Though virus RNA levels in the sample from a California child whose H5N1 avian flu infection was reported in November weren't enough for complete sequencing, complex analysis was able determine that is most closely resembles the B3.13 genotype found in cattle, the US Centers for Disease Control and Prevention (CDC) said today in a technical update.
In other developments, the CDC said yesterday that follow-up testing didn't confirm two recent cases from Arizona as H5 infections, though they are classified as probable cases, keeping the number of confirmed infections since the first of the year at 58 and lifting the number of probable cases to 6.
California health officials had identified the case during flu surveillance, and initial subtyping was done at the Stanford Medicine Clinical Virology Laboratory. So far, epidemiological and environmental investigations haven't been able to pin down how the child was exposed to the virus, and the CDC said that the sequencing challenges don't bode well for identifying the source.
Low levels of virus RNA in the child's sample made it difficult to sequence the virus with traditional methods, and attempts to isolate the virus from the sample were unsuccessful. However, using other techniques, scientists were able to sequence the full-length neuraminidase (NA) and nucleoprotein (NP) genes, as well as partial hemagglutinin (HA), polymerase basic 2 (PB2), and polymerase basic 1 (PB1) genes.
Phylogenetic analysis of the two full-length genes showed that the virus was most similar to the B3.13 genotype viruses detected in California's cattle, poultry, and recent human cases. Also, sequencing analysis shows that the case isn't closely related to the virus involved in the severe illness in a teen hospitalized in British Columbia.
Additional analysis found that the virus from the child had no concerning mutations that might suggest greater infectivity, transmissibility, or resistance to neuraminidase inhibitor drugs such as oseltamivir.
In other H5N1 developments, the US Department of Agriculture (USDA) Animal and Plant Health Inspection Service (APHIS) confirmed 22 more detections in dairy herds, including 21 from California and 1 recently announced by Nevada's agriculture department, the state's first. The new confirmations boost the number of affected herds to 742 from 16 states, 527 of them from California.
APHIS also confirmed more outbreaks in poultry flocks from four states, including one at a massive layer farm in Iowa's Sioux County that has more than 4.2 million birds. The new outbreaks also include two commercial turkey farms from two South Dakota counties, a commercial turkey hen breeding facility in Nebraska's Nemaha County, and a backyard flock in Arkansas' Lafayette County.