Open AccessPhylogenomics and Phylodynamics of SARS-CoV-2 Genomes Retrieved From India
Author(s) -
Sameera Farah,
Ashwin Atkulwar,
Manas Ranjan Praharaj,
Raja Ishaq Nabi Khan,
Ravi Kumar Gandham,
Mumtaz Baig
Publication year - 2020
Publication title -
future virology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.462
H-Index - 34
eISSN - 1746-0808
pISSN - 1746-0794
DOI - 10.2217/fvl-2020-0243
Subject(s) - phylogenomics , viral phylodynamics , genome , covid-19 , biology , computational biology , virology , pandemic , evolutionary biology , phylogenetics , genetics , medicine , gene , outbreak , clade , disease , pathology , infectious disease (medical specialty)
Background: This is the first phylodynamic study attempted on SARS-CoV-2 genomes from India to infer the current state of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution using phylogenetic network and growth trends. Materials & Methods: Out of 286 retrieved whole genomes from India, 138 haplotypes were used to build a phylogenetic network. The birth–death serial model (BDSIR) package of BEAST2 was used to calculate the reproduction number of SARS-CoV-2. Population dynamics were investigated using the stamp date method as implemented in BEAST2 and BEAST 1.10.4. Results: A median-joining network revealed two ancestral clusters. A high basic reproduction number of SARS-CoV-2 was found. An exponential rise in the effective population size of Indian isolates was detected. Conclusion: The phylogenetic network reveals dual ancestry and possibility of community transmission of SARS-CoV-2 in India.
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