pandemic and highlighted the multiple introductions of the disease and the missing data depicted in the transmission loop. In addition, we emphasized the significant role played by local and international travels in disease dissemination. Most importantly, we unveiled mutational patterns, the effect of unique mutations on corresponding proteins, and the relatedness regarding the Algerian sequences to other sequences worldwide. Our results revealed individual amino-acid replacements such as the deleterious replacement A23T in the orf3a gene in Algeria_EPI_ISL_418241. Additionally, a connection between Algeria_EPI_ISL_420037 and sequences originating from the USA was observed through a USA characteristic amino-acid replacement T1004I in the nsp3 gene, found in the aforementioned Algerian sequence. Similarly, successful tracing could be established, such as Algeria/G37318-8849/2020|EPI_ISL_766863, which was imported from Saudi Arabia during the pilgrimage. Lastly, we assessed the Algerian mitigation measures regarding disease containment using statistical analyses.

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Characterizing genomic variants and mutations in SARS-CoV-2 proteins from Indian isolates

Cited by 26 publications

References 55 publications

Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks

Acute SARS-CoV-2 infections harbor limited within-host diversity and transmit via tight transmission bottlenecks

Limited within-host diversity and tight transmission bottlenecks limit SARS-CoV-2 evolution in acutely infected individuals

The Algerian Chapter of SARS-CoV-2 Pandemic: An Evolutionary, Genetic, and Epidemiological Prospect

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