Evolution of Influenza A(H3N2) Viruses in 2 Consecutive Seasons of Genomic Surveillance, 2021–2023

Amary Fall; Lijie Han; Madeline Yunker; Yu Nong Gong; Tai Jung Li; Julie M. Norton; Omar Abdullah; Richard E. Rothman; Katherine Z.J. Fenstermacher; C. Paul Morris; Andrew Pekosz; Eili Klein; Heba H. Mostafa

doi:10.1093/ofid/ofad577

Evolution of Influenza A(H3N2) Viruses in 2 Consecutive Seasons of Genomic Surveillance, 2021–2023

Amary Fall, Lijie Han, Madeline Yunker, Yu Nong Gong, Tai Jung Li, Julie M. Norton, Omar Abdullah, Richard E. Rothman, Katherine Z.J. Fenstermacher, C. Paul Morris, Andrew Pekosz, Eili Klein, Heba H. Mostafa^*

^*Corresponding author for this work

International Master Degree Program for Molecular Medicine in Emerging Viral Infections

Research output: Contribution to journal › Journal Article › peer-review

9 Scopus citations

Abstract

Background. The circulation and the genomic evolution of influenza A(H3N2) viruses during the 2021/2022 and 2022/2023 seasons were studied and associated with infection outcomes. Methods. Remnant influenza A–positive samples following standard-of-care testing from patients across the Johns Hopkins Health System (JHHS) were used for the study. Samples were randomly selected for whole viral genome sequencing. The sequence-based pEpitope model was used to estimate the predicted vaccine efficacy (pVE) for circulating H3N2 viruses. Clinical data were collected and associated with viral genomic data. Results. A total of 121 683 respiratory specimens were tested for influenza at JHHS between 1 September 2021 and 31 December 2022. Among them, 6071 (4.99%) tested positive for influenza A. Of these, 805 samples were randomly selected for sequencing, with hemagglutinin (HA) segments characterized for 610 samples. Among the characterized samples, 581 were H3N2 (95.2%). Phylogenetic analysis of HA segments revealed the exclusive circulation of H3N2 viruses with HA segments of the 3C.2a1b.2a.2 clade. Analysis of a total of 445 complete H3N2 genomes revealed reassortments; 200 of 227 of the 2022/2023 season genomes (88.1%) were found to have reassorted with clade 3C.2a1b.1a. The pVE was estimated to be −42.53% for the 2021/2022 season and 30.27% for the 2022/2023 season. No differences in clinical presentations or admissions were observed between the 2 seasons. Conclusions. The increased numbers of cases and genomic diversity of influenza A(H3N2) during the 2022/2023 season were not associated with a change in disease severity compared to the previous influenza season.

Original language	English
Article number	ofad577
Journal	Open Forum Infectious Diseases
Volume	10
Issue number	12
DOIs	https://doi.org/10.1093/ofid/ofad577
State	Published - 01 12 2023

Bibliographical note

Publisher Copyright:
© The Author(s) 2023. Published by Oxford University Press on behalf of Infectious Diseases Society of America.

Keywords

H3N2
influenza
reassortment
vaccine

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1093/ofid/ofad577

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Fall, A., Han, L., Yunker, M., Gong, Y. N., Li, T. J., Norton, J. M., Abdullah, O., Rothman, R. E., Fenstermacher, K. Z. J., Paul Morris, C., Pekosz, A., Klein, E., & Mostafa, H. H. (2023). Evolution of Influenza A(H3N2) Viruses in 2 Consecutive Seasons of Genomic Surveillance, 2021–2023. Open Forum Infectious Diseases, 10(12), Article ofad577. https://doi.org/10.1093/ofid/ofad577

@article{b2b46a531eae4eb481e4e9c7ee464625,

title = "Evolution of Influenza A(H3N2) Viruses in 2 Consecutive Seasons of Genomic Surveillance, 2021–2023",

abstract = "Background. The circulation and the genomic evolution of influenza A(H3N2) viruses during the 2021/2022 and 2022/2023 seasons were studied and associated with infection outcomes. Methods. Remnant influenza A–positive samples following standard-of-care testing from patients across the Johns Hopkins Health System (JHHS) were used for the study. Samples were randomly selected for whole viral genome sequencing. The sequence-based pEpitope model was used to estimate the predicted vaccine efficacy (pVE) for circulating H3N2 viruses. Clinical data were collected and associated with viral genomic data. Results. A total of 121 683 respiratory specimens were tested for influenza at JHHS between 1 September 2021 and 31 December 2022. Among them, 6071 (4.99%) tested positive for influenza A. Of these, 805 samples were randomly selected for sequencing, with hemagglutinin (HA) segments characterized for 610 samples. Among the characterized samples, 581 were H3N2 (95.2%). Phylogenetic analysis of HA segments revealed the exclusive circulation of H3N2 viruses with HA segments of the 3C.2a1b.2a.2 clade. Analysis of a total of 445 complete H3N2 genomes revealed reassortments; 200 of 227 of the 2022/2023 season genomes (88.1%) were found to have reassorted with clade 3C.2a1b.1a. The pVE was estimated to be −42.53% for the 2021/2022 season and 30.27% for the 2022/2023 season. No differences in clinical presentations or admissions were observed between the 2 seasons. Conclusions. The increased numbers of cases and genomic diversity of influenza A(H3N2) during the 2022/2023 season were not associated with a change in disease severity compared to the previous influenza season.",

