Phylogenomics and Phylodynamics of SARS-CoV-2 Genomes Retrieved From India

Abstract

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.

Keywords:

• India
• phylodynamics
• SARS-nCoV-2

Supplementary data

To view the supplementary data that accompany this paper please visit the journal website at:www.tandfonline.com/doi/full/10.2217/fvl-2020-0243

Author contributions

S Farah and A Atkulwar retrieved and analyzed the data, MR Praharaj and R Khan assisted in data analysis, R Gandham and M Baig wrote the manuscript, study was conceptualized by M Baig.

Acknowledgments

We gratefully acknowledge all authors and submitting laboratories of the sequences from GISAID. S Farah and M Baig are thankful to Prof. Elizabeth Boulding and Compute Canada for providing access to high computation facilities at www.cedar.computecanada.ca

Financial & competing interests disclosure

The authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.

No writing assistance was utilized in the production of this manuscript.