Genetic divergence of Influenza A(H3N2) amino acid substitutions mark the beginning of the 2016–2017 winter season in Israel

Glatman‐Freedman, Aharona; Drori, Yaron; Beni, Sharon; Friedman, Nehemya; Pando, Rakefet; Sefty, Hanna; Tal, Ilana; McCauley, John W.; Rahav, Galia; Keller, Nathan; Shohat, Tamy; Mendelson, Ella; Hindiyeh, Musa; Mandelboim, Michal

doi:10.1016/j.jcv.2017.05.020

Cited by 20 publications

(15 citation statements)

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“…Group I and II strains in this study collectively represented clade 3C.2a1 designated by the WHO [ 32 ]. Group III strains in this study comprised some newer Israel strains and the proposed 3C.2a1 cluster III from the U.K., while group IV described additional Israel strains and the proposed 3C.2a2 clade [ 30 , 31 ]. Additionally, newly emergent A(H3N2) strains identified in this study necessitated further subdivision into a separate group V according to a number of significant variance from the A/Hong Kong/4801/2014 vaccine strain and other previously described variants.…”

Section: Discussionmentioning

confidence: 99%

Genetic and antigenic divergence in the influenza A(H3N2) virus circulating between 2016 and 2017 in Thailand

et al. 2017

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Influenza virus evolves rapidly due to the accumulated genetic variations on the viral sequence. Unlike in North America and Europe, influenza season in the tropical Southeast Asia spans both the rainy and cool seasons. Thus, influenza epidemiology and viral evolution sometimes differ from other regions, which affect the ever-changing efficacy of the vaccine. To monitor the current circulating influenza viruses in this region, we determined the predominant influenza virus strains circulating in Thailand between January 2016 and June 2017 by screening 7,228 samples from patients with influenza-like illness. During this time, influenza A(H3N2) virus was the predominant influenza virus detected. We then phylogenetically compared the hemagglutinin (HA) gene from a subset of these A(H3N2) strains (n = 62) to the reference sequences and evaluated amino acid changes in the dominant antigenic epitopes on the HA protein structure. The divergence of the circulating A(H3N2) from the A/Hong Kong/4801/2014 vaccine strain formed five genetic groups (designated I to V) within the 3C.2a clade. Our results suggest a marked drift of the current circulating A(H3N2) strains in Thailand, which collectively contributed to the declining predicted vaccine effectiveness (VE) from 74% in 2016 down to 48% in 2017.

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Section: Discussionmentioning

confidence: 99%

Genetic and antigenic divergence in the influenza A(H3N2) virus circulating between 2016 and 2017 in Thailand

et al. 2017

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“…Samples obtained from ILI patients were tested for influenza virus types and subtypes at the Central Virology Laboratory of the Israel Ministry of Health [4,9]. The viral genomic RNA was extracted using MagNApure 96 (Roche, Mannheim, Germany).…”

Section: Laboratory Methodsmentioning

confidence: 99%

“…Hemagglutinin (HA) gene sequencing was performed on a subset of viruses selected from different months throughout the 2018-2019 influenza season. The influenza A (H3N2) HA gene was partially amplified using specific primers [3,4,8,10]. The amplified HA RT-PCR products were sequenced as previously described [4].…”

Section: Laboratory Methodsmentioning

confidence: 99%

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Predominance of a Drifted Influenza A (H3N2) Clade and Its Association with Age-Specific Influenza Vaccine Effectiveness Variations, Influenza Season 2018–2019

et al. 2020

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Background: Influenza A (H3N2) clade 3C.3a was the predominant influenza virus in Israel throughout the 2018-2019 season, constituting a drift from the influenza A (H3N2) vaccine. We estimated the end-of season vaccine effectiveness (VE) by age, among community patients with influenza-like illness (ILI), considering the hemagglutinin (HA) gene mutations and amino acid substitutions of influenza A (H3N2) viruses detected. Methods: Nose-throat samples were analyzed for the presence of influenza virus, type/subtype, and HA gene sequence. HA gene sequences and amino acid substitutions were compared to the influenza A/Singapore/INFIMH-16-0019/2016 (H3N2)-like 2018-2019 vaccine virus, and a phylogenetic tree was generated. Influenza VE against influenza A (H3N2) was estimated using the test-negative design. VE was estimated by age group and by 15 year moving age intervals. Results: In total, 90% of the influenza A (H3N2) viruses belonged to the 3C.3a clade, constituting a unique situation in the northern hemisphere. Adjusted all-age influenza A (H3N2) VE was −3.5% (95% CI: −51.2 to 29.1). Although adjusted VEs were very low among infants, children, and young adults, a VE of 45% (95% CI: −19.2 to 74.6) was estimated among adults aged ≥45 years old. Conclusions: The higher VE point estimates among older adults may be related to previous exposure to similar influenza viruses.

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“…Presently, 18 HA and 11 NA subtypes are known . Several studies report a strong dominance of subtype A(H3N2), considered the main cause of seasonal influenza infections and associated with many deaths . The HA gene of influenza A(H3N2) has on its head 5 antigenic sites identified by epitopes A‐E, which are targets of the host immune response .…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity of influenza A(H3N2) viruses in Northern Cameroon during the 2014‐2016 influenza seasons

Njifon

Monamele

Vernet

et al. 2019

Journal of Medical Virology

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In Cameroon, genome characterization of influenza virus has been performed only in the Southern regions meanwhile genetic diversity of this virus varies with respect to locality. The Northern region characterized by a Sudan tropical climate might have distinct genetic characterization. This study aimed to better understand the genetic diversity of influenza A(H3N2) viruses circulating in Northern Cameroon. Sequences of three gene segments (hemagglutinin (HA), neuraminidase (NA) and matrix (M) genes) were obtained from 16 A(H3N2) virus strains collected during the 2014 to 2016 influenza seasons in Garoua. The HA gene segments were analysed with respect to reference strains while the NA and M gene was analysed for reported genetic markers of resistance to antivirals. Analysis of the HA sequences revealed that majority of the virus strains grouped together with the 2016‐2017 vaccine strain (3C.2a‐A/Hong Kong/4801/2014) while 3/5 (60%) of the 2015 viral strains grouped together with the 2015‐2016 vaccine strain 3C.3a‐A/Switzerland/9715293/2013. Within clade 3C.2a, Northern Cameroon sequences mostly grouped in sub‐clade A3 (10/16). Analysis of the coding regions of the NA and M genes showed that none had genetic markers of resistance to neuraminidase inhibitors but all strains possessed the S31N substitution of resistance to amantadine. Due to some discrepancies observed in this region with respect to the Southern regions of Cameroon, there is necessity of including all regions within a country in the sentinel surveillance of influenza. These data will enable to track changes in influenza viruses in Cameroon.

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Genetic divergence of Influenza A(H3N2) amino acid substitutions mark the beginning of the 2016–2017 winter season in Israel

Abstract: HighlightsA(H3N2) dominated the early stages of the 2016–2017 influenza season.36% of hospitalized infected patients received the influenza vaccine.Circulating A(H3N2) viruses were different from the vaccine strain.

Cited by 20 publications

References 20 publications

Genetic and antigenic divergence in the influenza A(H3N2) virus circulating between 2016 and 2017 in Thailand

Genetic and antigenic divergence in the influenza A(H3N2) virus circulating between 2016 and 2017 in Thailand

Predominance of a Drifted Influenza A (H3N2) Clade and Its Association with Age-Specific Influenza Vaccine Effectiveness Variations, Influenza Season 2018–2019

Genetic diversity of influenza A(H3N2) viruses in Northern Cameroon during the 2014‐2016 influenza seasons

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