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

Autor: Narendra Kumar, Tina Damodar, Shafeeq K. Shahul Hameed, Manjunatha M. Venkataswamy, Amrita Pattanaik, Vijayalakshmi Reddy, Ravi Vasanthapuram, Banerjee John, Anson K. George, Risha Rasheed, Kiran Hosallimath, B. G. Prakash Kumar, Prameela Dinesh, Chitra Pattabiraman, Farhat Habib, Pramada Prasad, Nakka Vijay Kiran Reddy, Anita Desai, Reeta S. Mani, Pulleri Kandi Harsha
Jazyk: angličtina
Rok vydání: 2020
Předmět:
0301 basic medicine
RNA viruses
Male
Viral Diseases
Coronaviruses
Epidemiology
Single Nucleotide Polymorphisms
law.invention
Disease Outbreaks
Geographical Locations
0302 clinical medicine
Medical Conditions
law
030212 general & internal medicine
Index case
Pathology and laboratory medicine
Phylogeny
Data Management
Respiratory Distress Syndrome
Travel
Multidisciplinary
biology
Phylogenetic Analysis
Genomics
Medical microbiology
Phylogenetics
Transmission (mechanics)
Infectious Diseases
Viral evolution
Viruses
Medicine
Female
SARS CoV 2
Pathogens
Research Article
Computer and Information Sciences
Lineage (genetic)
Asia
SARS coronavirus
Science
India
Genome
Viral
Microbiology
03 medical and health sciences
Genetics
Humans
Evolutionary Systematics
Taxonomy
Medicine and health sciences
Evolutionary Biology
SARS-CoV-2
Pangolin
Organisms
Viral pathogens
Biology and Life Sciences
COVID-19
Covid 19
biology.organism_classification
Microbial pathogens
030104 developmental biology
Evolutionary biology
People and Places
Contact Tracing
Contact tracing
Zdroj: PLoS ONE
PLoS ONE, Vol 15, Iss 12, p e0243412 (2020)
ISSN: 1932-6203
Popis: 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.
Databáze: OpenAIRE
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