National Weekly Bulletin

Year: Week:


Week 05.03.2018-11.03.2018

Influenza and ARI morbidity data

Epidemiological data show decrease of influenza and other ARI activity in Russia in comparison with previous week. The ILI & ARI incidence rate (70.0 per 10 000 of population) was below by 3.6% the new nationalwide baseline (72.6) calculated by RII NIC for 2017-2018 season.

ILI and ARI epidemic thresholds were exceeded in 5 of 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 54 RBLs and two WHO NICs. According to these data as a result of 3523 patients investigation the percent of samples positive for influenza was estimated as 26.5%. Proportion of influenza A(H1N1)pdm09, A(H3N2), type A and type B viruses was estimated as 40.3%, 26.4%, 5.2% and 28.1%, 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 RII2280172015052
(%) 0,07,58,86,60,022,8
BL of IV1430171411042
(%) 0,011,99,87,70,029,4
TOTAL3710343426094
(%) 0,09,29,27,00,025,3

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 RII767403813188252836206
(%) 5,25,01,72,31,03,33,74,726,9
BL of IV10622332781441
(%) 1,91,92,82,81,96,67,513,238,7
TOTAL8734240162110323650247
(%) 4,84,61,82,41,13,74,15,728,3

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 RII246648 / 24320 / 722158 / 22330 / 650211 / 2462293 / 232418 / 141349 / 1439109 / 1440
(%) 2,00,07,10,08,612,61,33,47,6
BL of IV4191 / 4190 / 5936 / 3630 / 5932 / 41945 / 3321 / 2242 / 22413 / 224
(%) 0,20,09,90,07,613,60,40,95,8
TOTAL288549 / 28510 / 781194 / 25960 / 709243 / 2881338 / 265619 / 163751 / 1663122 / 1664
(%) 1,70,07,50,08,412,71,23,17,3

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 RII302504021148228331818
(%) 0,01,37,01,67,510,927,0
BL of IV498023613445116
(%) 0,00,47,20,26,89,023,3
TOTAL352304224749262376934
(%) 0,01,27,01,47,410,726,5

Conclusion

Influenza and ARI morbidity data.  Decrease of influenza and other ARI activity was registered during week 10.2018 in Russia. The ILI & ARI incidence rate (70.0 per 10 000 of population) was below by 3.6% the nationalwide baseline.

Etiology of ILI & ARI morbidity. The overall percent of respiratory samples positive for influenza was estimated as 26.5%. Proportion of influenza A(H1N1)pdm09, A(H3N2), type A and type B viruses was estimated as 40.3%, 26.4%, 5.2% and 28.1%, respectively

Antigenic characterization. 180 influenza viruses were characterized antigenically in Moscow and Saint-Petersburg NICs, including 47 influenza A(H1N1)pdm09 viruses, 41 influenza A(H3N2) strains and 92 influenza type B strains. All influenza A(H1N1)pdm09 strains were related to influenza A/Michigan/45/2015, influenza A(H3N2) strains to A/Hong Kong/4801/2014 viruses. 86 influenza type B strains belonged to Yamagata lineage and were like B/Phuket/3073/2013 reference virus, 6 influenza type B strains belonged to Victoria lineage and were antigenically related to B/Brisbain/60/2008 strain.

Genetic characterizationFull-genome NGS of 58 influenza positive samples and viruses from 6 cities was conducted. 16 influenza A(H1N1)pdm09  viruses belonged to phylogenetic group 6B.1 with amino acid substitutions in HA S84N, S162N and I216T. According to phylogenetic analisis of HA 18 of 22 tested influenza A(H3N2) viruses belonged to clade 3C.2a carring aa substitutions L3I, N144S, F159Y, K160T, N225D and Q311H in HA1. Four influenza A(H3N2) viruses belonged to genetic subgroup 3C.2a1 and carried aa substitutions K92R, N121K, T135K and H311Q. 2 influenza B viruses of Victoria-lineage belonged to genetic subgroup 1A (B/Brisbane/60/2008-like). All 18 influenza B viruses of Yamagata-lineage belonged to clade 3 (B/Phuket/3073/2013-like) and had substitution L172Q and M251V in HA1.

Susceptibility to antivirals.Most viruses were susceptible to NA inhibitors excluding three influenza A(H1N1)pdm09 strains isolated in Moscow which had H275Y amino acid substitution in NA responsible for highly reduced susceptibility to oseltamivir and zanamivir. 14 influenza strains tested in MUNANA-assay for antiviral resistance to NA inhibitors in RII NIC, including 3 A(H1N1)pdm09 strains isolated in St.Petersburg, 4 A(H3N2), two B Victoria strains and 5 B Yamagata 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 17.0% of investigated patients by IFA and 11.6% by PCR. Last weeks RSV dominated among ARI agents.

In sentinel surveillance system clinical samples from 93 SARI and ILI/ARI patients were investigated by rRT-PCR. 16 (40.0%) influenza cases were detected among SARI patients, including 6 influenza A(H1N1)pdm09 cases, 4 influenza A(H3N2) cases and 6 influenza B cases. Among ILI/ARI patients 13 (24.5%) influenza cases were detected, including 6 influenza A(H1N1)pdm09, 6 influenza A(H3N2) and 1 influenza B case.