Assessing SARS-CoV-2 Rare Mutations and Transmission in New York City by NGS

SARS-CoV-2 undergoes frequent mutations that drive viral evolution and genomic diversity, influencing transmissibility, immune escape, and disease severity. In this study, we performed whole-genome sequencing on SARS-CoV-2 isolates from patients in New York City and identified several globally rare mutations across multiple viral lineages. The isolates analyzed for rare mutations belonged to three lineages: B.1.1.7 (Alpha), B.1.526 (Iota), and B.1.623. We identified 16 rare mutations (global incidence <1000) in non-structural protein genes, including <i>nsp2</i>, <i>nsp3</i>, <i>nsp4</i>, <i>nsp6</i>, <i>nsp8</i>, <i>nsp13</i>, <i>nsp14</i>, <i>ORF7a</i>, and <i>ORF8</i>. Three of these mutations-located in <i>nsp2, nsp13,</i> and <i>ORF8</i>-have been reported in fewer than 100 individuals worldwide. We also detected five rare mutations in structural proteins (<i>S</i>, <i>M</i>, and <i>N</i>), including two-one in <i>M</i> and one in <i>N</i>-previously reported in fewer than 100 cases globally. We present clinical profiles of three patients, each infected with genetically distinct viral isolates from the three lineages studied. Furthermore, we illustrate a local transmission chain inferred from unique mutation patterns identified in the Omicron genome. These findings underscore the importance of whole-genome sequencing for detecting rare mutations, tracking community spread, and identifying emerging variants with clinical and public health significance.