Epidemic Situation

Year: Week:


Week 02.04.2018-08.04.2018

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 (79.9 per 10 000 of population) was above by 10.1% the new nationalwide baseline (72.6) calculated by RII NIC for 2017-2018 season.

ILI and ARI epidemic thresholds were exceeded in 16 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 53 RBLs and two WHO NICs. According to these data as a result of 5292 patients investigation the percent of samples positive for influenza was estimated as 30.0%. Proportion of influenza A(H1N1)pdm09, A(H3N2), type A and type B viruses was estimated as 40.8%, 27.2%, 2.8% and 29.2%, 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 RII1750670270103
(%) 0,03,440,015,40,058,9
BL of IV10200915024
(%) 0,00,08,814,70,023,5
TOTAL2770679420127
(%) 0,02,228,515,20,045,8

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 RII8773722141310295864247
(%) 4,22,51,61,51,13,36,67,328,2
BL of IV19071134320141173
(%) 3,75,81,62,11,610,57,45,838,4
TOTAL10674433171713497275320
(%) 4,13,11,61,61,24,66,77,030,0

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 RII374043 / 37400 / 1254305 / 35790 / 1315326 / 3740484 / 372515 / 205420 / 210872 / 2076
(%) 1,10,08,50,08,713,00,70,93,5
BL of IV9162 / 9160 / 100101 / 9160 / 10072 / 916120 / 9162 / 3193 / 31919 / 319
(%) 0,20,011,00,07,913,10,60,96,0
TOTAL465645 / 46560 / 1354406 / 44950 / 1415398 / 4656604 / 464117 / 237323 / 242791 / 2395
(%) 1,00,09,00,08,513,00,70,93,8

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 RII4296034323433905271283
(%) 0,00,87,51,09,112,329,9
BL of IV99607109274122307
(%) 0,00,710,90,27,412,230,8
TOTAL5292041432454646491590
(%) 0,00,88,20,98,812,330,0

Conclusion

Influenza and ARI morbidity data.  Decrease of influenza and other ARI activity was registered during week 14.2018 in Russia. The ILI & ARI incidence rate (79.9 per 10 000 of population) was above by 10.1% the nationalwide baseline.

Etiology of ILI & ARI morbidity. The overall percent of respiratory samples positive for influenza was estimated as 30.0%. Proportion of influenza A(H1N1)pdm09, A(H3N2), type A and type B viruses was estimated as 40.8%, 27.2%, 2.8% and 29.2%, respectively.

Antigenic characterization. 379 influenza viruses were characterized antigenically in Moscow and Saint-Petersburg NICs, including 110 influenza A(H1N1)pdm09 viruses, 79 influenza A(H3N2) strains and 190 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. 184 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 next-generation sequencing of 71 influenza positive samples and viruses from cities located in differrent regions of Russian Feseration was conducted. 23 influenza A(H1N1)pdm09  viruses belonged to the phylogenetic group 6B.1. According to phylogenetic analisis of HA 21 of 26 tested influenza A(H3N2) viruses belonged to clade 3C.2a. 5 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 20 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 and zanamivir. 108 influenza strains tested in MUNANA-assay for antiviral resistance to NA inhibitors in RII NIC, including 20 A(H1N1)pdm09 strains, 12 A(H3N2) strains, two B Victoria strains and 74 B Yamagata viruses. All 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 21.1% of investigated patients by IFA and 5.4% by PCR. Last weeks RSV dominated among ARI agents.

In sentinel surveillance system clinical samples from 151 SARI and ILI/ARI patients were investigated by rRT-PCR. 32 (51.6%) influenza cases were detected among SARI patients, including 8 influenza A(H1N1)pdm09 cases, 14 influenza A(H3N2) cases and 10 influenza B cases. Among ILI/ARI patients 18 (20.2%) influenza cases were detected, including 9 influenza A(H1N1)pdm09, 8 influenza A(H3N2) and 1 influenza B case