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

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 ana...

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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
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creator Franke, Karl R
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Shapiro, Craig A
Lee, Mary M
Crowgey, Erin L
description 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.
doi_str_mv 10.1371/journal.pone.0262573
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source Publicly Available Content Database (Proquest) (PQ_SDU_P3); PubMed Central; Coronavirus Research Database
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
title Genomic surveillance of SARS-CoV-2 in the state of Delaware reveals tremendous genomic diversity
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