Genomic analysis of 16 Colorado human NL63 coronaviruses identifies a new genotype, high sequence diversity in the N-terminal domain of the spike gene and evidence of recombination
Autor: | Christopher D. Town, Kathryn V. Holmes, Christine C. Robinson, David E. Wentworth, Gregory E. Sims, Samuel R. Dominguez, Rebecca A. Halpin |
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Rok vydání: | 2012 |
Předmět: |
Male
Lineage (genetic) Colorado Time Factors Adolescent Genotype Molecular Sequence Data Genome Viral Biology Genome Virus stomatognathic system Viral Envelope Proteins Phylogenetics Virology Genetic variation Humans Child Gene Phylogeny Genetics Recombination Genetic Membrane Glycoproteins Phylogenetic tree Animal Infant Newborn Genetic Variation Infant respiratory system Protein Structure Tertiary Coronavirus NL63 Human Child Preschool Spike Glycoprotein Coronavirus Female Coronavirus Infections |
Zdroj: | Journal of General Virology |
ISSN: | 1465-2099 0022-1317 |
DOI: | 10.1099/vir.0.044628-0 |
Popis: | This study compared the complete genome sequences of 16 NL63 strain human coronaviruses (hCoVs) from respiratory specimens of paediatric patients with respiratory disease in Colorado, USA, and characterized the epidemiology and clinical characteristics associated with circulating NL63 viruses over a 3-year period. From 1 January 2009 to 31 December 2011, 92 of 9380 respiratory specimens were found to be positive for NL63 RNA by PCR, an overall prevalence of 1 %. NL63 viruses were circulating during all 3 years, but there was considerable yearly variation in prevalence and the month of peak incidence. Phylogenetic analysis comparing the genome sequences of the 16 Colorado NL63 viruses with those of the prototypical hCoV-NL63 and three other NL63 viruses from the Netherlands demonstrated that there were three genotypes (A, B and C) circulating in Colorado from 2005 to 2010, and evidence of recombination between virus strains was found. Genotypes B and C co-circulated in Colorado in 2005, 2009 and 2010, but genotype A circulated only in 2005 when it was the predominant NL63 strain. Genotype C represents a new lineage that has not been described previously. The greatest variability in the NL63 virus genomes was found in the N-terminal domain (NTD) of the spike gene (nt 1–600, aa 1–200). Ten different amino acid sequences were found in the NTD of the spike protein among these NL63 strains and the 75 partial published sequences of NTDs from strains found at different times throughout the world. |
Databáze: | OpenAIRE |
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