A Distinct Phylogenetic Cluster of Indian Severe Acute Respiratory Syndrome Coronavirus 2 Isolates

Banu, Sofia; Jolly, Bani; Mukherjee, Payel; Singh, Priya; Khan, Shagufta; Zaveri, Lamuk; Shambhavi, Sakshi; Gaur, Namami; Reddy, Shashikala; Kaveri, K; Srinivasan, Sivasubramanian; Raj, Gopal Dhinakar; Siva, Archana Bharadwaj; Thangaraj, Kumarasamy; Tallapaka, Karthik Bharadwaj; Mishra, Rakesh; Scaria, Vinod; Sowpati, Divya Tej

doi:10.1093/ofid/ofaa434

Cited by 65 publications

(61 citation statements)

References 22 publications

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“…The genome Wuhan/WH01 (EPI_ISL_406798) was used as the reference for constructing the tree. Clades were assigned according to the nomenclature defined by Nextstrain [ 15 ] The resulting phylogenetic tree suggests that out of 469 COVIDSeq genomes, 451 genomes (96%) fell into the A2a clade while 14 genomes (3%) mapped to the I/A3i clade, a distinct clade previously defined for genomes from India [ 16 ]. A total of 4 genomes mapped to the B4 clade.…”

Section: Resultsmentioning

confidence: 99%

High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing

et al. 2021

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The rapid emergence of coronavirus disease 2019 (COVID-19) as a global pandemic affecting millions of individuals globally has necessitated sensitive and high-throughput approaches for the diagnosis, surveillance, and determining the genetic epidemiology of SARS-CoV-2. In the present study, we used the COVIDSeq protocol, which involves multiplex-PCR, barcoding, and sequencing of samples for high-throughput detection and deciphering the genetic epidemiology of SARS-CoV-2. We used the approach on 752 clinical samples in duplicates, amounting to a total of 1536 samples which could be sequenced on a single S4 sequencing flow cell on NovaSeq 6000. Our analysis suggests a high concordance between technical duplicates and a high concordance of detection of SARS-CoV-2 between the COVIDSeq as well as RT-PCR approaches. An in-depth analysis revealed a total of six samples in which COVIDSeq detected SARS-CoV-2 in high confidence which were negative in RT-PCR. Additionally, the assay could detect SARS-CoV-2 in 21 samples and 16 samples which were classified inconclusive and pan-sarbeco positive respectively suggesting that COVIDSeq could be used as a confirmatory test. The sequencing approach also enabled insights into the evolution and genetic epidemiology of the SARS-CoV-2 samples. The samples were classified into a total of 3 clades. This study reports two lineages B.1.112 and B.1.99 for the first time in India. This study also revealed 1,143 unique single nucleotide variants and added a total of 73 novel variants identified for the first time. To the best of our knowledge, this is the first report of the COVIDSeq approach for detection and genetic epidemiology of SARS-CoV-2. Our analysis suggests that COVIDSeq could be a potential high sensitivity assay for the detection of SARS-CoV-2, with an additional advantage of enabling the genetic epidemiology of SARS-CoV-2.

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Section: Resultsmentioning

confidence: 99%

High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing

et al. 2021

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“…The novel VUI-NP13 L variant reported in this study also derived from B.1.1.248 (former B.1.1.28) and harbored an important mutation in the nucleocapsid protein. The P13 L mutation also emerged in a cluster from India from stochastic events independent from the Brazilian lineage ( Banu et al, 2020 ). No statistically significant difference was found in the CT values of VUI-NP13 L when compared to the other clusters.…”

Section: Discussionmentioning

confidence: 99%

Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil

et al. 2021

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Emergence of novel SARS-CoV-2 lineages are under the spotlight of the media, scientific community and governments. Recent reports of novel variants in the United Kingdom, South Africa and Brazil (B.1.1.28-E484 K) have raised intense interest because of a possible higher transmission rate or resistance to the novel vaccines. Nevertheless, the spread of B.1.1.28 (E484 K) and other variants in Brazil is still unknown. In this work, we investigated the population structure and genomic complexity of SARS-CoV-2 in Rio Grande do Sul, the southernmost state in Brazil. Most samples sequenced belonged to the B.1.1.28 (E484 K) lineage, demonstrating its widespread dispersion. We were the first to identify two independent events of co-infection caused by the occurrence of B.1.1.28 (E484 K) with either B.1.1.248 or B.1.91 lineages. Also, clustering analysis revealed the occurrence of a novel cluster of samples circulating in the state (named VUI-NP13 L) characterized by 12 lineage-defining mutations. In light of the evidence for E484 K dispersion, co-infection and emergence of VUI-NP13 L in Rio Grande do Sul, we reaffirm the importance of establishing strict and effective social distancing measures to counter the spread of potentially more hazardous SARS-CoV-2 strains.

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“…The novel VUI-NP13L variant reported in this study also derived from B.1.1.248 (former B.1.1.28) and harbored an important mutation in the nucleocapsid protein. The P13L mutation also emerged in a cluster from India from stochastic events independent from the Brazilian lineage (Banu et al, 2020). No statistically significant difference was found in the CT values of VUI-NP13L when compared to the other clusters.…”

Section: Discussionmentioning

confidence: 99%

Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil

Francisco

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Lamarca

et al. 2021

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Emergence of novel SARS-CoV-2 lineages are under the spotlight of the media, scientific community and governments. Recent reports of novel variants in the United Kingdom, South Africa and Brazil (B.1.1.28-E484K) have raised intense interest because of a possible higher transmission rate or resistance to the novel vaccines. Nevertheless, the spread of B.1.1.28 (E484K) and other variants in Brazil is still unknown. In this work, we investigated the population structure and genomic complexity of SARS-CoV-2 in Rio Grande do Sul, the southernmost state in Brazil. Most samples sequenced belonged to the B.1.1.28 (E484K) lineage, demonstrating its widespread dispersion. We were the first to identify two independent events of co-infection caused by the occurrence of B.1.1.28 (E484K) with either B.1.1.248 or B.1.91 lineages. Also, clustering analysis revealed the occurrence of a novel cluster of samples circulating in the state (named VUI-NP13L) characterized by 12 lineage-defining mutations. In light of the evidence for E484K dispersion, co-infection and emergence of VUI-NP13L in Rio Grande do Sul, we reaffirm the importance of establishing strict and effective social distancing measures to counter the spread of potentially more hazardous SARS-CoV-2 strains.HighlightsThe novel variant B.1.1.28 (E484K) previously described in Rio de Janeiro is currently spread across the southernmost state of Brazil;The novel variant VUI-NP13L was also identified by causing a local outbreak in Rio Grande do Sul;B.1.1.28 (E484K) is able to establish successful coinfection events co-occurring simultaneously with different lineages of SARS-CoV-2.

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A Distinct Phylogenetic Cluster of Indian Severe Acute Respiratory Syndrome Coronavirus 2 Isolates

Cited by 65 publications

References 22 publications

High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing

High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing

Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil

Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil

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