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Simultaneous H5N1 Acquisitions in Russia and Egypt

Recombinomics Commentary
April 14, 2007

Recently, US NAMRU-3 has sequenced the latest confirmed cases in Egypt, including the sibling from Qena (4M), A/Egypt/2629-NAMRU3/2007; the child from Sohag (7M), A/Egypt/2630-NAMRU3/2007; the child from Qalubiea (4F), A/Egypt/2631-NAMRU3/2007; the child from Menia (2F), A/Egypt/2750-NAMRU3/2007; and the teenager from Shoubra in Cairo (15F), A/Egypt/2751-NAMRU3.

These sequences had much in common with previous sequences from Egypt.  The Qena sibling sequence matched the index case (6F), A/Egypt/2621-NAMRU-3/2007 (see slide 54) and the Qalubiea sequence was also very similar, including the HA 3 BP deletion (see slide 53) that was also in the Beni Suef (27F), A/Egypt/0636/2007, and Fayyoum sequences (17F).  The Menia sequence was closely related to the sequences from Aswan, while the Shourbra sequences were like poultry sequences from Gharbiya (A/chicken/Egypt/1891N3-CLEVB.2007 and A/chicken/Egypt/1890-HK45/2007).  The Sohag sequence was unique.  The NA sequence had the common Egyptian markers C150T, C236T, A703G, A740G, T1088C, and G1280A.  However, appended onto this Egyptian, Qinghai genetic background was G743A.  G743A was in a large subset of the recently released sequences from northern Germany, as well as earlier Bavaria sequences, which were from dead wild birds or carnivores, collected in February, 2006.

As noted earlier, G743A was in chicken isolates in Gharbiya, collected a year later in February, 2007.  It was also in the Qena siblings, who were confirmed this month.  Thus, G743A has appeared in six recent Egyptian isolates in Gharbiya, Sohag, and Qena.  The HA and NA sequences from the isolates fall into three readily distinguishable isolates, yet they all contain A743G.  Moreover, the recent isolates from Moscow (A/chicken/Moscow/2/2007 and A/chicken/Russia_Moscow oblast_Odintsovo/1/2007) also have G743A, appended onto another easily distinguishable Clade 2.2 genetic background, similar to Azerbaijan isolates from last season.

The simultaneous appearance of G743A on four genetically distinguishable backgrounds is most easily explained by recombination.

Polymorphism tracing indicates the polymorphism moved from H5N1 in South Korea / Japan in 2004 to Clade 1 in southeast Asia in 2005, to Clade 2.1 and 2.3 isolates in China and Indonesia in 2006, to Clade 2.2 in Germany in 2006, and to readily distinguishable Clade 2.2 isolates in Moscow and three locations in Egypt in 2007.  The 2007 infections were between mid-February and early April.

The simultaneous G743A acquisitions onto genetically distinguishable Clade 2.2 isolates in Russia and Egypt are striking.

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