Wild Birds Are the H5N1 Common Source in Europe
Recombinomics Commentary
June 30, 2007
A comparison of parts of the hereditary property of the bird flu viruses of the type H5N1 Asia from Saxonia, Bavaria and the Czech republic at the reference laboratory for aviaere influenza of the Friedrich Loeffler institute resulted in a high similarity. Thus it is certain that all three outbreaks decrease/go back to a common origin.
Common molecular-biological analyses of the European Union reference laboratory (VLA Weybridge) and the national reference laboratory for aviaere influenza at the FLI, island Riems, show besides a high relationship (99,2% for the first section of the H5-Gens) between one the Virus isolate from Nuernberg and a H5N1-Isolat from the current happening in the Czech republic. The high degree at agreement refers to of common, so far not identified origin both viruses.
The above statements from the Friedlich Loeffler Institute (FLI) have created considerable confusion in the media and Promed commentaries, which assumed that a common source referred to a close linkage, as had been seen recently when sequences from H5N1 infected turkeys in England were compared to H5N1 isolates from Hungary. Those isolates had an identity of 99.96% across all eight gene segments, demonstrating that they recently originated from a common source.
However, the FLI comments above indicate that the identity between HA sequences from turkeys in the Czech Republic and wild birds in Nuremberg was 99.2%, which is much lower than the England / Hungary linkage, and is similar to identities between various Qinghai clade 2.2 sub-clades.
Last year, clade 2.2 was widespread in Europe, including three distinct sub-clades in Germany. Distinct sub-clades was a characteristic of H5N1 from wild birds. Last season, over 700 H5N1 isolates were collected from wild birds in Europe. All were clade 2.2, as expected for H5N1 transported and transmitted by migratory birds. Clade 2.2 was first reported in dead bar-headed geese at Qinghai Lake in May, 2005. Additional long range migratory bird species were subsequently identified. The spring outbreak at Qinghai Lake was followed by summer outbreaks in Russia, Kazakhstan, and Mongolia. These outbreaks also involved clade 2.2 and signaled a spread into Europe, the Middle East, and Africa.
As expected, H5N1 was subsequently found in these locations. In all cases, the “Asian” version of H5N1 was detected for the first time, and in all cases the H5N1 identified was clade 2.2. Moreover, in many countries the H5N1 in the wild birds were the only reported outbreaks. In Western Europe, some poultry on farms were infected, but those infections were after wild bird infections were found.
Although no country in western Europe reported H5N1 infections in 2005, the sequence of H5N1 from a cloacal swab from a healthy teal in the Nile Delta collected in December, 2005 strongly suggested that H5N1 was in western Europe in the fall of 2005, because the sequences were very similar to isolates from Austria. Moreover, the 2006 isolates in Western Europe were widespread, further suggesting that the H5N1 migrated into Western Europe in the fall of 2005, when it migrated into Eastern Europe.
The isolation of H5N1 in Germany and the Czech Republic this month followed a 12 month hiatus in the detection of H5N1 in Western Europe. Last week Ilaria Capua, at the Options VI influenza meeting in Toronto presented an update of H5N1 infections in Europe and Africa. She noted the large number of live wild birds that were negative for H5N1, and said that the wild bird infections were limited to the 2005/2006 season.
However, dead wild birds in western Europe and western Africa were positive for H5N1 in early 2006, but H5N1 in live wild birds has never been reported in those regions, indicating that the surveillance in those regions lacked the sensitivity to identify H5N1 in live wild birds. Ian Brown followed Ilaria Capua, and he noted that there were only two outbreaks in Western Europe. The outbreaks in Hungary and England were tightly linked suggesting a common source. He noted that 2007 outbreaks outside of Western Europe were largely limited to countries that had outbreaks in 2006, suggesting those countries had endemic populations.
Within minutes of the presentations, H5N1 infections were reported on a turkey farm in the Czech Republic. That report was followed by an outbreak on a nearby farm, but H5N1 was also found in wild birds in Bavaria and Saxony in Germany, as well as Lednice in southern Czech Republic, raising concerns that H5N1 was also endemic in wild bird populations throughout Western Europe. The H5N1 was once again found in dead wild birds, suggesting that the surveillance program still lacked the sensitivity to detect H5N1 in live wild birds and likely also missed H5N1 in dead wild birds since there were no positives in the prior 12 months. Moreover, the H5N1 positive birds died in June, when migration in Europe was minimal, and the dead birds were largely not migratory.
The HA phylogenetic tree of public sequences clearly demonstrated the segregation of last years isolates into three sub-clades, 2.2.2.1, 2.2.2.2, and 2.2.2.3. The public isolates are bolded below. However, most of the sequences from the 2005/2006 outbreak in Europe still have not been published. Over a year ago, Ian Brown presented data on almost 80 of the 700 European isolates and that data strongly suggests that the sub-clades defined by the German isolates represented sequences that were widely detected in Europe.
For clade 2.2.2.1, the public sequences were limited to northern Germany and Denmark. However, the sequences on the phylogentic presented over a year ago indicated clade 2.2.2.1 was also in Azerbaijan, Greece, Bosnia, Serbia, Croatia, Romania, Poland, Greece, and Scotland (see unbolded list below).
