Bird Flu Russian Recombinants
Recombinomics Commentary
January 8, 2005
A series of genes from H5 2001 duck (bird flu) isolates from Primorie in Russia show strong evidence of recombination. They contain some polymorphisms found primarily in Europe and others found primarily in Asian isolates from Hong Kong, Vietnam, and Thailand. The number of partial sequences made available today is small. They include HA, NP, and NS from an H5N2 isolate, A/duck/Primorie/2621/01(H5N2), and HA and NP from an H5N3 isolate, A/duck/Primorie/2633/01(H5N3), but the sequences clearly show evidence of recombination. Some of the polymorphisms can be found in the first H5N1, isolated from a chicken in Scotland, A/Chicken/Scotland/59 (H5N1), in 1959, while others are found in 2004 isolates from Vietnam and Thailand.
The conservation of polymorphisms from 1959 isolates demonstrate that the viral polymerase does not make frequent errors that lead to annual changes in human or avian influenza genomes. Instead these polymorphisms are simply recycled from earlier times or other places. This recycling is driven by recombination, which is ongoing.
Reassortment may facilitate more rapid change by bringing more distant genes into novel environments as demonstrated by the reassorted and recombined genes in the swine isolates in Korea. These Korean swine isolates have 2004 avian genes and 1933 human genes in the same isolates. Recombination has generated genes that are half human and half avian. The reassortment of additional genes facilitates rapid change via recombination with other human or avian dual infections.
However, the driver of viral evolution and emergence is recombination.