Insights from Genomes and Genetic Epidemiology of SARS-CoV-2 isolates from the state of Andhra Pradesh

Rani, Pallavali R.; Imran, Mohamed; Lakshmi, J Vijaya; Jolly, Bani; Afşar, Selim; Jain, Abhinav; Divakar, Mohit Kumar; Suresh, Pujar Venkatesh; Sharma, Disha; Rajesh, N.; Bhoyar, Rahul C.; Ankaiah, D.; Kumari, Shashi; Ranjan, Gyan; Lavanya, V. Anitha; Rophina, Mercy; Umadevi, S.; Sehgal, Paras; Devi, Anju; Surekha, A.; Chandra, Pritam; Hymavathy, R.; Vanaja, P. R.; Sivasubbu, Sridhar

doi:10.1101/2021.01.22.427775

Cited by 3 publications

(5 citation statements)

References 16 publications

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“…All nine amino acid changes, namely N440K, S477N, V483A, E484K/Q, F490S, S494L/P, N501Y are associated with immune escape 24 , 25 . Viruses with some of these amino acid changes were already known to be circulating in other parts of India 16 , 17 , 24 .…”

Section: Discussionmentioning

confidence: 99%

“…Genomic studies in India have shown that several lineages of SARS-CoV-2 have been introduced, have spread, and fallen below the limit of detection since January 2020 [12][13][14][15][16][17][18][19][20][21][22] . We have previously performed detailed genomic epidemiology of SARS-CoV-2 in the South Indian state of Karnataka, with a population of 64.1 million (Census 2014) 22 .…”

Section: Introductionmentioning

confidence: 99%

“…Multiple lineages of SARS-CoV-2 have been reported from across the world and in India 12,13,[15][16][17][19][20][21][22]27 . There are two ancestral lineages of SARS-CoV-2 in the PANGO classification system, A and B 28 .…”

Section: Introductionmentioning

confidence: 99%

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Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka

et al. 2022

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Background: As the coronavirus disease 2019 (COVID-19) pandemic continues, the selection of genomic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) associated with higher transmission, more severe disease, re-infection, and immune escape are a cause for concern. Such variants have been reported from the UK (B.1.1.7), South Africa (B.1.351) and, Brazil (P.1/B.1.1.28). We performed this study to track the importation, spread, and emergence of variants locally. Methods: We sequenced whole genomes of SARS-CoV-2 from international travellers (n=75) entering Karnataka, South India, between Dec 22, 2020 and Jan 31, 2021, and from positive cases in the city of Bengaluru (n=108), between Nov 22, 2020- Jan 22, 2021, as well as a local outbreak. We present the lineage distribution and analysis of these sequences. Results: Genomes from the study group into 34 lineages. Variant B.1.1.7 was introduced by international travel (24/73, 32.9%). Lineage B.1.36 and B.1 formed a major fraction of both imported (B.1.36: 20/73, 27.4%; B.1: 14/73, 19.2%), and circulating viruses (B.1.36: 45/103; 43.7%,. B.1: 26/103; 25.2%). The lineage B.1.36 was also associated with a local outbreak. We detected nine amino acid changes, previously associated with immune escape, spread across multiple lineages. The N440K change was detected in 45/162 (27.7%) of the sequences, 37 of these were in the B.1.36 lineage (37/65, 56.92%) Conclusions: Our data support the idea that variants of concern spread by travel. Viruses with amino acid replacements associated with immune escape are already circulating. It is critical to check transmission and monitor changes in SARS-CoV-2 locally.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka

