Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India

Sharma, Kuldeep; Singh, Priyanka; Bhargava, Anudita; Negi, Sanjay Singh; Sharma, Pratibha; Bhise, Mayuri; Tripathi, Manish Kumar; Jindal, Atul; Nagarkar, Nitin M.

doi:10.1016/j.micpath.2022.105404

Cited by 21 publications

(19 citation statements)

References 32 publications

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“…The role of each specific mutation has not been completely elucidated, but they have all been implicated in immune escape [36][37][38]. In addition, the mutation S:A222V, present in AY.26, slightly increases human cell receptor (ACE2) binding [39], while the mutations N:R203M, common to the three sublineages, and N:G215C, present in AY.20 and AY.100, have been shown to improve viral replication and assembly [40,41].…”

Section: Discussionmentioning

confidence: 99%

Dominance of Three Sublineages of the SARS-CoV-2 Delta Variant in Mexico

Taboada

Zárate

García-López

et al. 2022

Viruses

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In this study, we analyzed the sequences of SARS-CoV-2 isolates of the Delta variant in Mexico, which has completely replaced other previously circulating variants in the country due to its transmission advantage. Among all the Delta sublineages that were detected, 81.5 % were classified as AY.20, AY.26, and AY.100. According to publicly available data, these only reached a world prevalence of less than 1%, suggesting a possible Mexican origin. The signature mutations of these sublineages are described herein, and phylogenetic analyses and haplotype networks are used to track their spread across the country. Other frequently detected sublineages include AY.3, AY.62, AY.103, and AY.113. Over time, the main sublineages showed different geographical distributions, with AY.20 predominant in Central Mexico, AY.26 in the North, and AY.100 in the Northwest and South/Southeast. This work describes the circulation, from May to November 2021, of the primary sublineages of the Delta variant associated with the third wave of the COVID-19 pandemic in Mexico and highlights the importance of SARS-CoV-2 genomic surveillance for the timely identification of emerging variants that may impact public health.

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Section: Discussionmentioning

confidence: 99%

Dominance of Three Sublineages of the SARS-CoV-2 Delta Variant in Mexico

Taboada

Zárate

García-López

et al. 2022

Viruses

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“…The most commonly found Delta mutations seen in our sequences were T19R, G142D, ΔE156/F157, R158G, L452R, T478K, D614G, P681R, and D950N ( Figure 3 and Figure 4 ). T19R, G142D, ΔE156/F157 and R158G are located within the antigenic supersite of the S protein NTD and affect immune evasion [ 96 , 97 ]. Furthermore, ΔE156/F157 and R158G contribute to increased infectivity [ 98 ].…”

Section: Discussionmentioning

confidence: 99%

Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus from November 2020 to October 2021: The Passage of Waves of Alpha and Delta Variants of Concern

Chrysostomou¹,

Vrancken²,

Haralambous³

et al. 2022

Viruses

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The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019 resulted in the coronavirus disease 2019 (COVID-19) pandemic, which has had devastating repercussions for public health. Over the course of this pandemic, the virus has continuously been evolving, resulting in new, more infectious variants that have frequently led to surges of new SARS-CoV-2 infections. In the present study, we performed detailed genetic, phylogenetic, phylodynamic and phylogeographic analyses to examine the SARS-CoV-2 epidemic in Cyprus using 2352 SARS-CoV-2 sequences from infected individuals in Cyprus during November 2020 to October 2021. During this period, a total of 61 different lineages and sublineages were identified, with most falling into three groups: B.1.258 & sublineages, Alpha (B.1.1.7 & Q. sublineages), and Delta (B.1.617.2 & AY. sublineages), each encompassing a set of S gene mutations that primarily confer increased transmissibility as well as immune evasion. Specifically, these lineages were coupled with surges of new infections in Cyprus, resulting in the following: the second wave of SARS-CoV-2 infections in Cyprus, comprising B.1.258 & sublineages, during late autumn 2020/beginning of winter 2021; the third wave, comprising Alpha (B.1.1.7 & Q. sublineages), during spring 2021; and the fourth wave, comprising Delta (B.1.617.2 & AY. sublineages) during summer 2021. Additionally, it was identified that these lineages were primarily imported from and exported to the UK, Greece, and Sweden; many other migration links were also identified, including Switzerland, Denmark, Russia, and Germany. Taken together, the results of this study indicate that the SARS-CoV-2 epidemic in Cyprus was characterized by successive introduction of new lineages from a plethora of countries, resulting in the generation of waves of infection. Overall, this study highlights the importance of investigating the spatiotemporal evolution of the SARS-CoV-2 epidemic in the context of Cyprus, as well as the impact of protective measures placed to mitigate transmission of the virus, providing necessary information to safeguard public health.

