A Russian Influenza Epidemiology Report To Ponder

UPDATED:  See An Update On The Russian Influenza Epi Report

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Every winter since the end of the 2009 H1N1 pandemic we've seen frequent, vague, often hyperbolic reports of H1N1 outbreaks around the world carrying an unusually high mortality, often suggesting that a `mutation' was responsible.

In India and the Middle East, the (now) seasonal H1N1pdm virus is still regarded as a `swine flu' by the media, and is always good for a headline.  Doubly so if the `M' word can be incorporated.

Yet despite this yearly hype, over the seven years since it appeared A/H1N1pdm09 has remained remarkably stable. While the H3N2 vaccine strain has been changed repeatedly, nearly all circulating H1N1 viruses have remained antigenically similar to the H1N1 strain that appeared back in 2009.

We have seen some limited, sporadic mutations (see 2014's  EID Journal: Emergence of D225G Variant A/H1N1, 2013–14 Flu Season, Florida) linked to enhanced virulence, and recently the ECDC reported that a genetic subcluster of viruses within the 6B subgroup has emerged, defined by HA1 amino acid substitutions S162N and I216T (see  Influenza virus characterisation, Summary Europe, December 2015).

Despite these changes, the H1N1 viruses that have been examined have all reportedly been antigenically similar to the vaccine virus A/California/07/2009. 

Once again this winter we've been seeing numerous reports of large H1N1 outbreaks - mostly in the Middle East and Eastern Europe -  with supposedly high mortality rates. Over the past couple of weeks, there have been multiple reports coming out of Russia and the Ukraine.

This morning Sharon Sanders on FluTrackers posted the following (translated) report: 

Russia - Government says "high incidence" of flu is due to H1N1pdm09 mutation not covered by vaccine - January 26, 2016

Today, 05:44 AM

In Russia, died from the flu 50 people, a high incidence is related to a mutation of the H1N1 virus Society January 26th, 16:19 UTC + 3, 24 people died this week, said Head of the Laboratory of Biotechnology and Research Institute of Influenza diagnostic preparations


PETERSBURG, January 26. / Correspondent. Natalia Mihalchenko TASS /. High morbidity and mortality from influenza in certain regions of Russia is associated with a mutation of the virus H1N1 (Swine Flu). This was reported by TASS Head of the Laboratory of Biotechnology and Research Institute of Influenza diagnostic preparations Anna Sominina.

Total of 50 Russians died of influenza, including 24 this week," - she said. "Among the isolated and studied in laboratories around 40% of viruses are changes in the genome that do not contain the vaccine. All in all today was able to identify three mutations" - added Sominina. According to the Institute of influenza in the country weekly epidemic threshold was exceeded by 48.8%, the baseline - 32%. Among the types of circulating influenza virus H1N1 predominant (96%). 

(Continue . . . )

Granted, Tass isn't always the most reliable source.   But Sharon also found and posted the following (week 3) Epidemiological report from the WHO National Influenza Centre Of Russia, which lends some credence to the above report.

Week 11.01.2016-17.01.2016
Influenza and ARI morbidity data

Epidemiological data show increase of influenza and other ARI activity in Russia in comparison with previous week. The nationwide ILI & ARI morbidity level (60.6 per 10 000 of population) was lower than the national baseline (69.5 per 10 000) by 12.8%.

ILI and ARI epidemic thresholds were exceeded in 9 of 59 cities collaborating with two WHO NICs in Russia.

Cumulative number of diagnosed influenza cases

Cumulative results of influenza laboratory diagnosis by different tests were submitted by 50 RBLs and two WHO NICs. According to these data as a result of 2580 patients investigation the overall proportion of respiratory samples positive for influenza virus was estimated as 25.3% including 615 (94.1%) influenza A(H1N1)pdm09 cases, 17 (2.6%) influenza A(H3N2) cases, 10 (1.5%) influenza A cases and 12 (1.8%) influenza B case.
Results of influenza diagnosis

Conclusion

Influenza and ARI morbidity data.  Increase of influenza and other ARI activity was registered during the week 03.2016 in traditional surveillance system in Russia. The nationwide ILI & ARI morbidity level (60.6 per 10 000 of population) was lower than the national baseline by 12.8%.

Etiology of ILI & ARI morbidity. The overall proportion of respiratory samples positive for influenza  was estimated as 25.3%. Percent of positive ARI cases of non-influenza etiology (PIV, adeno- and RSV) was estimated as 22.2% of investigated patients by IFA and 16.0% by PCR.

Antigenic characterization. Totally 45 influenza A(H1N1)pdm09 and 2 A(H3N2) viruses were characterizated antigenically in two NICs of Russia since the beginning of the season. 35 (76.6%) influenza A(H1N1)pdm09 strains were related closely to influenza A/California/07/09 virus, 10 (23.4%) influenza A(H1N1)pdm09 viruses had decreased up to 1/16 titers. Two A(H3N2) strains were similar to influenza A/Hong-Kong/4801/2014 virus but reacted with antiserum to influenza A/Switzerland/9715293/2013  vaccine strain up to 1/4 - 1/8 of homological titer only.

Genetic characterization. Three influenza A(H1N1)pdm09 viruses were identical for 97.8% to A/California/07/09 virus and for 99.0% to influenza A/South Africa/3626/13  virus. All investigated strains had  substitutions S84N, S162N+ and I216T in HA.

In sentinel surveillance system clinical samples from 57 SARI and 50 ILI/ARI patients were investigated by rRT-PCR. 24 (35.6%) influenza SARI cases were detected including 21 influenza A(H1N1)pdm09, 1 influenza A(H3N2) and 2 influenza B cases. 5 (10.0%) influenza ILI/ARI cases were detected including 4 influenza A(H1N1)pdm09 and 1 influenza A(H3N2) cases.

 

Two of the amino acid substitutions mentioned in the above report (S162N+ & I216T) are associated with the new genetic subcluster within subgroup 6B mentioned by the ECDC, while the third change (S84N) has been linked to reduced antigenic reactivity (cite).

Going back through the Russian Epi Weekly reports, as of the last week of 2015, they reported 23 of the 23 viruses H1N1 viruses examined to be antigenically similar to the vaccine strain, meaning that these reduced titer samples have all appeared over the past three weeks.

It would not be a huge surprise to finally see some significant antigenic drift in the H1N1pdm09 virus.  It has remained stable far longer than anyone expected. But it remains to be seen whether these `reduced titer' viruses will spread beyond the region.



The reports of increased `morbidity and mortality' from these viruses  - while possible - appear to be anecdotal at this time, and are not reflected in the data provided by the Russian Epi report. 

Influenza viruses  - `mutated' or otherwise - are responsible for hundreds of thousands of deaths each year, and so these statements will require additional  data to substantiate. 

The timing here is important, as decisions on what vaccine strains to include in next fall's North American Influenza vaccine are normally made by the end of February.


So we'll keep an extra close eye on the Russian Influenza reports in the weeks to come.