Deletion in the C-terminal region of the envelope glycoprotein in some of the Indian SARS-CoV-2 genome

Kumar, Ballamoole Krishna; Rohit, Anusha; Prithvisagar, Kattapuni Suresh; Rai, Praveen; Karunasagar, Indrani

doi:10.1016/j.virusres.2020.198222

Cited by 18 publications

(12 citation statements)

References 14 publications

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“…In addition, we observed that the E gene was not detected in the samples with equivocal results while the ORF1ab gene was still present. These observations are consistent with the results of studies by other authors [33,34]. A possible explanation of this situation is the occurrence of a mutation in the nucleotide sequence of this gene for the used fluorescent primers or probes [34][35][36].…”

Section: Discussionsupporting

confidence: 92%

Reliable Diagnostics of SARS-CoV-2 Infections Using One- and Two-Gene Molecular Tests for a Viral RNA Detection—Results Questioning Previous Observations

2021

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SARS-CoV-2 is a new virus from the Coronaviridae family and its rapid spread is now the most important medical problem worldwide. Currently used tests vary in the number and selection of SARS-CoV-2 target genes. Meanwhile, the choice of the appropriate target gene may be important in terms of a reliable detection of a viral RNA. As some researchers questioned the sensitivity of the monogenic VIASURE SARS-CoV-2 S gene Real Time PCR Detection Kit (CerTest Biotec, Zaragoza, Spain) in mid-2020, the aim of the study was to evaluate the usefulness of this kit, used along with the BD MAX™ System (Becton Dickinson, East Rutherford, NJ, USA), and compare the results with two-gene Bosphore Novel Coronavirus (2019-nCoV) Detection Kit v1 (Anatolia Diagnostics and Biotechnology Products Inc., Istanbul, Turkey). Both tests were carried out on 306 nasopharyngeal/oropharyngeal swabs. The consistent results (72 positive and 225 negative results found simultaneously in both kits) were obtained for 297 (97.1%) samples altogether, while discrepancies between the results of the evaluated tests were observed for nine (2.9%) specimens. There were no statistically significant differences between the method used and the frequency of positive results. Both tests, targeted at detecting one and two genes, are effective in SARS-CoV-2 RNA detection.

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Section: Discussionsupporting

confidence: 92%

Reliable Diagnostics of SARS-CoV-2 Infections Using One- and Two-Gene Molecular Tests for a Viral RNA Detection—Results Questioning Previous Observations

2021

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“…As the mutant was not identified in clinical samples, it is possible the deletion event is a result of cell culture adaptation. However, there are other reports of clusters of clinical isolates from India containing comparable deletions in E [ 165 ]. It has been shown previously that SARS-CoV artificially engineered to lack E gene expression is highly attenuated in vitro and in vivo [ 166 ].…”

Section: Sars-cov-2 Mutations Outside the Spike Glycoproteinmentioning

confidence: 99%

SARS-CoV-2 one year on: evidence for ongoing viral adaptation

Peacock

Penrice-Randal

Hiscox

et al. 2021

Journal of General Virology

147

118

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SARS-CoV-2 is thought to have originated in the human population from a zoonotic spillover event. Infection in humans results in a variety of outcomes ranging from asymptomatic cases to the disease COVID-19, which can have significant morbidity and mortality, with over two million confirmed deaths worldwide as of January 2021. Over a year into the pandemic, sequencing analysis has shown that variants of SARS-CoV-2 are being selected as the virus continues to circulate widely within the human population. The predominant drivers of genetic variation within SARS-CoV-2 are single nucleotide polymorphisms (SNPs) caused by polymerase error, potential host factor driven RNA modification, and insertion/deletions (indels) resulting from the discontinuous nature of viral RNA synthesis. While many mutations represent neutral ‘genetic drift’ or have quickly died out, a subset may be affecting viral traits such as transmissibility, pathogenicity, host range, and antigenicity of the virus. In this review, we summarise the current extent of genetic change in SARS-CoV-2, particularly recently emerging variants of concern, and consider the phenotypic consequences of this viral evolution that may impact the future trajectory of the pandemic.

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“…An earlier study based on in silico analysis of 2086 whole-genome sequences from India documented extensive deletion of amino acid residues in the C-terminal region of the envelope glycoprotein in some SARS-CoV-2 genomes (Kumar et al 2021 ). These amino acid deletions map to the C-terminal region of E protein which is just beyond the reverse primer binding site used in the detection of positive cases; thus, E gene-based RT-qPCR could still detect these isolates.…”

Section: Genomic Epidemiology: Implications For Origin and Surveillanmentioning

confidence: 99%

SARS-CoV-2 genomics: An Indian perspective on sequencing viral variants

et al. 2021

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Since its emergence as a pneumonia-like outbreak in the Chinese city of Wuhan in late 2019, the novel coronavirus disease COVID-19 has spread widely to become a global pandemic. The first case of COVID-19 in India was reported on 30 January 2020 and since then it has affected more than ten million people and resulted in around 150,000 deaths in the country. Over time, the viral genome has accumulated mutations as it passes through its human hosts, a common evolutionary mechanism found in all microorganisms. This has implications for disease surveillance and management, vaccines and therapeutics, and the emergence of reinfections. Sequencing the viral genome can help monitor these changes and provides an extraordinary opportunity to understand the genetic epidemiology and evolution of the virus as well as tracking its spread in a population. Here we review the past year in the context of the phylogenetic analysis of variants isolated over the course of the pandemic in India and highlight the importance of continued sequencing-based surveillance in the country.

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Deletion in the C-terminal region of the envelope glycoprotein in some of the Indian SARS-CoV-2 genome

Cited by 18 publications

References 14 publications

Reliable Diagnostics of SARS-CoV-2 Infections Using One- and Two-Gene Molecular Tests for a Viral RNA Detection—Results Questioning Previous Observations

Reliable Diagnostics of SARS-CoV-2 Infections Using One- and Two-Gene Molecular Tests for a Viral RNA Detection—Results Questioning Previous Observations

SARS-CoV-2 one year on: evidence for ongoing viral adaptation

SARS-CoV-2 genomics: An Indian perspective on sequencing viral variants

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