Epidemic Situation

Year: Week:


Week 08.05.2017-14.05.2017

Influenza and ARI morbidity data

Epidemiological data indicated for decrease of influenza and other ARI activity in Russia in comparison with previous week. The nationwide ILI & ARI morbidity level (34.1 per 10 000 of population) was below the national baseline (69.7) by 51.1%.

ILI and ARI epidemic threshold was exceeded in one of 59 cities collaborating with two WHO NICs in Russia.

Exceeding of morbidity epidemic thresholds for overall population
 
- No data - less 20% - 20 - 49% - 50% and more


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 786 patients investigation the overall proportion of respiratory samples positive for influenza was estimated as 8.4%, including  1.0% for influenza A(H3N2) virus and 7.4% for influenza B virus

Results of influenza diagnosis
 
- No data
- No detection
- H1pdm09
- H1pdm09+H1
- H1pdm09+B
- H1pdm09+B+H1
- H1pdm09+H3
- H1pdm09+H3+H1
- H1pdm09+H3+B
- H1pdm09+H3+H1+B
- H1
- B
- B+H1
- H3
- H3+H1
- H3+B
- H3+H1+B


Influenza Virus Isolation



  - B - A(H1N1) - A(H3N2) - A(H1N1)pdm09  


Influenza Virus Antigen Detection by Immunofluorescence Assay (IFA)



  - B - A(H1N1) + A(H1N1)pdm09 - A(H3N2)  
  - PIV - AD - RS  


Influenza Virus RNA Detection by RT-PCR



  - B - A(H1N1) - A(H3N2) - A(H1N1)pdm09  
  - PIV - AD - RS    


Table 1. Influenza Virus Isolation
Base lab. Number of
investigated
patients
Number of viruses isolated
H1 H3 B H1pdm09 Untyped
virus
Total
BL of RII26001001
(%) 0,00,03,80,00,03,8
BL of IV360480012
(%) 0,011,122,20,00,033,3
TOTAL620490013
(%) 0,06,514,50,00,021,0

Table 2. Influenza Virus Antigen Detection by Immunofluorescence Assay (IFA)
Base lab. Number of
investigated
patients
Influenza Parainfluenza AD RS Total
H1+H1pdm09 H3 B I II III
BL of RII2340032510192059
(%) 0,00,01,30,92,14,38,18,525,2
BL of IV550012091215
(%) 0,00,01,83,60,016,41,83,627,3
TOTAL2890044519202274
(%) 0,00,01,41,41,76,66,97,625,6

Table 3. Influenza Virus RNA Detection by RT-PCR
Base lab. Number of
investigated
patients
Influenza PIV AD RS
A
(not subtyped)
H1 H3 H5 B H1pdm09
BL of RII5230 / 5230 / 2558 / 3450 / 26147 / 5230 / 28810 / 38819 / 38839 / 388
(%) 0,00,02,30,09,00,02,64,910,1
BL of IV1050 / 1050 / 170 / 390 / 3311 / 1050 / 390 / 551 / 553 / 55
(%) 0,00,00,00,010,50,00,01,85,5
TOTAL6280 / 6280 / 2728 / 3840 / 29458 / 6280 / 32710 / 44320 / 44342 / 443
(%) 0,00,02,10,09,20,02,34,59,5

Table 4. Cumulative number of diagnosed influenza cases
Base lab. Number of
investigated
patients
Number of diagnosed influenza cases
H1 H1+H1pdm09
(IFA)
H3 A
(not subtyped)
B H1pdm09 Total
BL of RII663008047055
(%) 0,00,01,20,07,10,08,3
BL of IV123000011011
(%) 0,00,00,00,08,90,08,9
TOTAL786008058066
(%) 0,00,01,00,07,40,08,4

Conclusion

Influenza and ARI morbidity data. Decreased influenza and other ARI activity was registered in traditional surveillance system in Russia during the week ending 14.05.2017. The nationwide ILI & ARI morbidity level (34.1 per 10 000 of population) was below the baseline by 51.1%.

Etiology of ILI & ARI morbidity. The overall proportion of respiratory samples positive for influenza  was estimated as 8.4%, including 1.0% for influenza A(H3N2) virus and 8.4% for influenza B virus.

Percent of positive ARI cases of non-influenza etiology (PIV, adeno- and RSV) was estimated as 25.5% of investigated patients by IFA and 16.3% by PCR. 

In sentinel surveillance system clinical samples from 28 SARI patients were investigated by rRT-PCR. Among them 3 (10.7%) case was associated with influenza A(H3N2) virus. A total 33 ILI/ARI cases were investigated and 3 (9.1%) influenza B cases were recognized.

Antigenic characterization. One influenza A(H1N1)pdm09 strain was similar to A/California/7/2009 virus. 266 influenza A(H3N2) strains were antigenically related to influenza A/Hong Kong/4801/2014 virus. 295 influenza B viruses belonged to Victoria lineage and were like influenza B/Brisbane/60/2008 virus and one influenza B virus belonged to Yamagata line and was like Influenza B/Phuket/3073/2013 referens strain.

Genetic characterizationFull-genome amplification of influenza A(H3N2) viruses from 6 isolated viruses and 69 clinical specimens obtained from 30 Regional Base Laboratories of NIC was performed according to Zhou et al. with modifications. Next-generation sequencing was performed using Illumina MiSeq. Sequences were submitted to Epiflu GISAID database (isolates Acc. Nos. EPI_ISL_242591- EPI_ISL_242665)

According to the phylogenetic analysis of the hemagglutinin (HA) gene of 2016-2017 influenza season in Russian Federation influenza A(H3N2) viruses were represented by clade 3C2a and genetic subgroup 3C2a.1. Most of the sequenced viruses belonged to 3C2a clade (A/HongKong/4801/2014 reference virus), bearing S144R/K and N121K substitutions. Some 3C2a viruses had also S262N and N122D substitutions in hemagglutinin, the latter leading to loss of potential N-glycosylation site. 18 viruses clustered in 3C2a.1 genetic subgroup (A/Bolzano/7/2016 reference-strain), bearing N171K substitution typical for this subgroup and two substitutions in HA2 – I61V and G139E. Several viruses of 3C2a.1 subgroup from European part of Russia possessed additional substitutions in HA1: I58V, K92R, N121K, and H311Q. All tested viruses were susceptible to both NA inhibitors and resistant to rimantadine by results of genetic analysis of NA and M gene, respectively. Additionally 73 viruses tested phenotypically were susceptible to NA inhibitors and resistant to rimantadine.