About: PAN-INDIA 1000 SARS-CoV-2 RNA Genome Sequencing Reveals Important Insights into the Outbreak

Facets (new session)
Description
Metadata
Settings
- owl:sameAs
- Inference Rule:

About: PAN-INDIA 1000 SARS-CoV-2 RNA Genome Sequencing Reveals Important Insights into the Outbreak Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	PAN-INDIA 1000 SARS-CoV-2 RNA Genome Sequencing Reveals Important Insights into the Outbreak
Creator	Sahu, Arvind Chinnaswamy, Sreedhar Das, Saumitra Maitra, Arindam Parida, Ajay Pati, Sanghamitra Dalal, Ashwin Mitra, Debashis Palakodeti, Dasaradhi Bashyam, Murali Biswas, Farhan, Ali Ghosh, Arup Jani, Kunal Kumar Bhat, Manoj Molin, Paynter Raghav, Sunil Sai, Aswin Sarin, Apurva Sauche, Yogesh Seshasayee, Narain
Source	BioRxiv
abstract	The PAN-INDIA 1000 SARS-CoV-2 RNA Genome Sequencing Consortium has achieved its initial goal of completing the sequencing of 1000 SARS-CoV-2 genomes from nasopharyngeal and oropharyngeal swabs collected from individuals testing positive for COVID-19 by Real Time PCR. The samples were collected across 10 states covering different zones within India. Given the importance of this information for public health response initiatives investigating transmission of COVID-19, the sequence data is being released in GISAID database. This information will improve our understanding on how the virus is spreading, ultimately helping to interrupt the transmission chains, prevent new cases of infection, and provide impetus to research on intervention measures. This will also provide us with information on evolution of the virus, genetic predisposition (if any) and adaptation to human hosts. One thousand and fifty two sequences were used for phylodynamic, temporal and geographic mutation patterns and haplotype network analyses. Initial results indicate that multiple lineages of SARS-CoV-2 are circulating in India, probably introduced by travel from Europe, USA and East Asia. A2a (20A/B/C) was found to be predominant, along with few parental haplotypes 19A/B. In particular, there is a predominance of the D614G mutation, which is found to be emerging in almost all regions of the country. Additionally, mutations in important regions of the viral genome with significant geographical clustering have also been observed. The temporal haplotype diversities landscape in each region appears to be similar pan India, with haplotype diversities peaking between March-May, while by June A2a (20A/B/C) emerged as the predominant one. Within haplotypes, different states appear to have different proportions. Temporal and geographic patterns in the sequences obtained reveal interesting clustering of mutations. Some mutations are present at particularly high frequencies in one state as compared to others. The negative estimate Tajimas D (D = −2.26817) is consistent with the rapid expansion of SARS-CoV-2 population in India. Detailed mutational analysis across India to understand the gradual emergence of mutants at different regions of the country and its possible implication will help in better disease management.
has issue date	2020-08-03(xsd:dateTime)
bibo:doi	10.1101/2020.08.03.233718
has license	biorxiv
sha1sum (hex)	722ff696d41fe1afd5935ff641b85bff457c6859
schema:url	https://doi.org/10.1101/2020.08.03.233718
resource representing a document's title	PAN-INDIA 1000 SARS-CoV-2 RNA Genome Sequencing Reveals Important Insights into the Outbreak
schema:publication	bioRxiv
resource representing a document's body	covid:722ff696d41fe1afd5935ff641b85bff457c6859#body_text
is schema:about of	named entity 'covering' named entity 'cases' named entity 'INDIA' named entity 'COLLECTED' named entity 'DATABASE' named entity 'HUMAN' named entity 'SARS-CoV-2' named entity 'helping' named entity 'India' named entity 'collected' named entity 'adaptation' named entity 'Sequencing' named entity 'Important' named entity 'virus' named entity 'Genome Sequencing' named entity 'virus' named entity 'GISAID' named entity 'PCR' named entity 'RNA' named entity 'Genome Sequencing' named entity 'RNA' named entity 'phylogenetic tree' named entity 'phylogenetic inference' named entity 'Western India' named entity 'Western India' named entity '6.68' named entity 'phylogenetic tree' named entity 'haplotype' named entity 'nucleotide sequence' named entity 'India' named entity 'nsp3' named entity 'RdRp' named entity 'correlation' named entity 'RNA sequences' named entity 'PCR' named entity 'Wuhan' named entity 'common ancestors' named entity 'haplotype' named entity 'genomes' named entity 'SARS-CoV-2' named entity 'China' named entity 'Gujarat' named entity 'Viral' named entity 'haplotypes' named entity 'Illumina' named entity 'mutation' named entity 'Southern India' named entity 'GISAID' named entity 'nsp6' named entity 'nasopharyngeal' named entity 'Illumina' named entity 'genomes' named entity 'RNA sequences' named entity 'Multiple Sequence Alignment' named entity 'SARS-CoV-2' named entity 'synonymous mutations' named entity 'Indian Council of Medical Research' named entity 'Eastern India' named entity 'GISAID' named entity 'reference genome' named entity 'haplotype' named entity 'SARS-CoV-2' named entity 'MRCA' named entity 'haplotype'

Faceted Search & Find service v1.13.91 as of Mar 24 2020

Alternative Linked Data Documents: Sponger | ODE Content Formats:

RDF

ODATA

Microdata

About

OpenLink Virtuoso version 07.20.3229 as of Jul 10 2020, on Linux (x86_64-pc-linux-gnu), Single-Server Edition (94 GB total memory)
Data on this page belongs to its respective rights holders.
Virtuoso Faceted Browser Copyright © 2009-2024 OpenLink Software