Wednesday, February 10, 2016

Russia's Flu Epidemic: Week 6 Epidemiology Report

Russian Research Institute of Influenza

# 10,993

Russia's flu epidemic has been raging for three weeks, forcing the closure of more than 11,000 schools, and as it consists primarily A(H1N1)pdm09, it is hitting younger adults and children particularly hard.

Today the Russian Research Institute of Influenza has published their latest (week 6) epidemiological report, which shows a slight reduction in flu activity, but still with ILI & ARI morbidity levels running very high.

First some excerpts from today's report, after which I'll have some brief comments.

Week 01.02.2016-07.02.2016

Influenza and ARI morbidity data

Epidemiological data slight (by 13.3%) decrease of influenza activity in Russia in comparison with previous week.  However the nationwide ILI & ARI morbidity level (125.2 per 10 000 of population) exceeded the national baseline (69.5 per 10 000) by 80.1%
ILI and ARI epidemic thresholds were exceeded in 44 of 58 cities collaborating with two WHO NICs in Russia.

Cumulative number of diagnosed influenza cases

Laboratory diagnosis data. Results of influenza laboratory diagnosis by different tests were submitted by 53 RBLs and two WHO NICs. According to these data as a result of 13246 patients investigation the overall proportion of respiratory samples positive for influenza virus was estimated as 4321 (32.6%) including 3982 (92.2%) influenza A(H1N1)pdm09 cases, 128 (3.0%) influenza A(H3N2) cases, 174 (4.0%) influenza A cases and 37 (0.9%) influenza B cases.


Influenza and ARI morbidity data. Influenza activity decreased slightly on the week 06.2016 however the nationwide ILI & ARI morbidity level (125.2 per 10 000 of population) exceeded still the national baseline by 80.1%.

Etiology of ILI & ARI morbidity. As a result of investigation of 13246 patients in 53 cities of Russia the overall proportion of respiratory samples positive for influenza in traditional surveillance system was estimated as 32.6%. Influenza A(H1N1)pdm09 dominated (92.2% of influenza cases). Influenza A(H3N2) and B cases registered sporadically.

The overall proportion of respiratory samples tested positive for parainfluenza, adenovirus and RSV was estimated in total as 4.5% (PCR) and 13.4% (IFA) of investigated samples.

In sentinel surveillance system clinical samples from 86 SARI and 112 ILI/ARI patients were investigated by rRT-PCR. 59 (68.8%) influenza cases including 55 influenza A(H1N1)pdm09 and 4 influenza A(H3N2) cases were detected among SARI patients. A total 40 (35.7%) influenza cases including 37 influenza A(H1N1)pdm09 and 3 influenza A(H3N2) cases were detected among ILI/ARI patients.

Antigenic characterization. Totally 123 influenza A(H1N1)pdm09, 2 influenza A(H3N2) and 5 influenza B viruses were characterizated antigenically in two NICs of Russia since the beginning of the season. According to St.Petersburg NIC data 21 influenza A(H1N1)pdm09 strains were related closely to influenza A/California/07/09 virus. 
Most of 102 influenza A(H1N1)pdm09 viruses investigated in Moscow NIC were similar to vaccine A/California/07/09 virus however 10 of them had decreased up to 1/16 titer in interaction with antiserum to this virus. Two A(H3N2) strains were similar to influenza A/Hong-Kong/5738/2014 virus, with antiserum to influenza A/Switzerland/9715293/2013 they reacted up to 1/4 - 1/8 of homological titer in HI.
All investigated 5 influenza B viruses belonged to Victorian lineage and were similar to influenza B/Brisbane/60/2008 reference strain reacting with antiserum to this virus up to 1 - 1/8 of homological titer in HI.

Genetic characterization54 investigated influenza A(H1N1)pdm09 virus strains were A/South Africa/3626/2013-like. All viruses bear clade 6B specific mutations in HA (S84N, S162+N and I216T) and formed new genetic group according to phylogenetic analysis. Two A(H1N1)pdm09 sequences obtained directly from autopsy sample showed the presence of additional mutation D222G in HA1.

Susceptibility to antiviral drugs. According to genetic investigations 54 influenza A(H1N1)pdm09 viruses were susceptible to oseltamivir and resistant to rimantadine. These results coincided with Munana testing of 10 strains isolated in St.-Petersburg.

Today's report indicates that 15 additional  A(H1N1)pdm09 viruses were antigenically characterized, and (based on the numeric differences from Week 5), all appear to be closely related to influenza A/California/07/09 virus. 
Additionally, the number of virus samples with decreased titers to the vaccine virus remained unchanged from last week at 10. 

Once again, this week's report once again states that - Two A(H1N1)pdm09 sequences obtained directly from autopsy sample showed the presence of additional mutation D222G in HA1. - although it seems likely this is a carry over from last week. 

In a final bit of good news, there doesn't appear to be any sign of a loss of susceptibility of the 6B clade of H1N1 to Oseltamivir - in contrast to last week's Eurosurveillance: Emergence of A(H1N1)pdm09 Genogroup 6B In India, 2015 report which found some (limited) detection of the H275Y resistance mutation. 

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