MORTALITY-ASSOCIATED SARS-COV-2 GENOMIC VARIANTS FROM PATIENTS HOSPITALIZED FOR SEVERE PNEUMONIA IN AGUASCALIENTES, MEXICO FROM 2020 TO 2023
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Background Genomic surveillance of SARS-CoV-2 is essential for understanding regional disease dynamics and supporting reproducible public health research. Latin America remains underrepresented in global datasets, despite high mutation frequencies reported in the region. Methods We sequenced 150 SARS-CoV-2 genomes from patients hospitalized with pneumonia in Aguascalientes, Mexico, between 2021 and 2023. Samples were confirmed by RT-qPCR, sequenced using the Illumina CovidSeq protocol, and analyzed with standardized bioinformatics workflows (CLC Genomics Workbench, BV-BRC annotation, and PANGO lineage assignment). Clinical metadata, including demographics, comorbidities, and symptom duration, were integrated with genomic data. Results Delta lineages predominated in 2021, while Omicron lineages became dominant from 2022 onward, with XBB accounting for most cases by 2023. Two mutations not previously reported in reference datasets—ORF8-L95M and ORF9-L46M—were identified in 31% and 23% of sequences, respectively. Both mutations occurred in regions associated with immune evasion. Hypertension and diabetes were the most frequent comorbidities, and symptom duration differed significantly between Delta and Omicron infections. Conclusions This study provides a reproducible workflow for genomic surveillance in a regional Mexican population, with all sequences deposited in GISAID for open access. The dataset contributes to educational and comparative studies, highlighting the importance of sustained surveillance in underrepresented populations.
