Pasteur Institute of Iran

We conducted this study to obtain a comprehensive picture of molecular epidemiology of HIV-1 in three neighboring countries, i.e. Afghanistan, Iran, and Pakistan as a basis for discussing possible hypothesis regarding between-country virus transmission. Our results showed that subtype composition differs between these countries with more variation in Pakistan than Iran and Afghanistan. The CRF35-AD clade was predominant in Afghanistan and Iran while the A1 subtype was predominant in Pakistan. HIV-1 sequences obtained from Pakistan (belonging either to B, A1, or CRF35_AD clades)  did not group with the sequences obtained from Afghanistan and Iran. However, CRF35_AD clades from Afghanistan made two significant clusters with those strains from Iran. The results also showed that CRF35_AD clades from Afghanistan had more diversity than those in Iran suggesting its older presence in this country. Putting these findings together and considering drug trafficking/immigration events from Afghanistan to Iran we hypothesized that HIV epidemics might have been transmitted from Iran to Afghanistan. However, the reverse order might also be true but with less support from the existing evidence. There was no indication of Iran-Pakistan HIV transmission. Performing sophisticated evolutionary analysis is needed to test these hypotheses about the origin and transmission pattern of the virus among these countries.

Bayesian evolutionary analysis provide a statistically sound and flexible framework for estimation of evolutionary parameters. In this method, posterior estimates of evolutionary rate (μ) are derived by combining evolutionary information in the data with researcher’s prior knowledge about the true value of μ. Nucleotide sequence samples of fast evolving pathogens that are taken at different points in time carry evolutionary information that allow for estimation of evolutionary rates and divergence dates. If the amount of genetic change in the data is proportional to the time elapsed since divergence from the common ancestor, then one can directly estimate the μ from the data. Otherwise, external sources should be used to select the μ value, and use it as a fixed prior in Bayesian evolutionary analysis. This note provides a brief overview on how to assess the adequacy of the evolutionary information in the data and provides some recommendations for obtaining proper evolutionary rate priors from external sources. The recommendations generally highlight the need for the candidate μ prior to be a good representative of the evolutionary rate in the data at hand. This will be achieved by ensuring that the samples that are the source of the candidate μ value have been under relatively similar evolutionary forces as the data at hand. As the evolutionary forces acting on a particular set of samples varies across different study settings and species type, selection of prior for μ should be founded on a thorough understanding of the species under study at biological and social levels.