High diversity in Delta variant across countries revealed via genome-wide analysis of SARS-CoV-2 beyond the Spike protein

Ghosh, Pritha; Suratekar, Rohit; Niesen, Michiel J.M.; Donadio, Gregory; Soundararajan, Venky; Venkatakrishnan, AJ

doi:10.1101/2021.09.01.458647

Cited by 9 publications

(8 citation statements)

References 30 publications

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“…This is similar to previous studies indicating the I82T mutation as one of the most frequent mutations in the M protein in the USA, with a 116-fold increase from October 2020 to February 2021 [32]. Suratekar et al also reported I82T as one of the most prevalent mutations in the Delta variant in a systematic analysis of mutations from nearly 2 million SARS-CoV-2 genomes from 176 countries [33]. However, till 2020, D3G was reported as the most common mutation in this protein [22].…”

Section: Mutational Insights Among the Structural Proteins Of Sars-co...supporting

confidence: 89%

Mutational insights among the structural proteins of SARS-CoV-2: frequencies and evolutionary trends in American countries

Abavisani

Rahimian

Khayami

et al. 2022

Preprint

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a role in the mortality of more than 6 million people worldwide. This virus owns the genome, which contains four structural proteins, including spike (S), envelope (E), membrane (M), and nucleocapsid (N). The occurrence of structural mutations can induce the emergence of new variants. Depending on the mutations, the variants may display different patterns of infectivity, mortality, and sensitivity toward drugs and vaccines. In this study, we analyzed samples of amino-acid sequences (AASs) for structural proteins from the coronavirus 2019 (COVID-19) declaration as a pandemic to April 2022 among American countries. The analysis process included considering mutations' frequencies, locations, and evolutionary trends utilizing sequence alignment to the reference sequence. In the following, the results were compared with the same analyses among the samples of the entire world. Results displayed that despite samples of North America and international countries that own the region of 508 to 635 with the highest mutation frequency among S AASs, the region with the same characteristic was concluded as 1 to 127 in South America. Besides, the most frequent mutations in S, E, M, and N proteins from North America and worldwide samples were concluded as D614G, T9I, I82T, and R203M. In comparison, R203K was the first frequent mutation in N samples in South America. Widely comparing mutations between North America and South America and between the Americas and the world can help scientists introduce better drug and vaccine development strategies.

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Section: Mutational Insights Among the Structural Proteins Of Sars-co...supporting

confidence: 89%

Mutational insights among the structural proteins of SARS-CoV-2: frequencies and evolutionary trends in American countries

Abavisani

Rahimian

Khayami

et al. 2022

Preprint

View full text Add to dashboard Cite

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“…A high variation rate in genomes belonging to Delta has been described before (Suratekar et al . 2021 ), but in which direction is the VoC evolving? Although theoretically possible, is it likely that a given VoC will independently evolve to collect mutations similar to those that resulted in increased fitness in previous VoC, thus creating an ever more ‘successful’ VoC?…”

Section: What Do These Observations Mean For the Evolution Of Sars-co...mentioning

confidence: 99%

The first three waves of the Covid-19 pandemic hint at a limited genetic repertoire for SARS-CoV-2

Wassenaar

Wanchai

Buzard³

et al. 2022

FEMS Microbiology Reviews

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The genomic diversity of SARS-CoV-2 is the result of a relatively low level of spontaneous mutations introduced during viral replication. With millions of SARS-CoV-2 genome sequences now available, we can begin to assess the overall genetic repertoire of this virus. We find that during 2020 there was a global wave of one variant that went largely unnoticed, possibly because its members were divided over several sub-lineages (B.1.177 and sub-lineages B.1.177.XX). We collectively call this Janus, and it was eventually replaced by the Alpha (B.1.1.7) Variant of Concern (VoC), next replaced by Delta (B.1.617.2), which itself might soon be replaced by a fourth pandemic wave consisting of Omicron (B.1.1.529). We observe that splitting up and redefining variant lineages over time, as was the case with Janus and is now happening with Alpha, Delta, and Omicron, is not helpful to describe the epidemic waves spreading globally. Only about five percent of the 30,000 nucleotides of the SARS-CoV-2 genome are found to be variable. We conclude that a fourth wave of the pandemic with the Omicron variant might not be that different from other VoCs, and that we may already have the tools in hand to effectively deal with this new VoC.

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“…The Delta variant has multiple mutations distributed throughout its genome of which at least five are located within the S gene that encodes the spike protein [Suratekar et al, 2021]. Some of these individual mutations are shared by other variants but we noted that the combination of spike mutations L452R and T478K (corresponding to nucleotide positions T22917G and C22995A, respectively) within the receptor binding domain can effectively differentiate Delta from other variants.…”

Section: Primer and Probe Designmentioning

confidence: 81%

Highly sensitive and specific detection of the SARS-CoV-2 Delta variant by double-mismatch allele-specific PCR

Garson

Badru

Parker

et al. 2021

Preprint

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The highly transmissible Delta variant of SARS-CoV-2 (B.1.617.2), first identified in India, is currently replacing pre-existing variants in Europe, the USA, and many other parts of the world. It is essential to monitor efficiently its spread to help guide public health policies. Genome sequencing is the gold standard for identification of Delta, but is time-consuming, expensive, and unavailable in many regions. We describe here a rapid and relatively inexpensive alternative to sequencing for specific identification of the Delta variant, by application of double-mismatch allele-specific RT-PCR (DMAS-RT-PCR). The technique exploits forward and reverse allele-specific primers, targeting two spike gene mutations, L452R and T478K, within the same amplicon. The discriminatory power of each primer is enhanced by the presence of an additional mismatch located at the fourth nucleotide from the 3' end. Amplicons are detected in real-time by means of a conventional fluorescently-labelled hydrolysis probe. Specificity was assessed by testing a range of well characterised cell culture-derived viral isolates and clinical samples, most of which had previously been fully sequenced. In all cases the results of viral genotyping by DMAS-RT-PCR were entirely concordant with the results of sequencing, and the assay was shown to discriminate reliably between the Delta variant and other variants of concern (Alpha, B.1.1.7 and Beta, B.1.351), and 'wild-type' SARS-CoV-2. Other respiratory viruses, including influenza A and respiratory syncytial virus, were non-reactive in the assay. The sensitivity of DMAS-RT-PCR matched that of the diagnostic SARS-CoV-2 RT-qPCR screening assay, which targets the E gene. Several samples that could not be sequenced due to insufficient virus could successfully be genotyped by DMAS-RT-PCR. The method we describe would be simple to establish in any laboratory that has the ability to conduct PCR assays and should greatly facilitate monitoring of the spread of the Delta variant throughout the world, and its proportional representation in any SARS-CoV-2-infected population.

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High diversity in Delta variant across countries revealed via genome-wide analysis of SARS-CoV-2 beyond the Spike protein

Cited by 9 publications

References 30 publications

Mutational insights among the structural proteins of SARS-CoV-2: frequencies and evolutionary trends in American countries

Mutational insights among the structural proteins of SARS-CoV-2: frequencies and evolutionary trends in American countries

The first three waves of the Covid-19 pandemic hint at a limited genetic repertoire for SARS-CoV-2

Highly sensitive and specific detection of the SARS-CoV-2 Delta variant by double-mismatch allele-specific PCR

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