Wisconsin Virus Commits Zoonosis and Fails; Influenza Flux at Work

JCVI / the Medical College of Wisconsin submitted a set of sequences to GenBank on 2009-11-11. The sub-segment genomic variance that occurs when viral diseases commit zoonosis is demonstrated. We’ve discussed the coinage, Influenza Flux, in the past.  One particular Wisconsin sequence provides a useful discussion point for the sub-segment, bidirectional influx / reflux (emergence / reversion) of genetic material between distinct species-adapted, viral reservoirs.
WiscD0117 considered alongside WiscD1058 may demonstrate with simplicity an observable situation early in the pandemic where a viral reservoir attempted species-specific (human) adaptation and failed. Documenting the reservoir’s failures to adapt may be as important to future scholars as analysing the path of beneficial adaptation within the zoonosis to humans.

The two Hemagglutinins are homologous, but for a single silent nucleotide variance. WiscD1058 is identical to Canadian sequences (2) to the immediate north and Mexican sequences (2) on the same continent to the distant south.  WiscD0117 from the 3 year old, however, stands alone at the nucleotide level though matching hundreds of PF11 sequences at the amino acid coding.

A silent SNP at the third base codon, A592G, sets this sequence as novel within ΣPF11 even today (5 months later), revising “CTa -> CTg” and coding for a synonymous Leucine at residue 179, (syn179L). The A592G SNP appears at GenBank within A/swine/Hong Kong/1110/2006 of serotype H1N2.

We widened the input series for a geographic match and temporal proximity to enhance the results.

Influenza Flux Dataset
Samples Selected for Evaluation
Samples in purple show 100% Homology

A/Mexico/InDRE13551, sampled 2009-04-28
A/Mexico/InDRE13555, sampled 2009-04-29
A/Wisconsin/629-D01058, sampled 2009-05-04
A/Canada-PQ/RV1758, sampled 2009-05-08
A/Canada-QC/RV1954, sampled 2009-05-17
A/Wisconsin/629-D00117, sampled 2009-05-28
A/Wisconsin/629-D00829, sampled 2009-05-28 (324I)
A/Wisconsin/629-D01026, sampled 2009-05-28
A/Wisconsin/629-D01083, sampled 2009-05-28 (252L)
A/Wisconsin/629-D02144, sampled 2009-05-28 (324I, identical to WiscD0829)
A/Wisconsin/629-D00223, sampled 2009-05-30 (159T)
A/Wisconsin/629-D02013, sampled 2009-05-30 (35I)

Note the reasonable number of data points around the WiscD0117 sequence of interest. Many of these carry independent recombinations, including 35I, 159T, 252L and 324I.  All sequences shown on the list demonstrate the wild type 592A, except WiscD0117, including the two sequences that were sampled AFTER the original A592G SNP. 

Either an attractant signal was very strong to revert the silent SNP in the subsequent Wisconsin samples or the SNP was never transmitted.  In either case, ΣPF11 tried a new identity and then determined that the previous genetic footprint was more suitable.

Wisconsin is an area of interest for our evaluations due to the unusual clinical presentations and outcomes.  Influenza Flux may be more strongly driven in Wisconsin and causality must be determined.  ΣPF11 is on record as attempting new permutations in this geography, fixing them when useful like 324I from 1918 and discarding them like the syn179L when unneeded.

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