Interpatient mutational spectrum of human coronavirus‐OC43 revealed by illumina sequencing
| Autor: | Gira B. Patel, Geoffrey J. Gorse, Xiaofeng Fan |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Nonsynonymous substitution hepatitis C virus Adult Male Mutation rate Genotype viruses 030106 microbiology coronavirus Biology Gene mutation medicine.disease_cause Coronavirus OC43 Human 03 medical and health sciences Mutation Rate Virology humoral immunity genetic variability medicine Cluster Analysis Humans Human coronavirus OC43 Mutation frequency Illumina dye sequencing Research Articles Phylogeny Coronavirus Genetics Aged 80 and over Reverse Transcriptase Polymerase Chain Reaction virus diseases Genetic Variation Sequence Analysis DNA Middle Aged biology.organism_classification 030104 developmental biology Infectious Diseases Mutation Spike Glycoprotein Coronavirus Coronavirus Infections Research Article |
| Zdroj: | Journal of Medical Virology |
| ISSN: | 1096-9071 0146-6615 |
| Popis: | Human coronaviruses (HCoV) are RNA viruses that cause respiratory tract infections with viral replication of limited duration. The host and viral population heterogeneity could influence clinical phenotypes. Employing long RT-PCR with Illumina sequencing, we quantified the gene mutation load at 0.5% mutation frequency for the 4529 bp-domain spanning the Spike gene (4086 bp) of HCoV-OC43 in four upper respiratory clinical specimens obtained during acute illness. There were a total of 121 mutations for all four HCoV samples with the average number of mutations at 30.3 ± 10.2, which is significantly higher than that expected from the Illumina sequencing error rate. There were two mutation peaks, one at the 5' end and the other near position 1 550 in the S1 subunit. Two coronavirus samples were genotype B and two were genotype D, clustering with HCoV-OC43 strain AY391777 in neighbor-joining tree phylogenetic analysis. Nonsynonymous mutations were 76.1 ± 14% of mutation load. Although lower than other RNA viruses such as hepatitis C virus, HCoV-OC43 did exhibit quasi-species. The rate of nonsynonymous mutations was higher in the HCoV-OC43 isolates than in hepatitis C (HCV) virus genotype 1a isolates analyzed for comparison in this study. These characteristics of HCoV-OC43 may affect viral replication dynamics, receptor binding, antigenicity, evolution, transmission, and clinical illness. |
| Databáze: | OpenAIRE |
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