Similarly, the public sequences indicated clade 2.2.2.2 was in Germany, Austria, Egypt, Slovenia, Italy, and the Czech Republic. However, the withheld sequences indicated clade 2.2.2.2 was also in Slovakia, Ukraine, Greece, France, Bulgaria, Romania, Azerbaijan, and Turkey.
These data leave little doubt that the common source for the recent outbreaks in Germany and the Czech Republic is wild birds. More the H5N1 is endemic in the region, and the infections in the wild birds have been largely undected throughout western Europe, as also happened in the fall of 2005.
The endemic nature of H5N1 in Europe extends well beyond the countries reporting H5N1 infections this year, and an increased surveillance, with improved sensitivity, is indicated for Europe, the Middle East, and Africa.
Clade 2.2.2.1
A/stork/Germany/R1239/06
A/cormorant/Germany/R292/06
A/duck/Germany/R751/06
A/goose/Germany/R696/06
A/duck/Germany/R338/06
A/coot/Germany/R655/06
A/buzzard/Denmark/8370/06
A/whooper swan/Germany/R88/06
A/stone marten/Germany/R747/2006
A/Canada goose/Germany/R1207/06
A/cat/Germany/R606/06
A/turkey/Germany/R1077/06
A/Canada goose/Germany/R71/06
A/swan/Germany/R65/2006
A/mute swan/Germany/R854/06
A/dog/Azerbaijan/1413-06-(6)
A/fox/Azerbaijan/1413-06-(7)
A/ck/Azerbaijan/Av107-06-K7-2
A/swan/Greece/Av119-06-106
A/swan/Bosnia/Av265-2
A/peacock/Denmark/Av6014-06
A/swan/Serbia/Av1077-06-1155(1)
A/ck/Serbia/Av1077-06-1307(2)
A/swan/Croatia/1265-05T
A/swan/Germany/Av159-2
A/swan/Romania/Av1496-05-1
A/swan/Poland/Av709-4
A/buzzard/Denmark/Av1075-06
A/ck/Romania/Av/170-06-2
A/swan/Greece/Av119-06-1
A/ck/Albania/Av1079-06-1
A/swan/Bosnia/Av265-1
A/swan/Scotland/1430-06A
A/turkey/Germany/Av3603-06
Clade 2.2.2.2
A/cat/Austria/649/2006
A/teal/Egypt/14051-NAMRU3/2005
A/swan/Slovenia/760/2006
A/swan/Austria/216/2006
A/mute swan/Bavaria/12/2006
A/great crested grebe/Bavaria/22/2006
A/common bussard/Bavaria/2/2006
A/Cygnus olor/Czech Republic/5170/2006
A/mallard/Italy/835/2006
A/falcon/Slovakia/AV305-246
A/pheasant/Ukraine/Av598-2
A/smew/Slovakia/Av305-212
A/ck/Ukraine/Av598-3
A/pigeon/Ukraine/Av598-4
A/swan/Austria/Av917-06(P4227)-7
A.swan/Czech Rep/Av1324-06
A/falcon/Ukraine/Av598-6
A/go/Greece/Av128-06-167-1
A/go/Greece/Av128-06-167-2
A/ck/Ukraune/Av27-06B
A/ck/Ukraine/Av27-06L
A/common pochard/France/Av1142-06 06167
A/swan/Bulgaria/Av118-06
A/he/Romania/1266-05
A/ck-ty/Romania/Av266-06-1
A/swan/Azerbaijan/Av160/216B
A/swanAustria/Av160-216B
A/cat/Austria/Av917-06'K3.2
A/ck/Turkey/Av73-06-2
A/ck/Romania/1210-05
A/swan/Slovenia/Av136-06
A/swan/Romania/1212-05
A/ck/Romania/1212-05
A/turkey/France/Av1142-06-1
Clade 2.2.2.3
A/swan/Bavaria/14/2006
A/goosander/Switzerland/V82/06
A/falcon/Germany/R899/06
A/gull/Germany/R882/06
A/falcon/Bavaria/15/2006
A/tufted duck/Bavaria/4/2006
A/buzzard/Bavaria/5/2006
A/swan/Bavaria/17/2006
A/mallard/Bavaria/1/2006
A/goosander/Bavaria/20/2006
A/goosander/Bavaria/18/2006
A/duck/Germany/R603/06
A/duck/Germany/R592/06
A/buzzard/Bavaria/13/2006
A/swan/Bavaria/6/2006
A/swan/Bavaria/16/2006
A/eagle owl/Bavaria/10/2006
A/eagle owl/Germany/R1166/06
A/pochard/Germany/R348/06
A/great crested grebe/Germany/R1226/06
A/common coot/Switzerland/V544/06
A/common buzzard/Bavaria/11/2006
A/swan/Bavaria/21/2006
A/tufted duck/Germany/R1240/06
A/tufted duck/Bavaria/8/2006
Media sources
Recombinomics Presentations