Five Waves, 110 Lineages: The Complete SARS-CoV-2 Genomic Record of Goa, India (2020–2025)

Background: Goa, India's smallest state and major international tourism destination, represents a unique epidemiological setting for SARS-CoV-2 genomic surveillance. No comprehensive state-level genomic analysis of Goa's SARS-CoV-2 record has been published previously. Methods: We analysed all 1,274 GISAID EpiCoV genome sequences and associated metadata from Goa, India (extracted 5 June 2026; collection dates 2020-12-23 to 2025-06-16). Sequence quality metrics were computed directly from FASTA files. A systematic metadata transposition error affecting 118 records was detected and corrected. Statistical analyses included Shapiro-Wilk, Kruskal-Wallis, Welch t-test, chi-square, Mann-Whitney U, and Spearman rank correlation. Shannon entropy and Simpson's reciprocal index were computed for lineage diversity. Results: The dataset encompasses 110 unique Pango lineages across 8 GISAID clades. Delta (B.1.617.2 + AY sub-lineages): 663 sequences (52.0%); Omicron and all descendants: 467 (36.7%). N-content analysis reveals 46.8% high-quality sequences and 25.9% low-quality (>10% N). N-content is significantly correlated with submission lag (Spearman r=0.469, p<0.001). Shannon diversity peaked in 2022 (H=3.13) and was lowest in 2021 (H=1.48, Delta dominance). Corrected sex ratio: 1.28:1 (689M:540F). Submission lag: median 95.5 days (IQR 49-194d). Mann-Whitney U confirms highly significant institutional lag disparity (NCCS Pune median 199d vs NIV-NIC median 46d; p<0.001). Conclusions: This is the first comprehensive genomic epidemiological analysis of SARS-CoV-2 in Goa, India, covering five pandemic waves over 54 months. Key findings include detection and correction of a 118-record metadata transposition error, N-content quality profiling, the Kappa-Delta co-circulation cluster at Mapusa (April 2021), BA.2.75/Centaurus over-representation (n=62), complete Arcturus wave documentation (n=156 XBB sequences), and genomic continuity through 2025 recombinant lineages XFC and XFG. Genomic data: GISAID EPI_SET_260610gh (https://doi.org/10.55876/gis8.260610gh)