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“…Our study identified the predominance of BA.2 and its sub-lineage (93.5%) followed by BA.5.2 and its sub-lineage BA. 5 11). An earlier study from Denmark and India has reasoned a higher fusogenicity and reproduction number (R0) of 2.445 for BA.2 predominance (12).…”

Section: Discussionmentioning

confidence: 99%

Mutational characterization of Omicron SARS-CoV-2 lineages circulating in Chhattisgarh, a central state of India

et al. 2023

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IntroductionThe emergence of the Omicron SARS-CoV-2 variant from various states of India in early 2022 has caused fear of its rapid spread. The lack of such reports from Chhattisgarh (CG), a central state in India, has prompted us to identify the Omicron circulating lineages and their mutational dynamics.Materials and methodsWhole-genome sequencing (WGS) of SARS-CoV-2 was performed in 108 SARS-CoV-2 positive combined samples of nasopharyngeal and oropharyngeal swabs obtained from an equal number of patients.ResultsAll 108 SARS-CoV-2 sequences belonged to Omicron of clade 21L (84%), 22B (11%), and 22D (5%). BA.2 and its sub-lineages were predominantly found in 93.5% of patients, BA.5.2 and its sub-lineage BA.5.2.1 in 4.6% of patients, and B.1.1.529 in 2% of patients. Various BA.2 sub-lineages identified were BA.2 (38%), BA.2.38 (32%), BA.2.75 (9.25%), BA.2.56, BA.2.76, and BA.5.2.1 (5% each), BA.2.74 (4.6%), BA.5.2.1 (3.7%), BA.2.43 and B.1.1.529 (1.8% each), and BA.5.2 (0.9%). Maximum mutations were noticed in the spike (46), followed by the nucleocapsid (5), membrane (3), and envelope (2) genes. Mutations detected in the spike gene of different Omicron variants were BA.1.1.529 (32), BA.2 (44), BA.2.38 (37), BA.2.43 (38), BA.2.56 (30), BA.2.74 (31), BA.2.75 (37), BA.2.76 (32), BA.5.2, and BA.5.2.1 (38 similar mutations). The spike gene showed the signature mutations of T19I and V213G in the N-terminal domain (NTD), S373P, S375F, T376A, and D405N in receptor-binding domain (RBD), D614G, H655Y, N679K, and P681H at the furin cleavage site, N764K and D796K in fusion peptide, and Q954H and N969K in heptapeptide repeat sequence (HR)1. Notably, BA.2.43 exhibited a novel mutation of E1202Q in the C terminal. Other sites included ORF1a harboring 13 mutations followed by ORF1b (6), ORF3a (2), and ORF6 and ORF8 (1 mutation each).ConclusionBA.2 followed by BA.2.38 was the predominant Omicron lineage circulating in Chhattisgarh. BA.2.75 could supersede other Omicron due to its mutational consortium advantage. The periodical genomic monitoring of Omicron variants is thus required for real-time assessment of circulating strains and their mutational-induced severity.

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Genomic characterization unravelling the causative role of SARS-CoV-2 Delta variant of lineage B.1.617.2 in 2nd wave of COVID-19 pandemic in Chhattisgarh, India

Cited by 21 publications

References 32 publications

Dominance of Three Sublineages of the SARS-CoV-2 Delta Variant in Mexico

Dominance of Three Sublineages of the SARS-CoV-2 Delta Variant in Mexico

Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus from November 2020 to October 2021: The Passage of Waves of Alpha and Delta Variants of Concern

Mutational characterization of Omicron SARS-CoV-2 lineages circulating in Chhattisgarh, a central state of India

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