keywords = "H3N2, influenza, reassortment, vaccine",

author = "Amary Fall and Lijie Han and Madeline Yunker and Gong, {Yu Nong} and Li, {Tai Jung} and Norton, {Julie M.} and Omar Abdullah and Rothman, {Richard E.} and Fenstermacher, {Katherine Z.J.} and {Paul Morris}, C. and Andrew Pekosz and Eili Klein and Mostafa, {Heba H.}",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2023. Published by Oxford University Press on behalf of Infectious Diseases Society of America.",

year = "2023",

month = dec,

day = "1",

doi = "10.1093/ofid/ofad577",

language = "英语",

volume = "10",

journal = "Open Forum Infectious Diseases",

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publisher = "Oxford University Press",

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TY - JOUR

T1 - Evolution of Influenza A(H3N2) Viruses in 2 Consecutive Seasons of Genomic Surveillance, 2021–2023

AU - Fall, Amary

AU - Han, Lijie

AU - Yunker, Madeline

AU - Gong, Yu Nong

AU - Li, Tai Jung

AU - Norton, Julie M.

AU - Abdullah, Omar

AU - Rothman, Richard E.

AU - Fenstermacher, Katherine Z.J.

AU - Paul Morris, C.

AU - Pekosz, Andrew

AU - Klein, Eili

AU - Mostafa, Heba H.

PY - 2023/12/1

Y1 - 2023/12/1

N2 - Background. The circulation and the genomic evolution of influenza A(H3N2) viruses during the 2021/2022 and 2022/2023 seasons were studied and associated with infection outcomes. Methods. Remnant influenza A–positive samples following standard-of-care testing from patients across the Johns Hopkins Health System (JHHS) were used for the study. Samples were randomly selected for whole viral genome sequencing. The sequence-based pEpitope model was used to estimate the predicted vaccine efficacy (pVE) for circulating H3N2 viruses. Clinical data were collected and associated with viral genomic data. Results. A total of 121 683 respiratory specimens were tested for influenza at JHHS between 1 September 2021 and 31 December 2022. Among them, 6071 (4.99%) tested positive for influenza A. Of these, 805 samples were randomly selected for sequencing, with hemagglutinin (HA) segments characterized for 610 samples. Among the characterized samples, 581 were H3N2 (95.2%). Phylogenetic analysis of HA segments revealed the exclusive circulation of H3N2 viruses with HA segments of the 3C.2a1b.2a.2 clade. Analysis of a total of 445 complete H3N2 genomes revealed reassortments; 200 of 227 of the 2022/2023 season genomes (88.1%) were found to have reassorted with clade 3C.2a1b.1a. The pVE was estimated to be −42.53% for the 2021/2022 season and 30.27% for the 2022/2023 season. No differences in clinical presentations or admissions were observed between the 2 seasons. Conclusions. The increased numbers of cases and genomic diversity of influenza A(H3N2) during the 2022/2023 season were not associated with a change in disease severity compared to the previous influenza season.

AB - Background. The circulation and the genomic evolution of influenza A(H3N2) viruses during the 2021/2022 and 2022/2023 seasons were studied and associated with infection outcomes. Methods. Remnant influenza A–positive samples following standard-of-care testing from patients across the Johns Hopkins Health System (JHHS) were used for the study. Samples were randomly selected for whole viral genome sequencing. The sequence-based pEpitope model was used to estimate the predicted vaccine efficacy (pVE) for circulating H3N2 viruses. Clinical data were collected and associated with viral genomic data. Results. A total of 121 683 respiratory specimens were tested for influenza at JHHS between 1 September 2021 and 31 December 2022. Among them, 6071 (4.99%) tested positive for influenza A. Of these, 805 samples were randomly selected for sequencing, with hemagglutinin (HA) segments characterized for 610 samples. Among the characterized samples, 581 were H3N2 (95.2%). Phylogenetic analysis of HA segments revealed the exclusive circulation of H3N2 viruses with HA segments of the 3C.2a1b.2a.2 clade. Analysis of a total of 445 complete H3N2 genomes revealed reassortments; 200 of 227 of the 2022/2023 season genomes (88.1%) were found to have reassorted with clade 3C.2a1b.1a. The pVE was estimated to be −42.53% for the 2021/2022 season and 30.27% for the 2022/2023 season. No differences in clinical presentations or admissions were observed between the 2 seasons. Conclusions. The increased numbers of cases and genomic diversity of influenza A(H3N2) during the 2022/2023 season were not associated with a change in disease severity compared to the previous influenza season.

KW - H3N2

KW - influenza

KW - reassortment

KW - vaccine

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U2 - 10.1093/ofid/ofad577

DO - 10.1093/ofid/ofad577

M3 - 文章

AN - SCOPUS:85180267491

SN - 2328-8957

VL - 10

JO - Open Forum Infectious Diseases

JF - Open Forum Infectious Diseases

IS - 12

M1 - ofad577

ER -

Evolution of Influenza A(H3N2) Viruses in 2 Consecutive Seasons of Genomic Surveillance, 2021–2023

Abstract

Bibliographical note

Keywords

UN SDGs

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