INTRA-PATIENT EVOLUTION OF HCV IN EARLY STAGES OF ACUTE INFECTION

Hepatitis C virus (HCV) is estimated to affect approximately 70 million people worldwide and is a major cause of chronic liver diseases. In its acute stage, the viral infection is mostly asymptomatic, and thus often overlooked by clinicians and researchers. We study a cohort of twelve patients who were subject to nosocomial transmission of HCV and diagnosed ~50 days post infection. All patients underwent a CT scan with contrast material on the same day, and due to a medical error, were given an IV flush from a shared saline bottle also used for a patient known to be infected with chronic HCV.

We performed accurate next-generation sequencing on the viral samples including the twelve patients, the alleged source, and two unrelated control samples. First, we verified by phylogenetic analysis that the most likely source of infection was indeed the alleged source. We next sought to compare and contrast the intra-patient diversity among the twelve patients. Our results showed highly different levels of intra-genetic diversity in each one of the patients: some displayed extremely heterogeneous viral populations whereas others did not. We found that the level of diversity was negatively correlated with the order of the CT examination, suggesting that the number of transmitted viruses decreased with time. We next used a mathematical model to infer the transmitted population size based on the difference in allele frequencies between the source and each patient. Our results revealed the effective transmission size was roughly between 10² and 10⁴ for most patients. This study thus affords a rare glimpse into the potentially parallel evolution occurring across twelve patients infected at the same time from the same source.