Almaty, Kazakhstan - Unique Cross-Segment Quadruple Combination (QC1)

A sequence from Kazakhstan's largest city, the capital Almaty, was deposited at GenBank on 2009-08-18 by the Russian Vector lab using the nomenklatura's nomenclature of A/Almati/01/2009 with no collection date. Elevation and population density of the host geography raised our interest in this particular specimen and the signal was correlated upon inspection.

At the amino acid level, Almati01 matches the HA of NewJersey01 and Sapporo1, the NA of Amagasaki1, Amagasaki2 and Hyogo1.  Bear in mind that NewJersey01 is closely related to the Tamiflu-resistant HongKong2369 specimen.

Of a more compelling interest is the first deposited emergence of a particular Cross-Segment Quadruple Combination (QC1) that may prepare the virus for additional human-fitness acquisitions. This Almati01 sequence appears to be the singular ΣPF11 sequence on file that carries the quadruple set of amino acids:

  • HA 206T
  • HA 225E
  • NA 106I
  • NA 248N
The introduction appears to be NA 248N, but the collection date is absent on Almati01 so conclusions may not be drawn. Comparison data is sparse because the neuraminidase segment is unavailable or unpublished on many of the 13 candidate ΣPF11 dual HA combinations of 206T and 225E. Plainly stated, the database coverage to investigate this quadruple combination is far from broad. However, in this case, scarcity breeds clarity, sharpening a focus for future monitoring in anticipation of a more robust dataset. 

Movement within and around the Receptor Binding Domain (RBD) always draws focus on a new specimen.  The genetic acquisition path of ΣPF11, including this profiled specimen, suggests a non-random pattern of polymorphisms.

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