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Commuting-driven competition between transmission chains shapes seasonal influenza virus epidemics in the United States.

ABSTRACT: Despite intensive study, much remains unknown about the dynamics of seasonal influenza virus epidemic establishment and spread in the United States (US) each season. By reconstructing transmission lineages from seasonal influenza virus genomes collected in the US from 2014 to 2023, we show that most epidemics consisted of multiple distinct transmission lineages. Spread of these lineages exhibited strong spatiotemporal hierarchies and lineage size was correlated with timing of lineage establishment in the US. Mechanistic epidemic simulations suggest that mobility-driven competition between lineages determined the extent of individual lineages' geographical spread. Based on phylogeographic analyses and epidemic simulations, lineage-specific movement patterns were dominated by human commuting behavior. These results suggest that given the locations of early-season epidemic sparks, the topology of inter-state human mobility yields repeatable patterns of which influenza viruses will circulate where, but the importance of short-term processes limits predictability of regional and national epidemics.

SUBMITTER: de Jong SPJ

PROVIDER: S-EPMC11326338 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature

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Commuting-driven competition between transmission chains shapes seasonal influenza virus epidemics in the United States.

de Jong Simon P J SPJ Conlan Andrew A Han Alvin X AX Russell Colin A CA

medRxiv : the preprint server for health sciences 20240809

Despite intensive study, much remains unknown about the dynamics of seasonal influenza virus epidemic establishment and spread in the United States (US) each season. By reconstructing transmission lineages from seasonal influenza virus genomes collected in the US from 2014 to 2023, we show that most epidemics consisted of multiple distinct transmission lineages. Spread of these lineages exhibited strong spatiotemporal hierarchies and lineage size was correlated with timing of lineage establishme ...[more]

PMID: 39148829

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Project description:To analyze absenteeism among healthcare workers (HCWs) at a large Italian hospital and to estimate the increase in absenteeism that occurred during seasonal flu periods.Retrospective observational study.The absenteeism data were divided into three "epidemic periods," starting at week 42 of one year and terminating at week 17 of the following year (2010-2011, 2011-2012, 2012-2013), and three "non-epidemic periods," defined as week 18 to week 41 and used as baseline data. The excess of the absenteeism occurring among HCWs during periods of epidemic influenza in comparison with baseline was estimated. All data, obtained from Hospital's databases, were collected for each of the following six job categories: medical doctors, technical executives (i.e., pharmacists), nurses and allied health professionals (i.e., radiographers), other executives (i.e., engineers), nonmedical support staff, and administrative staff. The HCWs were classified by: in and no-contact; vaccinated and unvaccinated.5,544, 5,369, and 5,291 workers in three years were studied. The average duration of absenteeism during the epidemic periods increased among all employees by +2.07 days/person (from 2.99 to 5.06), and the relative increase ranged from 64-94% among the different job categories. Workers not in contact with patients experienced a slightly greater increase in absenteeism (+2.28 days/person, from 2.73 to 5.01) than did employees in contact with patients (+2.04, from 3.04 to 5.08). The vaccination rate among HCWs was below 3%, however the higher excess of absenteeism rate among unvaccinated in comparison with vaccinated workers was observed during the epidemic periods (2.09 vs 1.45 days/person).The influenza-related absenteeism during epidemic periods was quantified as totaling more than 11,000 days/year at the Italian hospital studied. This result confirms the economic impact of sick leave on healthcare systems and stresses on the necessity of encouraging HCWs to be immunized against influenza.

Project description:Protective antibody immunity against the influenza A virus wanes in 2-7 years due to antigenic drift of the virus' surface proteins. The duration of immune protection is highly variable because antigenic evolution of the virus is irregular. Currently, the variable nature of the duration of immunity has had little attention in analyses of the impact of vaccination, including cost-effectiveness studies.We developed a range of mathematical transmission models to investigate the effect of variable duration of immunity on the size of seasonal epidemics. The models range from simple conceptual to more realistic, by distinguishing between infection- versus vaccination-induced immunity, by inclusion of primary vaccine failure, by assuming a leaky vaccine, and by the inclusion of age-dependent contact patterns.We show that annual variation in the duration of immunity causes large variation in the size of epidemics, and affects the effectiveness of vaccination. Accumulation of susceptible individuals in one or more mild seasons results in a disproportionately large outbreak in a subsequent season. Importantly, variation in the duration of immunity increases the average infection attack rate when the vaccination coverage is around the outbreak threshold. Specifically, in a tailored age-stratified model with a realistic reproduction number (R 0 = 1.4) and vaccination coverage of 25%, we find that the attack rate in unvaccinated children (<10 years old) is negligible if the duration of immunity is constant, while on average 2.8% (2.5-97.5% percentiles: 1.8-4.1%) of the children are infected if the duration of immunity is variable. These findings stem from the buildup of susceptibility over multiple seasons by waning of immunity, and the nonlinear relation between susceptibility and infection attack rates.The models illustrate that variation in the duration of immunity impacts the long-term effectiveness of vaccination, and that vaccine effectiveness cannot be judged for each year in isolation. Our findings have implications for vaccination strategies that aim to maximize the vaccination coverage while extending the age range of persons eligible for vaccination.

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Commuting-driven competition between transmission chains shapes seasonal influenza virus epidemics in the United States.

Publications

Commuting-driven competition between transmission chains shapes seasonal influenza virus epidemics in the United States.

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