Genomic surveillance of SARS-CoV-2 in the state of Delaware reveals tremendous genomic diversity

• Published in: PloS one 2022-01, Vol.17 (1), p.e0262573-e0262573
• Main Authors: Franke, Karl R, Isett, Robert, Robbins, Alan, Paquette-Straub, Carrie, Shapiro, Craig A, Lee, Mary M, Crowgey, Erin L
• Format: Article
• Language: English
• Subjects: Acids; Airports; Biological diversity; Biology and life sciences; Computer and Information Sciences; Coronaviruses; COVID-19; COVID-19 - epidemiology; COVID-19 - pathology; COVID-19 - virology; Delaware - epidemiology; Disease transmission; Gene mutations; Genetic Linkage; Genome, Viral; Genomes; Genomics; Health aspects; Health surveillance; High-Throughput Nucleotide Sequencing; Humans; Identification and classification; Infections; Infectivity; Medicine and health sciences; Mutation; Next-generation sequencing; People and places; Phylogenetics; Phylogeny; Proteins; Research and analysis methods; RNA, Viral - chemistry; RNA, Viral - metabolism; SARS-CoV-2 - classification; SARS-CoV-2 - genetics; SARS-CoV-2 - isolation & purification; Severe acute respiratory syndrome; Severe acute respiratory syndrome coronavirus 2; Surveillance; Viral infections; Viruses
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0262573

The use of next generation sequencing is critical for the surveillance of severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, transmission, as single base mutations have been identified with differences in infectivity. A total of 1,459 high quality samples were collected, sequenced, and analyzed in the state of Delaware, a location that offers a unique perspective on transmission given its proximity to large international airports on the east coast. Pangolin and Nextclade were used to classify these sequences into 16 unique clades and 88 lineages. A total of 411 samples belonging to the Alpha 20I/501Y.V1 (B.1.1.7) strain of concern were identified, as well as one sample belonging to Beta 20H/501.V2 (B.1.351), thirteen belonging to Epsilon 20C/S:452R (B.1.427/B.1.429), two belonging to Delta 20A/S:478K (B.1.617.2), and 15 belonging to Gamma 20J/501Y.V3 (p.1). A total of 2217 unique coding mutations were observed with an average of 17.7 coding mutations per genome. These data paired with continued sample collection and sequencing will give a deeper understanding of the spread of SARS-CoV-2 strains within Delaware and its surrounding areas.