Quantifying Pathogen Surveillance Using Temporal Genomic Data

Chan, Joseph M.; Rabadan, Raul

The swine is another animal that demands adequate surveillance (13) . Researchers have observed that epithelial cells in the pig trachea contain sialyloligosaccharides SA␣2,3 and SA␣2,6, which are unique host determinants for birds and humans, respectively (14) . This feature confers tropism in pigs on both avian and human influenza viruses (15) , allowing swine to serve as mixing vessels for antigenic shift, in which different strains infecting the same host can reassort RNA segments to create a novel viral strain (16) . Such reassortments have engendered at least two major human pandemics in the 20th century, in 1957 and 1968 (17) . The most recent pandemic of swine origin influenza virus (SOIV) in 2009, in particular, was a reassortant between Eurasian and North American swine lineages, and although the virus most likely came from a pig, a definitive geographic origin has yet to be determined (13, 18) . Interestingly, the closest ancestors of the 2009 pandemic virus were related to viruses isolated from swine more than a decade prior (13, 19) , suggesting that relevant strains circulating in swine herds have escaped detection because of inadequate sampling (18) .