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In addition, the equine isolate lacks
aa S145. This deletion is also present in all other viruses grouped
into 2.2 sublineage A1, which also includes sequences from human H5N1
isolates (Fig. 2). The significance of this deletion is unknown, but it
should be noted that this position is close to a domain modulating
Interestingly, strains with this deletion appear to evolve towards a receptor usage that is similar to that of the seasonal human H1N1.
The above comments are from the paper, “Isolation and characterization of highly pathogenic avian influenza virus subtype H5N1 from donkeys” and notes the prior paper on H5N1 in Egypt which identified sequences with the 3 BP deletions as those most likely to have a high affinity for human H1N1 receptors. Sequences with the deletion were of interest because they were linked to mild cases of H5N1 in Egyptian children in 2007 and 2009. The sequences in 2007 included closely related sequences in southern Egypt, raising concerns of human to human transmission. These concerns increased in 2009 when virtually all initial confirmed cases were mild and in toddlers.
It was at this time in early 2009 that the H5N1 was isolated from donkeys, A/equine/Egypt/av1/2009, and as noted above had the same deletion. Moreover, the donkeys were only symptomatic for three days and there were no fatalities. Further serological analysis indicated the H5N1 was widespread in donkeys in the Beni Suef governorate, and therefore were likely throughout Egypt because in 2009 the H5N1 with deletion was the most common H5N1 sub-clade detected in Egypt in humans and poultry, including waterfowl.
The detection of H5N1 in donkeys raised concerns that H5N1 was also in horses and camels as well as other mammals, including humans, but was not described because of a lack of testing / reporting, which extends to other regions and sub-clades.
The identical 3 BP deletion was also found in China in clade 7 in Shanxi and Hunan province in 2006, raising concerns of widespread transmission in mammals in China including humans. The lack of testing / reporting increases those concerns. The mild nature of many of the cases in Egypt raise concerns of silent spread and recombination in humans or other mammals co-infected with pH1N1, giving rise to more recombinants including H5N1 which is more transmissible in humans, or H1N1 which is more lethal in humans.
The lack of testing and reporting continues to be hazardous to the world’s health.