Epidemic Situation

Year: Week:


Week 06.03.2017-12.03.2017

Influenza and ARI morbidity data

Epidemiological data show decrease of influenza and other ARI registration in Russia in comparison with previous week. The nationwide ILI & ARI morbidity level (62.9 per 10 000 of population) was below than the national baseline (69.7) by 9.8%.

ILI and ARI epidemic thresholds were exceeded in 3 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 53 RBLs and two WHO NICs. According to these data as a result of 2578 patients investigation the overall proportion of respiratory samples positive for influenza was estimated as 23.9%, including 0.04% for A(H1N1)pdm09 virus, 5.6% for influenza A(H3N2) virus, 0.2% for influenza A and 18.0% 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 RII244018210039
(%) 0,07,48,60,00,016,0
BL of IV2904110015
(%) 0,013,837,90,00,051,7
TOTAL273022320054
(%) 0,08,111,70,00,019,8

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 RII701022332613153948196
(%) 0,03,14,73,71,92,15,66,828,0
BL of IV10101160476539
(%) 0,01,015,80,04,06,95,95,038,6
TOTAL802023492617224553235
(%) 0,02,96,13,22,12,75,66,629,3

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 RII17513 / 17300 / 668111 / 14610 / 665336 / 17301 / 104914 / 111128 / 111591 / 1136
(%) 0,20,07,60,019,40,101,32,58,0
BL of IV2801 / 2800 / 426 / 1790 / 4296 / 2800 / 421 / 1443 / 1443 / 144
(%) 0,40,03,40,034,30,00,72,12,1
TOTAL20314 / 20100 / 710117 / 16400 / 707432 / 20101 / 109115 / 125531 / 125994 / 1280
(%) 0,20,07,10,021,50,091,22,57,3

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 RII22450013933661509
(%) 0,00,06,20,116,30,0422,7
BL of IV3330061990106
(%) 0,00,01,80,329,70,031,8
TOTAL25780014544651615
(%) 0,00,05,60,218,00,0423,9

Conclusion

Influenza and ARI morbidity data. Decreased influenza and other ARI reporting was registered in traditional surveillance system in Russia during the week ending 12.03.2017. The nationwide ILI & ARI morbidity level (62.9 per 10 000 of population) was below the baseline by 9.8%.

Etiology of ILI & ARI morbidity. The overall proportion of respiratory samples positive for influenza  was estimated as 23.9%, including 0.04% for A(H1N1)pdm09 virus, 5.6% for influenza A(H3N2) virus, 0.2% for influenza A and 18.0% for influenza B virus.

Percent of positive ARI cases of non-influenza etiology (PIV, adeno- and RSV) was estimated as 20.2% of investigated patients by IFA and 11.0% by PCR. 

In sentinel surveillance system Clinical samples from 65 SARI patients were investigated by rRT-PCR. Among them 19 (29.2%) cases were associated with influenza, including 6 A(H3N2) cases and 13 influenza B cases. A total 63 ILI/ARI cases were investigated and 30 (47.6%) influenza cases were recognized, among them 3 influenza A(H3N2) and 27 influenza B cases.

Antigenic characterization. One influenza A(H1N1)pdm09 strain was similar to A/California/7/2009 virus. 128 influenza A(H3N2) strains were antigenically related to influenza A/Hong Kong/4801/2014 virus. 89 influenza B viruses belonged to Victoria lineage and were like influenza B/Brisbane/60/2008 virus.

Genetic characterization7 influenza A(H3N2) viruses were characterized. 2 of them belonged to genetic subgroup 3C.2a1 and were like A/Bolzano/7/2016 reference-strain. 5 influenza A(H3N2) viruses belonged to genetic subgroup 3C.2a and were like A/HongKong/4801/2014 virus.

Full-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 in the beginning 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, 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, 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.