et al. 2022

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show abstract

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka

et al. 2021

View full text Add to dashboard Cite

Background: As the coronavirus disease 2019 (COVID-19) pandemic continues, the selection of genomic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) associated with higher transmission, more severe disease, re-infection, and immune escape are a cause for concern. Such variants have been reported from the UK (B.1.1.7), South Africa (B.1.351) and, Brazil (P.1/B.1.1.28). We performed this study to track the importation, spread, and emergence of variants locally. Methods: We sequenced whole genomes of SARS-CoV-2 from international travellers (n=75) entering Karnataka, South India, between Dec 22, 2020 and Jan 31, 2021, and from positive cases in the city of Bengaluru (n=108), between Nov 22, 2020- Jan 22, 2021, as well as a local outbreak. We present the lineage distribution and analysis of these sequences. Results: Genomes from the study group into 34 lineages. Variant B.1.1.7 was introduced by international travel (24/73, 32.9%). Lineage B.1.36 and B.1 formed a major fraction of both imported (B.136: 20/73, 27.4%; B.1: 14/73, 19.2%), and circulating viruses (B.1.36: 45/103; 43.7%, B.1: 26/103; 25.2%). The lineage B.1.36 was also associated with a local outbreak. We detected nine amino acid changes, previously associated with immune escape, spread across multiple lineages. The N440K change was detected in 45/162 (27.7%) of the sequences. Conclusions: Our data support the idea that variants of concern spread by travel. Viruses with amino acid replacements associated with immune escape are already circulating. It is critical to check transmission and monitor changes in SARS-CoV-2 locally.

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Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian State of Karnataka

Pattabiraman

Prasad

George

et al. 2021

Preprint

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As the pandemic of COVID-19 caused by the coronavirus SARS-CoV-2 continues, the selection of genomic variants which can influence how the pandemic progresses is of growing concern. Of particular concern, are those variants that carry mutations/amino acid changes conferring higher transmission, more severe disease, re-infection, and immune escape. These can broadly be classified as Variants of Concern (VOCs). VOCs have been reported from several parts of the world- UK (lineage B.1.1.7), South Africa (lineage B.1.351) and, Brazil (lineage P.1/B.1.1.28). The conditions that contribute to the emergence of VOCs are not well understood. International travel remains an important means of spread. To track importation, spread, and the emergence of variants locally; we sequenced whole genomes of SARS-CoV-2 from international travellers (n=75) entering Karnataka, a state in South India, between Dec 22, 2020- Jan 31, 2021, and from positive cases in the city of Bengaluru (n=108), between Nov 22, 2020- Jan 22, 2021. The resulting 176 SARS-CoV-2 genomes could be classified into 34 lineages, that were either imported (73/176) or circulating (103/176) in this time period. The lineage B.1.1.7 (a.k.a the UK variant) was the major lineage imported into the state (24/73, 32.9%), followed by B.1.36 (20/73, 27.4%) and B.1 (14/73, 19.2%). We identified B.1.36 (45/103; 43.7%), B.1 (26/103; 25.2%), B.1.1.74 (5/103; 4.9%) and B.1.468 (4/103; 3.9%) as the major variants circulating in Bengaluru city. A distinct clade within the B.1.36 lineage was associated with a local outbreak. Analysis of the complete genomes predicted multiple amino acid replacements in the Spike protein. In total, we identified nine amino acid changes (singly or in pairs) in the Receptor Binding Domain of the Spike protein. Of these, the amino acid replacement N440K was found in 37/65 (56.92%) sequences in the B.1.36 lineage. The E484K amino acid change which is present in both VOCs, B.1.351 and P.1/B.1.1.28, was found in a single circulating virus in the B.1.36 lineage. This study highlights the introduction of VOCs by travel and the local circulation of viruses with amino acid replacements in the Spike protein. These were spread across lineages, suggesting that multiple paths can lead to the emergence of VOCs, this, in turn, highlights the need to sequence and limit outbreaks of SARS-CoV-2 locally. Our data support the use of concentrated and continued genomic surveillance of SARS-CoV-2 to direct public health measures, suggest revisions to vaccines, and serve as an early warning system to prepare for a surge in COVID-19 cases.

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Insights from Genomes and Genetic Epidemiology of SARS-CoV-2 isolates from the state of Andhra Pradesh

Cited by 3 publications

References 16 publications

Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka

Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka

Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian state of Karnataka

Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian State of Karnataka

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