A binning tool to reconstruct viral haplotypes from assembled contigs

Jiao Chen; Jiayu Shang; Jianrong Wang; Yanni Sun

High genetic diversity within viral populations has been observed in patients with chronic infection with RNA viruses such as HIV, HCV, etc (Sullivan et al., 2007; Perrin and Telenti, 1998) . The genetic diversity could be caused by multiple infections of different strains or by mutations during the virus replication inside the host. In the latter case, the high replication rate, coupled with the low fidelity of the viral polymerase in most RNA viruses, results in a group of different but related strains infecting the same host, which is often termed as "quasispecies" (Nowak, 2006) . Previous studies have revealed that patients with chronic virus infections, such as AIDS, are often the reservoir of new viral variants, which are likely produced during the replication process (MacLachlan and Dubovi, 2017) . Because different strains could have very different biological properties such as virulence, transmissibility, antiviral drug resistance etc, characterizing the genetic diversity within viral populations is very important for developing effective prevention and treatment strategies. For example, if some strains have developed antiviral drug resistance, they may become the dominant strains and lead to treatment failure. Thus, characterization of the strain-level diversity of viral populations is indispensable for understanding the viruses and is of great clinical importance.