Five Waves, One Phylogeny: Molecular Clock, Lineage Diversity, and Temporal Phylodynamics of SARS-CoV-2 in Goa, India (2020–2025)

This study presents the first phylogenetic analysis of SARS-CoV-2 in Goa, India. A Nextclade neighbour-joining tree for 1,274 Goa sequences (EPI_SET_260610gh) was analysed for root-to-tip distances, branch length distributions, co-circulation patterns, and lineage diversity. Root-to-tip regression showed a strong molecular clock signal (Pearson r=0.877, p<0.001) with an evolutionary rate of approximately 21.5 substitutions per year. RTT distances differed highly significantly across variant groups (Kruskal-Wallis H=566.70, p<0.001): Omicron mean RTT was 2.1-fold higher than Delta. 75 unique PANGO lineages were identified across 495 good-quality sequences; Shannon diversity peaked in 2022 (H'=2.943). A complete circular phylogenetic tree of all 1,274 sequences is presented. Part of the West Coast and Western Ghats SARS-CoV-2 Genomic Surveillance Series. Data: GISAID EpiCoV EPI_SET_260610gh (https://doi.org/10.55876/gis8.260610gh). We gratefully acknowledge all data contributors, i.e., the Authors and their Originating laboratories responsible for obtaining the specimens, and their Submitting laboratories for generating the genetic sequence and metadata and sharing via the GISAID Initiative, on which this research is based. GISAID citations: Elbe & Buckland-Merrett (2017) Global Challenges 1:33–46. doi:10.1002/gch2.1018 | Shu & McCauley (2017) Euro Surveill 22(13):30494. doi:10.2807/1560-7917.ES.2017.22.13.30494 | Khare et al. (2021) China CDC Weekly 3(49):1049–1051. doi:10.46234/ccdcw2021.255