Severe cases of seasonal influenza and detection of seasonal A(H1N2) in Russia in 2018–2019

Kolosova, Natalia; Ilyicheva, T. N.; Danilenko, Alexey V.; Svyatchenko, Svetlana V.; Гончарова, Н. И.; Bulanovich, Julia A.; Torzhkova, P. Yu.; Durymanov, A. G.; Gudymo, Andrey S.; Shvalov, Аlexander N.; Susloparov, Ivan M.; Трегубчак, Т. В.; Gavrilova, Elena V.; Maksyutov, Rinat А.; Ryzhikov, Alexander B.

doi:10.1007/s00705-020-04699-z

Cited by 5 publications

(11 citation statements)

References 13 publications

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“…A relatively high vaccine effectiveness was noted for the A(H1N1)pdm2009 vaccine component in the 2018-2019 epidemiological season [14,43]. The absence of a significant effect of D222G/N mutations on the antigenic properties of the virus was shown in our previous studies [13,14] and another study [42]. This indicates that the vaccine remains effective in protecting against variants of viruses with D222G/N mutations.…”

Section: Epidemiological Significance Of D222g/n Mutationsmentioning

confidence: 60%

“…During the four epidemic seasons in Russia from 2015-2019, D222G/N mutations were observed in up to 32-57% of fatal cases [12][13][14], and the HA 222D/G polymorphism in A (H1N1)pdm09 was observed in 30-60% of fatal and severe influenza cases in other studies in Russia [15], Germany [8] and Italy [9,16].…”

Section: Introductionmentioning

confidence: 75%

“…The D222G/N mutations were not detected in non-lethal cases in major or minor virus variants at frequencies of more than 1% in a sample in influenza cases in Russia during the 2017-2019 epidemiological seasons [13,14]. Other studies also note the identification of these mutations mainly in severe and fatal cases.…”

Section: Epidemiological Significance Of D222g/n Mutationsmentioning

confidence: 90%

“…An analysis of influenza morbidity in Russia in the 2018-2019 season revealed that among fatal cases A(H1N1)pdm09-associated illness was more prevalent (70%) than A(H3N2) infection, while in the general circulation there was an approximately equal distribution of influenza A(H1N1)pdm09 and A(H3N2) among type A viruses [14]. A similar increased proportion of A(H1N1)pdm09-associated fatal cases compared to the proportion of A(H1N1) pdm09 in general circulation was reported for the 2017-2018 epidemic season [13].…”

Section: Epidemiological Significance Of D222g/n Mutationsmentioning

confidence: 99%

“…The A(H1N1)pdm09 virus, which appeared in 2009, caused an epidemic in the 2015-2016 season in Russia with an increased rate of severe cases of the disease, which were often fatal [12]. Increased mortality from H1N1pdm09 compared to H3N2 was observed in Russia in 2017-2019 [13,14].…”

Section: Introductionmentioning

confidence: 99%

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Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018–2019

et al. 2021

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Outbreaks of influenza, which is a contagious respiratory disease, occur throughout the world annually, affecting millions of people with many fatal cases. The D222G/N mutations in the hemagglutinin (HA) gene of A(H1N1)pdm09 are associated with severe and fatal human influenza cases. These mutations lead to increased virus replication in the lower respiratory tract (LRT) and may result in life-threatening pneumonia. Targeted NGS analysis revealed the presence of mutations in major and minor variants in 57% of fatal cases, with the proportion of viral variants with mutations varying from 1% to 98% in each individual sample in the epidemic season 2018–2019 in Russia. Co-occurrence of the mutations D222G and D222N was detected in a substantial number of the studied fatal cases (41%). The D222G/N mutations were detected at a low frequency (less than 1%) in the rest of the studied samples from fatal and nonfatal cases of influenza. The presence of HA D222Y/V/A mutations was detected in a few fatal cases. The high rate of occurrence of HA D222G/N mutations in A(H1N1)pdm09 viruses, their increased ability to replicate in the LRT and their association with fatal outcomes points to the importance of monitoring the mutations in circulating A(H1N1)pdm09 viruses for the evaluation of their epidemiological significance and for the consideration of disease prevention and treatment options.

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Section: Epidemiological Significance Of D222g/n Mutationsmentioning

confidence: 60%

Section: Introductionmentioning

confidence: 75%

Section: Epidemiological Significance Of D222g/n Mutationsmentioning

confidence: 90%

Section: Epidemiological Significance Of D222g/n Mutationsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018–2019

et al. 2021

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High-throughput droplet-based analysis of influenza A virus genetic reassortment by single-virus RNA sequencing

Chen

Karuppusamy

O’Neill

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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The segmented RNA genome of influenza A viruses (IAVs) enables viral evolution through genetic reassortment after multiple IAVs coinfect the same cell, leading to viruses harboring combinations of eight genomic segments from distinct parental viruses. Existing data indicate that reassortant genotypes are not equiprobable; however, the low throughput of available virology techniques does not allow quantitative analysis. Here, we have developed a high-throughput single-cell droplet microfluidic system allowing encapsulation of IAV-infected cells, each cell being infected by a single progeny virion resulting from a coinfection process. Customized barcoded primers for targeted viral RNA sequencing enabled the analysis of 18,422 viral genotypes resulting from coinfection with two circulating human H1N1pdm09 and H3N2 IAVs. Results were highly reproducible, confirmed that genetic reassortment is far from random, and allowed accurate quantification of reassortants including rare events. In total, 159 out of the 254 possible reassortant genotypes were observed but with widely varied prevalence (from 0.038 to 8.45%). In cells where eight segments were detected, all 112 possible pairwise combinations of segments were observed. The inclusion of data from single cells where less than eight segments were detected allowed analysis of pairwise cosegregation between segments with very high confidence. Direct coupling analysis accurately predicted the fraction of pairwise segments and full genotypes. Overall, our results indicate that a large proportion of reassortant genotypes can emerge upon coinfection and be detected over a wide range of frequencies, highlighting the power of our tool for systematic and exhaustive monitoring of the reassortment potential of IAVs.

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Comparative analysis of influenza viruses isolated from first and severe cases in Russia in epidemiological seasons before and during COVID-19 pandemic (2019—2023)

Boldyrev,

Panova,

Kolosova

et al. 2023

Mol. genet. mikrobiol. virusol.

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Severe cases of seasonal influenza and detection of seasonal A(H1N2) in Russia in 2018–2019

Cited by 5 publications

References 13 publications

Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018–2019

Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018–2019

High-throughput droplet-based analysis of influenza A virus genetic reassortment by single-virus RNA sequencing

Comparative analysis of influenza viruses isolated from first and severe cases in Russia in epidemiological seasons before and during COVID-19 pandemic (2019—2023)

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