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Widespread D225G/N In Fatal Ukraine Cases
Recombinomics Commentary 14:43
January 25, 2010

Mill Hill released 32 HA sequences at GISAID.  28 were from Ukraine and were from autopsy lung.  These were collected between the end of October through mid-November. 10 of the Ukraine samples had D225G and D225N.  Three had D225N and one was mixed for D225N.  Four has D225G and three more were mixed for D225G.  Thus, 21/28 had D225G, D225N, or both.

The widespread detection of D225G and D225N in these samples support earlier data which had D225G, D225N, or both in 8 of 8 fatal cases.  Although the new sequences include the first sequences from clear fatal cases in Ukraine lacking the position 225 changes, the vast majority of samples had the changes, and for regions in western Ukraine, like Lviv, all samples had 225 changes.

The large number of cases with both D225G and D225N (including one sample from the Azores), greatly reduces the likelihood that these are random copy errors, which appears to be the WHO working hypothesis.  Similarly, the high concentration of these changes in fatal cases again supports transmission.  Earlier 22 sequences were released, from patients that were not likely to be fatal, and only one had D225G (as a mixture).

The vast majority of the new sequences are also mixture, either because samples had D225G and D225N, or had one or the other along with wild type.  These combinations may facilitate spread by allowing for infections in both the upper respiratory tract as well as the lower respiratory tract.

Moreover, a pair sample from a patient in Kathmandu had D225G (as a mixture) in the nasal sample, while the throat sample had a wild type RBD.  Similarly, the fatal samples in Ukraine were from multiple oblasts and represented multiple sub-clades.  Most sub-clades had at least one sample lacking the RBD change, further supporting acquistion of the position 225 chnages via recombination.

The current series of sequences did not have excessive copy errors, and analysis of this clade in Russia demonstrates that all samples have PB2 K340N, reducing the likelihood that the PB2 change has any direct impact on the changes at position 225.  K340N is in samples lacking position 225 changes and other clades which lack K340N have position 225 changes.  K340N at this time appears to just be a marker for the dominant clade in Ukraine (and much of eastern Russia).

The high frequency of 225 changes in Ukraine is of concern because recent media reports indicate an uptick in cases in eastern Ukraine, especially in Donetsk (see map), where schools are closing again.  Donetsk has recorded the largest number of fatalities, and the rate this month is about 4 fold higher that 2009, raising concerns that position 225 changes are on the rise.

Sequences from these recent cases would be useful.

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