The rapid molecular evolution of hepatitis C virus (HCV) has been used to help incriminate the source of an outbreak in two Spanish hospitals in the late nineties. The evolutionary techniques used, described in BioMed Central's open access journal BMC Biology, also helped separate those who were infected by the person in question from those infected elsewhere during the same time period.
In the days before deep sequencing became a cheap option scientists used partial sequencing of HCV to help convict an anesthetist of infecting 275 patients with this virus. Back in 1998 an anesthetist was alleged to have injected himself with opioid painkillers, using some of the dose meant for his patients, before giving them the rest using the same needle and syringe. It is only now, after the experts' testimony and appeals, that the science used to track the outbreak and the spread of the virus is being made public.
The main difficulty in establishing a link between the source and the infected patients is that the virus continues to evolve in its host. Also unlike HIV, HCV can remain silent in an infected patient for years even though it is still capable of being transmitted.
Prof Fernando González-Candelas from the Universidad de Valencia, who led this multicentre study explained, "We sequenced 322 patients who were suspected to have been infected by the donor and 44 local, unrelated controls. Our analysis of over 4000 sequences from the E1-E2 region of the viral genome allowed us to exclude 47 patients as having been infected elsewhere. Because we knew the dates of infection for some patients we were able to use their data to validate a molecular clock and construct an estimated date of infection for each patient and of the source."
The patients were all infected between 1988 and 1998 shortly after the estimated date of infection of the source.
Improvements in sequencing techniques and computing now make it easier to obtain whole viral genomes and the phylogenetic analysis of RNA viruses, especially the molecular clock technique, is increasingly used today to analyze disease outbreaks in order to help plan control measures.
Prof González-Candelas continued, "Naturally, there are very limited possibilities for a single infected patient of infecting so many recipients, but the recent case of a medical technician in New Hampshire (USA), and eight other states, shows that more such events might be revealed."