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Uvs Lake H5N1 Precursors in Kazakhstan
Recombinomics Commentary 08:22
December 22, 2008

Kazakhstan recently released sequence data at Genbank from an H5N1 infected chicken, A/chicken/Astana/6/2005.  This sequence is related to the Uvs Lake strain, which is a clade 2.2.3 variant isolated a year later at Uvs Lake in Mongolia, and adjacent Tyva in Siberia.  Thus, although the Kazakhstan sequences were released more than three years after the fact, the data plays an important role in mapping out the origins and spread of Qinghai H5N1 that subsequently lead to first ever reports of H5N1 in over 50 countries west of China.

The Qinghai strain (clade 2.2) was first detected at the Qinghai Lake Nature Reserve in May of 2005.  The massive outbreak in long range migratory birds raised concern that H5N1 would spread rapidly out of China because the nature reserve hosted over 100 species of wild bids and was at the intersection of several major flyways.

However, various conservation groups maintained that “dead birds don’t fly” and the lethal infections would burn out at Qinghai Lake. The major flaw in this prediction was the ability of these birds to fly long distances.  Most of the infections were in bar headed geese, which could fly 1000 miles in one day.  Thus, even if a bird was lethally infected, if asymptomatic for one day, the H5N1 could migrate 1000 miles.  Moreover, the movement of the virus was not dependent on a single host.  An H5N1 positive brid could move the virus 1000 miles and then infected another bird, which could move the H5N1 another 1000 miles.

The first hint that H5N1 did not die out came from northwestern China in June, when waterfowl began dying in to distinct locations.  However, those sequences were not released, so the involvement of the Qinghai strain was indirect (most H5N1 does not kill waterfowl, so the death of ducks and geese suggested the H5N1 was the Qinghai strain).

The May outbreak was followed by reports from Chany Lake in Siberia in mid-July.  Waterfowl (dead, dying, and asymptomatic) was H5N1 positive for the Qinghai strain demonstrating that the virus did not burn itself out.  Kazakhstan also filed an OIE report on August 2, describing an outbreak at Pavoldar, which began July 23, 2005.

However, conservation groups maintained that wild bird migration to the north happened prior to July or August, so the H5N1 in Russia and Kazakhstan were examples of “wild birds as victims” and had been infected by the H5N1 transported to farms in the area.  The OIE reports from Russia cited wild birds as the cause, but the conservation groups maintained that the poultry infected the wild birds.

The characterization sheet of the H5N1 Astana indicated the sample was collected in June, 2005.  The sequence is clearly a Qingahi sub-clade (2.2.3).  Thus, in 2005 the H5N1 had migrated north earlier, and was already in Astana in June.  Moreover, this early movement to the north and west helps explain the spread in Russia and Kazakhstan, which was reported in areas to the west of Chany Lake, which was used by conservation groups to deny the involvement of migratory birds, since they were not migrating from east to west in August. False negatives in Mongolia were also used to deny the role of migratory birds in teh spread of H5N1.

However, the latest sequence demonstrated that although H5N1 was a reportable disease, there was no mention of the June outbreak in the August 2 OIE report, which was the “first report of H5N1 in Kazakhstan,” as was the Russia report in July.  Therefore, the recent sequences demonstrate that lack of an H5N1 report does not always correlate with the lack of H5N1 (see satellite map).

The Kazakhstan sequence also impacts subsequent spread.  In the summer of 2006 there was a massive wild bird outbreak at Uvs Lake in Mongolia, which was on a par with the outbreak a year early.  The relationship of the Kazakhstan sequence to the Uvs Lake sequence indicates it was in circulation in Kazakhstan a year prior to the outbreak in June of 2006 in Mongolia and Tyva or Chany Lake in July of 2007, which once again demonstrates surveillance and reporting shortfalls.

The shortfalls are somewhat like the H5N1 that was detected in a healthy teal in the Nile Delta in December, 2005.  At that time western Europe and Africa were denying any H5N1, yet the teal sequence matched cat and poultry H5N1 reported in Austria in early 2006.  Since the wild birds are migrating south in December, the sequences in Egypt in 2005 indicated that H5N1 had been in Austria in 2005.

Similar shortfalls are found in India.  The bar-headed geese and many additional species at Qinghai Lake winter in India and although H5N1 has been detected in Qinghai province every year since 2005, India has never reported H5N1 in wild birds.  This season, warnings are being issued, but there have been no confirmations in migratory birds.  Recently, India confirmed H5N1 in dead crows in Guwahhati.  However, dead crows have been associated with H5N1 poultry outbreaks in India since 2006.

Recently, India also acknowledged dead wild birds in the jungles of Karbi Anglang and Nagaland, yet H5N1 has yet to be confirmed.  Confirmation failures in wild birds are largely linked to testing procedures.  The Qinghai strain is at very low levels in cloacal swabs. Wild birds experimentally infected with the Qinghai strain have detectable shedding in nasopharyngeal swabs, while cloacal swabs are negative.  Thus, India’s reliance on serum and cloacal swabs leads to false negatives and failures to confirm.

Therefore, the Kazakhstan sequences, released more than three years after the fact help explain the role of wild birds in the transport and transmission of H5N1, which is important for current outbreaks, where false negatives are still being reported for the Qinghai strain in wild birds in India and Bangladesh.

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