Via CIDRAP, Robert Roos writes: Study: New H5N1 strain in Egypt may be tied to rise in human cases. Excerpt:
A new strain of H5N1 avian influenza virus that has apparently gained predominance in Egypt in recent months may be associated with the sharp increase in human H5N1 cases there during that same time frame, an international team of scientists reported yesterday in Eurosurveillance.
The researchers said the new strain has spread widely in Egypt's poultry and that two recent H5N1 isolates from human patients fall into the same group. It's too early to tell if the strain has gained a greater ability to jump from birds to humans, they wrote, and further studies are needed to find out if that's the case.
At this point it can't be "excluded with certainty that the emerging phylotype of viruses may have increased zoonotic potential and may be transmitted more efficiently to humans, although this assumption cannot be drawn from the molecular evidence described here," the report states. The authors are from Egypt, Germany, and the United Nations Food and Agriculture Organization.
435 outbreaks in 5 months
The steep increase in human cases and poultry outbreaks in Egypt in the past several months has stirred speculation about whether mutations in the virus are better equipping it to spread in poultry and from poultry to humans. The report says 435 poultry outbreaks were reported by Egyptian veterinary authorities from October 2014 through February 2015.
Human H5N1 cases first occurred in Egypt in 2006, and a total of 204 confirmed cases were reported from 2006 through 2014, with a case-fatality rate of 35.8%, the researchers say. This year, the case total reached 116 as of Mar 21, with 36 deaths, or more than half the count for the preceding 9 years, they add.
For the study, the team selected a sample of 29 H5N1 isolates representing different poultry species, locations, and operations (commercial farms, backyard flocks, and live-bird markets). They generated sequence data for the hemagglutinin (HA) segments of all 29 viruses and for the neuraminidase (NA) genes of 15 isolates. In addition, they sequenced the entire genomes of four isolates.
Through a phylogenetic analysis to see where the viruses fit on the H5N1 family tree, the team concluded that they belong in a separate cluster within a previously defined clade, 126.96.36.199. They further found that none of the older viruses from that clade have been detected in Egypt since last October, indicating that the new strain has become predominant.
The sequence data for the internal genes of the viruses agree with the findings for the HA and NA sequences, "indicating that the new viruses represent a distinct cluster that originated from previously circulating viruses of clade 188.8.131.52," the report says.
In addition, the team found that two H5N1 viruses collected from infected humans last November "are part of the same expanding cluster," with similar mutation patterns. The two are the only publicly available sequences of viruses from recent human cases in Egypt.