Genome Sequence Quality Assessment and Annotation Analysis of SARS-CoV-2 in Goa, India (2020–2025): A Nextclade-Based Evaluation of 1,274 Sequences from Five Submitting Institutions

This study provides the first systematic genome quality evaluation for SARS-CoV-2 sequences from Goa, India. All 1,274 sequences (GISAID EPI_SET_260610gh; 2020–2025) were evaluated using Nextclade v3.21.2. Of 1,274 sequences, 495 (38.9%) passed good-quality thresholds, 68 (5.3%) were mediocre, and 711 (55.8%) bad quality. GMCH Bambolim achieved 88% good quality; NCCS Pune only 8%. Inter-institutional quality differences were highly significant (Kruskal-Wallis H=163.42, p<0.001). Deletion hotspots were identified at Nsp6 (~11,083) and the ORF8/N boundary (~28,248–28,268). Frame shifts detected in 47.9% of sequences are predominantly sequencing artefacts. 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