Epidemic Situation

Year: Week:


Week 14.05.2018-20.05.2018

Influenza and ARI morbidity data

Epidemiological data show increase of influenza and other ARI activity in Russia in comparison with previous week. The ILI & ARI incidence rate (39.9 per 10 000 of population) was lower by 45.0% the new nationalwide baseline (72.6) calculated by RII NIC for 2017-2018 season.

ILI and ARI epidemic thresholds were not exceeded in all 61 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 49 RBLs and two WHO NICs. According to these data as a result of 1712 patients investigation the percent of samples positive for influenza was estimated as 11.0%. Proportion of influenza A(H1N1)pdm09, A(H3N2), type A and type B viruses was estimated as 28.7%, 38.3%, 1.1% and 31.9%, respectively

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 RII95016236045
(%) 0,016,824,26,30,047,4
BL of IV21033006
(%) 0,014,314,30,00,028,6
TOTAL116019266051
(%) 0,016,422,45,20,044,0

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 RII4141069711141765
(%) 0,20,01,42,21,72,73,44,115,7
BL of IV38010002306
(%) 0,02,60,00,00,05,37,90,015,8
TOTAL4521169713171771
(%) 0,20,21,32,01,52,93,83,815,7

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 RII11661 / 11660 / 34839 / 8380 / 44131 / 116640 / 89215 / 85138 / 87432 / 874
(%) 0,090,04,70,02,74,51,84,33,7
BL of IV2031 / 2030 / 3417 / 1500 / 343 / 2039 / 984 / 1282 / 1282 / 128
(%) 0,50,011,30,01,59,23,11,61,6
TOTAL13692 / 13690 / 38256 / 9880 / 47534 / 136949 / 99019 / 97940 / 100234 / 1002
(%) 0,10,05,70,02,54,91,94,03,4

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 RII1494015515743156
(%) 0,00,073,70,073,82,910,4
BL of IV2180017131132
(%) 0,00,07,80,51,45,014,7
TOTAL1712017226054188
(%) 0,00,064,20,13,53,211,0

Conclusion

Influenza and ARI morbidity data.  Increase of influenza and other ARI activity was registered during week 20.2018 in Russia. The ILI & ARI incidence rate (39.9 per 10 000 of population) was lower by 45.0% the nationalwide baseline.

Etiology of ILI & ARI morbidity. The overall percent of respiratory samples positive for influenza was estimated as 11.0%. Proportion of influenza A(H1N1)pdm09, A(H3N2), type A and type B viruses was estimated as 28.7%, 38.3%, 1.1% and 31.9%, respectively

Antigenic characterization. 825 influenza viruses were characterized antigenically in Moscow and Saint-Petersburg NICs, including 257 influenza A(H1N1)pdm09 viruses, 166 influenza A(H3N2) strains and 402 influenza type B strains. All influenza A(H1N1)pdm09 strains were related to influenza A/Michigan/45/2015, influenza A(H3N2) strains related to A/Hong Kong/4801/2014 viruses with the except for one virus that interacts with a homologous antiserum in HI with a low titer. 392 influenza type B strains belonged to Yamagata lineage and were like B/Phuket/3073/2013 reference virus, 10 influenza type B strains belonged to Victoria lineage and were antigenically related to B/Brisbain/60/2008 strain.

Genetic characterizationFull-genome next-generation sequencing of 89 influenza positive samples and viruses from cities located in differrent regions of Russian Feseration was conducted. 22 influenza A(H1N1)pdm09  viruses belonged to the phylogenetic group 6B.1. According to phylogenetic analisis of HA 22 of 33 tested influenza A(H3N2) viruses belonged to clade 3C.2a. 11 influenza A(H3N2) viruses belonged to genetic subgroup 3C.2a1. 2 influenza B viruses of Victoria-lineage belonged to genetic subgroup 1A (B/Brisbane/60/2008-like). All 32 influenza B viruses of Yamagata-lineage belonged to clade 3 (B/Phuket/3073/2013-like).

Susceptibility to antivirals. Most viruses were susceptible to NA inhibitors excluding 5 influenza A(H1N1)pdm09 strains isolated in Moscow which had H275Y amino acid substitution in NA responsible for highly reduced susceptibility to oseltamivir. 

256 influenza strains tested in MUNANA-assay for antiviral resistance to NA inhibitors in RII NIC, including 112 A(H1N1)pdm09 strains, 47 A(H3N2) strains, two B Victoria strains and 95 B Yamagata viruses. One influenza A(H1N1)pdm09 strain isolated in Samara was resistant to oseltamivir. All other viruses were susceptible to oseltamivir and zanamivir. All influenza A strains tested were resistant to rimantadine.

Percent of positive ARI cases of non-influenza etiology (PIV, adeno- and RSV) was estimated as 14.0% of investigated patients by IFA and 9.3% by PCR. 

In sentinel surveillance system clinical samples from 71 SARI and ILI/ARI patients were investigated by rRT-PCR. 5 influenza cases were detected including 2 influenza A(H1N1)pdm09 cases, 1  influenza A(H3N2) case and 2 influenza B cases. Clinical samples from 28 ILI/ARI patients were investigated by rRT-PCR. No influenza case was detected.