Natural intragenotypic and intergenotypic HCV recombinants are rare in southwest China even among patients with multiple exposures.

Background: Both intragenotypic and intergenotypic hepatitis C virus (HCV) recombinants were recently identified, whereas the frequency of HCV recombinants in circulation in certain parts of the world remains uncertain.

Objectives: To assess the frequency of natural intragenotypic and intergenotypic HCV recombinants in southwest China and that of multitypic HCV infection, which is the prerequisite factor for recombination.

Study Design: Comparison of the genotyping results based on core-envelope 1 and non-structural 5B sequence phylogenetic analyses to detect the possible recombinants. Multitypic HCV infection was detected by colony analysis of the core-envelope 1 region.

Results: There was no discrepancy between genotyping results based on the core-envelope 1 and non-structural 5B regions in 243 sera from 222 patients, including 107 samples from 92 intravenous drug users, 26 samples from 20 hemodialysis patients, and 110 samples from 110 other patients. Multitypic HCV carriage was identified in 9 (47.4%) of the 19 patients with multiple exposures who were randomly selected, and 11 (45.8%) of the 24 specimens. There were 26 repeatedly exposed patients who had more than one HCV RNA positive sera at different time points, but neither of their HCV subtypes had switched over time.

Conclusion: Although the high frequency of multitypic HCV infection was identified in patients with multiple exposures, intergenotypic or intragenotypic recombination remains an infrequent event in southwest China; thus, routine genotyping with more than one subgenomic region for clinical use is not warranted.