More of the H7N9 mystery has been solved (or almost solved) in an article published online in Nature today (Wed. Aug. 21, 2013). Let’s remember that H7N9 was first noted earlier this year in China; so far there have been >130 human cases reported, and 40 deaths, for a case fatality ratio of approx. 31%. The public health community–and I–have been concerned about this strain not because of the actual morbidity and mortality, but because of its potential for spread and increase.

Today’s article, published online in Nature (Lam, Wang, Shen et al, The genesis and source of the H7N9 influenza viruses causing human infections in China, doi:10.1038/nature12515) consists of a painstaking process of sampling from the environment as well as oropharyngeal and cloacal swabs from a variety of avian spp., including ducks, geese, and chickens. Phylogenies were then identified using quantitative reverse transciptase PCR (qRT-PCR). Based upon phylogenetic similarity, some of the article’s conclusions are:

1) Transfer of H7 viruses from domestic duck to chicken populations probably occurred at least twice in China;

2) Enzootic H9N2 viruses combined with the H7 viruses to produce H7N9, and a novel H7N7 virus that had not previously been identified. This was in chicken populations, and the novel virus has been shown, experimentally, to infect mammals.

3) Live poultry markets which are found widely in parts of China and other areas of Asia were implicated as potential foci of spread because of the presence of H7N9 in these markets. The authors caution that the H7N9 virus, and H7N7 viruses may be widespread in chickens, and therefore have the possibility of widespread species transfer to humans in these foci.

Echoing so many similar calls and observations, the authors warn that “Long-term influenza surveillance remains essential for early warning of novel reassortant viruses and interspecies transmission.”

This article is the latest of a series of articles on the molecular epidemiology of this novel virus. I argue that a big challenge is to combine two types of analysis: 1) molecular epidemiology identifying “clusters” of similar genomic configurations; and 2) geospatial analysis using GIS, spatial statistics, and spatial modeling, in combination with molecular epidemiology to understand patterns of spread of variants, and, indeed, to serve as early warning and surveillance instruments as new strains of flu and other viruses spread from localized foci, and threaten a more widespread population.