Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of Karnataka

Karnataka, a state in south India, reported its first case of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection on March 8, 2020, more than a month after the first case was reported in India. We used a combination of contact tracing and genomic epidemiology to trace the spread o...

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Veröffentlicht in:	PloS one Jg. 15; H. 12; S. e0243412
Hauptverfasser:	Pattabiraman, Chitra, Habib, Farhat, P. K., Harsha, Rasheed, Risha, Prasad, Pramada, Reddy, Vijayalakshmi, Dinesh, Prameela, Damodar, Tina, Hosallimath, Kiran, George, Anson K., Kiran Reddy, Nakka Vijay, John, Banerjee, Pattanaik, Amrita, Kumar, Narendra, Mani, Reeta S., Venkataswamy, Manjunatha M., Shahul Hameed, Shafeeq K., Kumar B. G., Prakash, Desai, Anita, Vasanthapuram, Ravi
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	United States Public Library of Science 17.12.2020 Public Library of Science (PLoS)
Schlagworte:	Biology and Life Sciences Clusters Computer and Information Sciences Contact Tracing Coronaviruses COVID-19 COVID-19 - epidemiology COVID-19 - genetics COVID-19 - transmission Disease Outbreaks Disease transmission Epidemiology Female Genetic aspects Genome, Viral Genomes Genomics Humans India - epidemiology Male Medicine and health sciences Mental health Neurosciences Pandemics People and Places Phylogeny Public health Respiratory Distress Syndrome - epidemiology Respiratory Distress Syndrome - genetics Respiratory Distress Syndrome - virology SARS-CoV-2 - genetics Severe acute respiratory syndrome Severe acute respiratory syndrome coronavirus 2 Software Spreaders Travel Viral diseases Viruses India Karnataka India Europe China
ISSN:	1932-6203, 1932-6203
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Abstract	Karnataka, a state in south India, reported its first case of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection on March 8, 2020, more than a month after the first case was reported in India. We used a combination of contact tracing and genomic epidemiology to trace the spread of SARS-CoV-2 in the state up until May 21, 2020 (1578 cases). We obtained 91 genomes of SARS-CoV-2 which clustered into seven lineages (Pangolin lineages—A, B, B.1, B.1.80, B.1.1, B.4, and B.6). The lineages in Karnataka were known to be circulating in China, Southeast Asia, Iran, Europe and other parts of India and are likely to have been imported into the state both by international and domestic travel. Our sequences grouped into 17 contact clusters and 24 cases with no known contacts. We found 14 of the 17 contact clusters had a single lineage of the virus, consistent with multiple introductions and most (12/17) were contained within a single district, reflecting local spread. In most of the 17 clusters, the index case (12/17) and spreaders (11/17) were symptomatic. Of the 91 sequences, 47 belonged to the B.6 lineage, including eleven of 24 cases with no known contact, indicating ongoing transmission of this lineage in the state. Genomic epidemiology of SARS-CoV-2 in Karnataka suggests multiple introductions of the virus followed by local transmission in parallel with ongoing viral evolution. This is the first study from India combining genomic data with epidemiological information emphasizing the need for an integrated approach to outbreak response.
AbstractList	Karnataka, a state in south India, reported its first case of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection on March 8, 2020, more than a month after the first case was reported in India. We used a combination of contact tracing and genomic epidemiology to trace the spread of SARS-CoV-2 in the state up until May 21, 2020 (1578 cases). We obtained 91 genomes of SARS-CoV-2 which clustered into seven lineages (Pangolin lineages-A, B, B.1, B.1.80, B.1.1, B.4, and B.6). The lineages in Karnataka were known to be circulating in China, Southeast Asia, Iran, Europe and other parts of India and are likely to have been imported into the state both by international and domestic travel. Our sequences grouped into 17 contact clusters and 24 cases with no known contacts. We found 14 of the 17 contact clusters had a single lineage of the virus, consistent with multiple introductions and most (12/17) were contained within a single district, reflecting local spread. In most of the 17 clusters, the index case (12/17) and spreaders (11/17) were symptomatic. Of the 91 sequences, 47 belonged to the B.6 lineage, including eleven of 24 cases with no known contact, indicating ongoing transmission of this lineage in the state. Genomic epidemiology of SARS-CoV-2 in Karnataka suggests multiple introductions of the virus followed by local transmission in parallel with ongoing viral evolution. This is the first study from India combining genomic data with epidemiological information emphasizing the need for an integrated approach to outbreak response. Karnataka, a state in south India, reported its first case of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection on March 8, 2020, more than a month after the first case was reported in India. We used a combination of contact tracing and genomic epidemiology to trace the spread of SARS-CoV-2 in the state up until May 21, 2020 (1578 cases). We obtained 91 genomes of SARS-CoV-2 which clustered into seven lineages (Pangolin lineages-A, B, B.1, B.1.80, B.1.1, B.4, and B.6). The lineages in Karnataka were known to be circulating in China, Southeast Asia, Iran, Europe and other parts of India and are likely to have been imported into the state both by international and domestic travel. Our sequences grouped into 17 contact clusters and 24 cases with no known contacts. We found 14 of the 17 contact clusters had a single lineage of the