Sequenced but Unseen: Geographic Gaps, Institutional Disparities, Surveillance Lags, and the Demographics of SARS-CoV-2 Genomic Surveillance in Goa, India (2020–2025)

This study analyses the surveillance infrastructure behind 1,274 Goa SARS-CoV-2 sequences (EPI_SET_260610gh; 2020–2025) using complete GISAID metadata. The median submission lag was 95.5 days; 52.7% of sequences exceeded the 90-day operational threshold. GMCH Bambolim had a median lag of 174 days; ICMR-NIV Pune 45 days (Kruskal-Wallis H=546.43, p=7.52×10⁻¹²¹). Only 4 of Goa's 12 talukas appear by name in GISAID metadata; 45.8% of sequences carry only state-level location. The WHO 5% sequencing rate threshold was exceeded only in 2023 when case counts had collapsed. A 527-day surveillance gap in 2024 left Goa invisible to global genomic surveillance. Patient mean age was 42.3 years; a sex ratio reversal was observed in 2023 (M:F=0.77:1 vs 1.36:1 in 2021–2022). 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