tetano
Editor, Senior Moderator
Open Forum Infect Dis
. 2020 Nov 13;8(6)
faa551.
doi: 10.1093/ofid/ofaa551. eCollection 2021 Jun.
High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19
Utsav Pandey[SUP] 1 [/SUP], Rebecca Yee[SUP] 1 [/SUP], Lishuang Shen[SUP] 1 [/SUP], Alexander R Judkins[SUP] 1 2 [/SUP], Moiz Bootwalla[SUP] 1 [/SUP], Alex Ryutov[SUP] 1 [/SUP], Dennis T Maglinte[SUP] 1 [/SUP], Dejerianne Ostrow[SUP] 1 [/SUP], Mimi Precit[SUP] 1 [/SUP], Jaclyn A Biegel[SUP] 1 2 [/SUP], Jeffrey M Bender[SUP] 3 2 [/SUP], Xiaowu Gai[SUP] 1 2 [/SUP], Jennifer Dien Bard[SUP] 1 2 [/SUP]
Affiliations
Abstract
Background: The full spectrum of the disease phenotype and viral genotype of coronavirus disease 2019 (COVID-19) have yet to be thoroughly explored in children. Here, we analyze the relationships between viral genetic variants and clinical characteristics in children.
Methods: Whole-genome sequencing was performed on respiratory specimens collected for all SARS-CoV-2-positive children (n = 141) between March 13 and June 16, 2020. Viral genetic variations across the SARS-CoV-2 genome were identified and investigated to evaluate genomic correlates of disease severity.
Results: Higher viral load was detected in symptomatic patients (P = .0007) and in children <5 years old (P = .0004). Genomic analysis revealed a mean pairwise difference of 10.8 single nucleotide variants (SNVs), and the majority (55.4%) of SNVs led to an amino acid change in the viral proteins. The D614G mutation in the spike protein was present in 99.3% of the isolates. The calculated viral mutational rate of 22.2 substitutions/year contrasts the 13.5 substitutions/year observed in California isolates without the D614G mutation. Phylogenetic clade 20C was associated with severe cases of COVID-19 (odds ratio, 6.95; P = .0467). Epidemiological investigation revealed major representation of 3 of 5 major Nextstrain clades (20A, 20B, and 20C) consistent with multiple introductions of SARS-CoV-2 in Southern California.
Conclusions: Genomic evaluation demonstrated greater than expected genetic diversity, presence of the D614G mutation, increased mutation rate, and evidence of multiple introductions of SARS-CoV-2 into Southern California. Our findings suggest a possible association of phylogenetic clade 20C with severe disease, but small sample size precludes a definitive conclusion. Our study warrants larger and multi-institutional genomic evaluation and has implications for infection control practices.
Keywords: COVID-19; D614G; SARS-CoV-2; children; clade 20C; genomic epidemiology; viral sequencing.
. 2020 Nov 13;8(6)
faa551.doi: 10.1093/ofid/ofaa551. eCollection 2021 Jun.
High Prevalence of SARS-CoV-2 Genetic Variation and D614G Mutation in Pediatric Patients With COVID-19
Utsav Pandey[SUP] 1 [/SUP], Rebecca Yee[SUP] 1 [/SUP], Lishuang Shen[SUP] 1 [/SUP], Alexander R Judkins[SUP] 1 2 [/SUP], Moiz Bootwalla[SUP] 1 [/SUP], Alex Ryutov[SUP] 1 [/SUP], Dennis T Maglinte[SUP] 1 [/SUP], Dejerianne Ostrow[SUP] 1 [/SUP], Mimi Precit[SUP] 1 [/SUP], Jaclyn A Biegel[SUP] 1 2 [/SUP], Jeffrey M Bender[SUP] 3 2 [/SUP], Xiaowu Gai[SUP] 1 2 [/SUP], Jennifer Dien Bard[SUP] 1 2 [/SUP]
Affiliations
- PMID: 34095334
- PMCID: PMC7717363
- DOI: 10.1093/ofid/ofaa551
Abstract
Background: The full spectrum of the disease phenotype and viral genotype of coronavirus disease 2019 (COVID-19) have yet to be thoroughly explored in children. Here, we analyze the relationships between viral genetic variants and clinical characteristics in children.
Methods: Whole-genome sequencing was performed on respiratory specimens collected for all SARS-CoV-2-positive children (n = 141) between March 13 and June 16, 2020. Viral genetic variations across the SARS-CoV-2 genome were identified and investigated to evaluate genomic correlates of disease severity.
Results: Higher viral load was detected in symptomatic patients (P = .0007) and in children <5 years old (P = .0004). Genomic analysis revealed a mean pairwise difference of 10.8 single nucleotide variants (SNVs), and the majority (55.4%) of SNVs led to an amino acid change in the viral proteins. The D614G mutation in the spike protein was present in 99.3% of the isolates. The calculated viral mutational rate of 22.2 substitutions/year contrasts the 13.5 substitutions/year observed in California isolates without the D614G mutation. Phylogenetic clade 20C was associated with severe cases of COVID-19 (odds ratio, 6.95; P = .0467). Epidemiological investigation revealed major representation of 3 of 5 major Nextstrain clades (20A, 20B, and 20C) consistent with multiple introductions of SARS-CoV-2 in Southern California.
Conclusions: Genomic evaluation demonstrated greater than expected genetic diversity, presence of the D614G mutation, increased mutation rate, and evidence of multiple introductions of SARS-CoV-2 into Southern California. Our findings suggest a possible association of phylogenetic clade 20C with severe disease, but small sample size precludes a definitive conclusion. Our study warrants larger and multi-institutional genomic evaluation and has implications for infection control practices.
Keywords: COVID-19; D614G; SARS-CoV-2; children; clade 20C; genomic epidemiology; viral sequencing.