Clinical and molecular epidemiology of influenza viruses from Romanian patients hospitalized during the 2019/20 season

PLoS One. 2021 Nov 12;16(11):e0258798. doi: 10.1371/journal.pone.0258798. eCollection 2021.

Abstract

Two main mechanisms contribute to the continuous evolution of influenza viruses: accumulation of mutations in the hemagglutinin and neuraminidase genes (antigenic drift) and genetic re-assortments (antigenic shift). Epidemiological surveillance is important in identifying new genetic variants of influenza viruses with potentially increased pathogenicity and transmissibility. In order to characterize the 2019/20 influenza epidemic in Romania, 1042 respiratory samples were collected from consecutive patients hospitalized with acute respiratory infections in the National Institute for Infectious Diseases "Prof. Dr. Matei Balș", Bucharest Romania and tested for influenza A virus, influenza B virus and respiratory syncytial virus (RSV) by real-time PCR. Out of them, 516 cases were positive for influenza, with relatively equal distribution of influenza A and B. Two patients had influenza A and B co-infection and 8 patients had influenza-RSV co-infection. The most severe cases, requiring supplemental oxygen administration or intensive care, and the most deaths were reported in patients aged 65 years and over. Subtyping showed the predominance of A(H3N2) compared to A(H1N1)pdm09 pdm09 (60.4% and 39.6% of all subtyped influenza A isolates, respectively), and the circulation of Victoria B lineage only. Influenza B started to circulate first (week 47/2019), with influenza A appearing slightly later (week 50/2019), followed by continued co-circulation of A and B viruses throughout the season. Sixty-eight samples, selected to cover the entire influenza season and all circulating viral types, were analysed by next generation sequencing (NGS). All A(H1N1)pdm09 sequences identified during this season in Romania were clustered in the 6b1.A clade (sub-clades: 6b1.A.183P -5a and 6b1.A.187A). For most A(H1N1)pdm09 sequences, the dominant epitope was Sb (pepitope = 0.25), reducing the vaccine efficacy by approximately 60%. According to phylogenetic analysis, influenza A(H3N2) strains circulating in this season belonged predominantly to clade 3C.3A, with only few sequences in clade 3C.2A1b. These 3C.2A1b sequences, two of which belonged to vaccinated patients, harbored mutations in antigenic sites leading to potential reduction of vaccine efficacy. Phylogenetic analysis of influenza B, lineage Victoria, sequences showed that the circulating strains belonged to clade V1A3. As compared to the other viral types, fewer mutations were observed in B/Victoria strains, with limited impact on vaccine efficiency based on estimations.

Publication types

  • Historical Article
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Adult
  • Aged
  • Aged, 80 and over
  • Child
  • Child, Preschool
  • Coinfection
  • Epidemics*
  • Female
  • History, 21st Century
  • Hospitalization*
  • Humans
  • Infant
  • Infant, Newborn
  • Influenza A Virus, H1N1 Subtype / genetics*
  • Influenza A Virus, H3N2 Subtype / genetics*
  • Influenza B virus / genetics*
  • Influenza Vaccines / therapeutic use
  • Influenza, Human / epidemiology*
  • Influenza, Human / history*
  • Influenza, Human / prevention & control
  • Influenza, Human / virology
  • Male
  • Middle Aged
  • Phylogeny
  • RNA, Viral / genetics
  • Respiratory Syncytial Virus Infections / epidemiology*
  • Respiratory Syncytial Virus Infections / history*
  • Respiratory Syncytial Virus Infections / virology
  • Respiratory Syncytial Viruses / genetics*
  • Romania / epidemiology
  • Vaccine Efficacy
  • Young Adult

Substances

  • Influenza Vaccines
  • RNA, Viral

Grants and funding

The study received funding from the Global Influenza Hospital Surveillance Network (GIHSN) project and the Development of Robust and Innovative Vaccine Effectiveness (DRIVE) project, as follows: GIHSN project was co-funded by the Foundation for Influenza Epidemiology; the DRIVE study has received support from the EU/EFPIA Innovative Medicines Initiative 2 Joint Undertaking (DRIVE, grant n° 777363). Both studies were co-funded by the National Institute for Infectious Diseases "Prof. Dr. Matei Balș”, Bucharest, Romania. GIHSN and DRIVE contributed to study design but had no role in data collection and analysis, decision to publish, or preparation of the manuscript. The National Institute for Infectious Diseases „Prof. Dr. Matei Balș” contributed to study design, data collection and analysis, but had no role in the decision to publish, or preparation of the manuscript. The authors VDM, LB, OS, SP, MS, DF, OV, Anca S-C, AB, DO, DP, Adrian S-C and ACD were supported by GIHSN project. MS was supported by Research Institute of the University of Bucharest (ICUB) grant no. 20964/30.10.2020. The funder ICUB provided support in the form of fellowship for the author MS, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.