TABLE 4.
Identification of single nucleotide polymorphisms in the HCV 5′-UTR sequences detected in CD4+ or CD8+ T lymphocytes infected in vitro with authentic genotype 1a inoculum HCV-11/M
| Cell type | Expt | Days postinfection | Polymorphism(s) (% identity) of nucleotide substitution at positionsa: |
||
|---|---|---|---|---|---|
| 68–150 | 151–220 | 221–311 | |||
| CD4+ | 1 | 10 | 126insC (10), A134G (5) | A260G (5) | |
| 3 | 10 | T228C (5), T282C (5) | |||
| 3 | 14 | A96G (5), 126delC (5), T149C (5) | G153A (5), T164C (5), G189T (5), T216C (5) | T269C (5) | |
| 5 | 7 | C112T (5), T144C (5) | G148A (5) | ||
| 5 | 14 | A252G (5) | |||
| CD8+ | 1 | 10 | T160 (5), C183T (20) | G286A (15), T287C (15) | |
| 3 | 7 | C115T (40), A116G (5) | C187T (5) | C255T (5) | |
| 5 | 7 | T144C (10) | A165G (5) | A252G (5), C272T (5), T282C (5) | |
HCV 5′-UTR amplicons detected in CD4+ and CD8+ T cells infected with HCV-11/M (genotype 1a) at the time points when the HCV RNA negative strand was detectable were analyzed by clonal sequencing. In total, 20 clones from each amplicon were sequenced. The percentage of clones carrying a given virus variant is noted in parentheses. The 5′-UTR sequence of the HCV-11/M plasma inoculum was used as a reference. For the designation of nucleotide positions, prototype genotype 1a HCV was used (GenBank accession number M67463). Variants detected in both CD4+ and CD8+ T cells are marked in boldface type, boldface italic type, or boldface underlined type. ins, insertion; del, deletion.