Estimating Transmission Potential of H5N1 Viruses Among Humans in Egypt Using Phylogeny, Genetic Distance and Sampling Time Interval

In 2014 and 2015, the number of human cases of H5N1 avian influenza virus infections had increased dramatically in Egypt. This increase might be related to increase in the transmission potential of the virus among humans. To clarify the cause of the increase in H5N1 human cases, we investigate the transmissibility of H5N1 viruses among humans via estimating the basic reproduction number R(0) using nucleotide sequences and sampling dates of viruses. To this end, full-length hemagglutinin gene sequences of human and avian H5N1 influenza viruses isolated from 2006 to 2016 in Egypt were obtained from the NCBI influenza virus resource. Taking into account the phylogeny, genetic distance, sampling time difference among viruses, R(0) was estimated to be 0.05 (95% CI: 0.01, 0.13) assuming that human-to-human transmissions occurred within a city, 0.23(95% CI: 0.14, 0.35) assuming human-to-human transmissions among cities. Our results indicate that human-to-human transmission of H5N1 viruses in Egypt is limited, and the large increase in human cases is likely attributed to other factor than increase in human-to-human transmission potential.