virus, consistent with multiple introductions and most (12/17) were contained within a single district, reflecting local spread. In most of the 17 clusters, the index case (12/17) and spreaders (11/17) were symptomatic. Of the 91 sequences, 47 belonged to the B.6 lineage, including eleven of 24 cases with no known contact, indicating ongoing transmission of this lineage in the state. Genomic epidemiology of SARS-CoV-2 in Karnataka suggests multiple introductions of the virus followed by local transmission in parallel with ongoing viral evolution. This is the first study from India combining genomic data with epidemiological information emphasizing the need for an integrated approach to outbreak response.Karnataka, a state in south India, reported its first case of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection on March 8, 2020, more than a month after the first case was reported in India. We used a combination of contact tracing and genomic epidemiology to trace the spread of SARS-CoV-2 in the state up until May 21, 2020 (1578 cases). We obtained 91 genomes of SARS-CoV-2 which clustered into seven lineages (Pangolin lineages-A, B, B.1, B.1.80, B.1.1, B.4, and B.6). The lineages in Karnataka were known to be circulating in China, Southeast Asia, Iran, Europe and other parts of India and are likely to have been imported into the state both by international and domestic travel. Our sequences grouped into 17 contact clusters and 24 cases with no known contacts. We found 14 of the 17 contact clusters had a single lineage of the virus, consistent with multiple introductions and most (12/17) were contained within a single district, reflecting local spread. In most of the 17 clusters, the index case (12/17) and spreaders (11/17) were symptomatic. Of the 91 sequences, 47 belonged to the B.6 lineage, including eleven of 24 cases with no known contact, indicating ongoing transmission of this lineage in the state. Genomic epidemiology of SARS-CoV-2 in Karnataka suggests multiple introductions of the virus followed by local transmission in parallel with ongoing viral evolution. This is the first study from India combining genomic data with epidemiological information emphasizing the need for an integrated approach to outbreak response.
Audience	Academic
Author	John, Banerjee George, Anson K. Reddy, Vijayalakshmi Kiran Reddy, Nakka Vijay P. K., Harsha Pattabiraman, Chitra Prasad, Pramada Hosallimath, Kiran Venkataswamy, Manjunatha M. Vasanthapuram, Ravi Dinesh, Prameela Pattanaik, Amrita Kumar, Narendra Rasheed, Risha Mani, Reeta S. Shahul Hameed, Shafeeq K. Habib, Farhat Kumar B. G., Prakash Damodar, Tina Desai, Anita
AuthorAffiliation	3 Directorate of Health and Family Welfare Services, Government of Karnataka, Bengaluru, India 2 TruFactor-InMobi Group, Bengaluru, India Centers for Disease Control and Prevention, UNITED STATES 1 Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
AuthorAffiliation_xml	– name: 2 TruFactor-InMobi Group, Bengaluru, India – name: 3 Directorate of Health and Family Welfare Services, Government of Karnataka, Bengaluru, India – name: 1 Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India – name: Centers for Disease Control and Prevention, UNITED STATES
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CitedBy_id	crossref_primary_10_1016_j_cell_2023_08_026 crossref_primary_10_1186_s12920_021_00990_3 crossref_primary_10_4103_ijmr_ijmr_3247_21 crossref_primary_10_1093_cid_ciab588 crossref_primary_10_3389_fmicb_2021_703933 crossref_primary_10_1007_s11357_021_00443_w crossref_primary_10_12688_wellcomeopenres_16768_2 crossref_primary_10_1371_journal_pcbi_1012682 crossref_primary_10_12688_wellcomeopenres_16768_1 crossref_primary_10_1016_j_ijmmb_2022_12_009 crossref_primary_10_1038_s41598_021_95822_w crossref_primary_10_1371_journal_pone_0248792 crossref_primary_10_4103_jgid_jgid_97_21 crossref_primary_10_1038_s41588_021_00862_7
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Notes	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 Competing Interests: FH is an employee of TruFactor-InMobi group company, however, he was permitted to participate as a volunteer in this study and his employer neither had access to data, nor any say in the design of the study or the decision to publish. This does not alter our adherence to PLOS ONE policies on sharing data and materials. All other authors are employees of state (PD, PK) or central government. The employers had no role in the design of the study or the decision to publish. The authors declare that they do not have any other financial or non-financial relationships that could present a conflict of interest.
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Snippet	Karnataka, a state in south India, reported its first case of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection on March 8, 2020, more...
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SubjectTerms	Biology and Life Sciences Clusters Computer and Information Sciences Contact Tracing Coronaviruses COVID-19 COVID-19 - epidemiology COVID-19 - genetics COVID-19 - transmission Disease Outbreaks Disease transmission Epidemiology Female Genetic aspects Genome, Viral Genomes Genomics Humans India - epidemiology Male Medicine and health sciences Mental health Neurosciences Pandemics People and Places Phylogeny Public health Respiratory Distress Syndrome - epidemiology Respiratory Distress Syndrome - genetics Respiratory Distress Syndrome - virology SARS-CoV-2 - genetics Severe acute respiratory syndrome Severe acute respiratory syndrome coronavirus 2 Software Spreaders Travel Viral diseases Viruses
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Title	Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of Karnataka
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