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Genomic epidemiology of seasonal influenza circulation in China during prolonged border closure from 2020 to 2021.

ABSTRACT: China experienced a resurgence of seasonal influenza activity throughout 2021 despite intermittent control measures and prolonged international border closure. We show genomic evidence for multiple A(H3N2), A(H1N1), and B/Victoria transmission lineages circulating over 3 years, with the 2021 resurgence mainly driven by two B/Victoria clades. Phylodynamic analysis revealed unsampled ancestry prior to widespread outbreaks in December 2020, showing that influenza lineages can circulate cryptically under non-pharmaceutical interventions enacted against COVID-19. Novel haemagglutinin gene mutations and altered age profiles of infected individuals were observed, and Jiangxi province was identified as a major source for nationwide outbreaks. Following major holiday periods, fluctuations in the effective reproduction number were observed, underscoring the importance of influenza vaccination prior to holiday periods or travel. Extensive heterogeneity in seasonal influenza circulation patterns in China determined by historical strain circulation indicates that a better understanding of demographic patterns is needed for improving effective controls.

SUBMITTER: Xie R

PROVIDER: S-EPMC9338706 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Genomic epidemiology of seasonal influenza circulation in China during prolonged border closure from 2020 to 2021.

Xie Ruopeng R Adam Dillon C DC Edwards Kimberly M KM Gurung Shreya S Wei Xiaoman X Cowling Benjamin J BJ Dhanasekaran Vijaykrishna V

Virus evolution 20220713 2

China experienced a resurgence of seasonal influenza activity throughout 2021 despite intermittent control measures and prolonged international border closure. We show genomic evidence for multiple A(H3N2), A(H1N1), and B/Victoria transmission lineages circulating over 3 years, with the 2021 resurgence mainly driven by two B/Victoria clades. Phylodynamic analysis revealed unsampled ancestry prior to widespread outbreaks in December 2020, showing that influenza lineages can circulate cryptically ...[more]

PMID: 35919872

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Project description:Background. In mid-2020, there was significant concern that the overlapping 2020-2021 influenza season and COVID-19 pandemic would overwhelm already stressed health care systems in the Northern Hemisphere, particularly if influenza immunization rates were low. Methods. Using a mathematical susceptible-exposed-infected-recovered (SEIR) compartmental model incorporating the age-specific viral transmission rates and disease severity of Austin, Texas, a large metropolitan region, we projected the incidence and health care burden for both COVID-19 and influenza across observed levels of SARS-CoV-2 transmission and influenza immunization rates for the 2020-2021 season. We then retrospectively compared scenario projections made in August 2020 with observed trends through June 2021. Results. Across all scenarios, we projected that the COVID-19 burden would dwarf that of influenza. In all but our lowest transmission scenarios, intensive care units were overwhelmed by COVID-19 patients, with the levels of influenza immunization having little impact on health care capacity needs. Consistent with our projections, sustained nonpharmaceutical interventions (NPIs) in Austin prevented COVID-19 from overwhelming health care systems and almost completely suppressed influenza during the 2020-2021 respiratory virus season. Limitations. The model assumed no cross-immunity between SARS-CoV-2 and influenza, which might reduce the burden or slow the transmission of 1 or both viruses. Conclusion. Before the widespread rollout of the SARS-CoV-2 vaccine, COVID-19 was projected to cause an order of magnitude more hospitalizations than seasonal influenza because of its higher transmissibility and severity. Consistent with predictions assuming strong NPIs, COVID-19 strained but did not overwhelm local health care systems in Austin, while the influenza burden was negligible. Implications. Nonspecific NPI efforts can dramatically reduce seasonal influenza burden and preserve health care capacity during respiratory virus season.HighlightsAs the COVID-19 pandemic threatened lives worldwide, the Northern Hemisphere braced for a potential "twindemic" of seasonal influenza and COVID-19.Using a validated mathematical model of influenza and SARS-CoV-2 co-circulation in a large US city, we projected the impact of COVID-19-driven nonpharmaceutical interventions combined with influenza vaccination on health care capacity during the 2020-2021 respiratory virus season.We describe analyses conducted during summer 2020 to help US cities prepare for the 2020-2021 influenza season and provide a retrospective evaluation of the initial projections.

Project description:BackgroundDespite the substantial global impact of influenza, there are limited economic data to guide influenza vaccination programs investments in middle-income countries. We measured the costs of influenza and the costs of an influenza vaccination program in Armenia, using a societal perspective.MethodsDuring December 2022 through March 2023, retrospective cost data were collected from case-patients and healthcare providers through structured questionnaires at 15 healthcare facilities selected through stratified sampling. Medical costs included medications, laboratory costs, laboratory and diagnostic tests, and routine health care service costs and direct and indirect societal costs were included. Vaccination program costs from the 2021-2022 influenza season were identified using accounting records and categorized as: planning, distribution, training, social mobilization and outreach, supervision and monitoring, procurement, and national- and facility-level administration and storage.ResultsThe mean costs per episode for SARI and ILI case-patients were $US 823.6 and $US 616.57, respectively. Healthcare service costs were the largest direct expenses for ILI and SARI case-patients. Total costs of the 2021-2022 influenza vaccination program to the government were $US 4,353,738, with the largest costs associated with national- and facility-level administration and storage (30% and 65% respectively). The total cost per dose administered was $US 25.61 ($US 7.73 per dose for procurement and $US 17.88 for the marginal administration cost per dose).ConclusionsThese data on the costs of seasonal influenza prevention programs and the societal costs of influenza illness in Armenia may inform national vaccine policy decisions in Armenia and may be useful for other middle-income countries. Influenza vaccines, like other vaccine programs, are recognized as substantially contributing to the reduction disease burden and associated mortality and further driving economic growth. However, a formal cost-effectiveness analysis should be performed once burden of disease data are available.

Dataset Information

Genomic epidemiology of seasonal influenza circulation in China during prolonged border closure from 2020 to 2021.

Publications

Genomic epidemiology of seasonal influenza circulation in China during prolonged border closure from 2020 to 2021.

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