The impact of climate and antigenic evolution on seasonal influenza virus epidemics in Australia

Competition between transmission lineages mediated by human mobility shapes seasonal influenza epidemics in the US

Due to its climatic variability, complex mobility networks and geographic expanse, the United States represents a compelling setting to explore the transmission processes that lead to heterogeneous yearly seasonal influenza epidemics. By analyzing genomic and epidemiological data collected in the US from 2014 to 2023, we show that epidemics consisted of multiple co-circulating transmission lineages that could emerge from all regions and often rapidly expanded. Lineage spread was characterized by strong spatiotemporal hierarchies and lineage size correlated with timing of establishment in the US. Mechanistic epidemic simulations, supported by phylogeographic analyses, suggest that competition between lineages on a network of human mobility consistent with commuting flows drove lineage dynamics. Our results suggest that the processes that disseminate viruses nationwide are highly structured, but variability in the short-term processes that determine the locations, timing, and explosiveness of initial epidemic sparks limits predictability of regional and national epidemics.

Epidemiological characteristics of RSV in pediatric inpatients with lower respiratory tract infections in Suzhou and their correlation with meteorology and atmospheric pollutants

BACKGROUND

Lower respiratory infections are the leading cause of illness and death in children under 5, primarily due to respiratory syncytial virus(RSV). Climate and pollution influence disease and pathogen prevalence. This study investigates the correlation between meteorological factors, atmospheric pollutants, and RSV infections in children, aiming to implement effective clinical measures and reduce RSV risk in children by enhancing the environment.

METHODS

This study included patients with lower respiratory tract infections who were hospitalized in the Department of Respiratory Medicine at Children's Hospital of Soochow University from January 2006 to December 2019 as the research subjects. This study analyzed detection rates across different ages, genders, and seasons, while also examining the relationship of RSV infection between meteorological factors and atmospheric pollutants. RSV was detected using direct immunofluorescence, and an LS-SVM prediction model with lag nonlinear curves was established in conjunction with meteorological data. In this model, monthly average temperature, atmospheric pollutant levels, and average monthly wind speed were used as predictive variables for construction and prediction. A distributed lag nonlinear model (DLNM) was developed, which included the creation of a lag nonlinear curve by integrating meteorological data.

RESULTS

A total of 19,637 pediatric cases of lower respiratory tract infections were included in this study. The detection rate of RSV over 14 years averaged 14.9% (2934/19637). The male-to-female ratios for positive detection was 1.2:1. The primary detection season for RSV is winter, with a detection rate of 33.7%. The prevalence of RSV was correlated with climatic factors and atmospheric pollution. Utilizing the monthly average temperature, monthly average wind speed, and levels of atmospheric pollutants as the predictive factors in LS-SVM for model construction and prediction, a DLNM identified that the relative risk (RR) of RSV infection fluctuated with changes in the temperature and wind speed.

CONCLUSION

RSV has the highest detection rate in infants and is often detected during winter.The influence of meteorological factors and atmospheric pollutants on RSV infection rates cannot be overlooked, with observation of a lag effect.

Characterization of serum metabolome and respiratory microbiota in children with influenza A virus infection

The risk of children being infected with Influenza A virus (IAV) is high, and if not treated promptly, it can lead to serious illness. Compared with control group, IAV infection decreased the contents of platelet, white blood cell, lymphocyte, eosinophil, basophil, CD3+ T cells, CD4+ T cells, CD8+ T cells, and B cells, while increasing the number of red blood cell. Additionally, IAV infection increased serum concentrations of total protein, albumin and lipase, while decreasing the contents of calcium, triglyceride, total bilirubin, direct bilirubin, indirect bilirubin and gamma-glutamyltransferase. However, the interactions between the respiratory microbiome and metabolites and their impact on IAV in children remains unclear. Ultra performance liquid chromatography quadrupole time of flight mass spectrometry (UPLC-QTOF/MS) and 16S rRNA gene sequencing were employed to analysis the respiratory microbiome and serum metabolic characteristics of 85 patients with IAV infection and age-matched 55 controls with respiratory disease who tested negative for 13 types of respiratory pathogens. The serum metabolic profile of IAV patients was significantly changed, and the purine metabolism was destroyed. Purine metabolism was also enriched in H3N2 patients compared to H1N1, with increased xanthine, deoxyguanosine, and inosine. The respiratory microbiome structure in children with IAV, including H1N1 and H3N2, was significantly different from that of the control, with significantly increased Chao index. The Mantel test revealed the correlation and consistency in the trends of Haemophilus, Ureaplasma and Inosine. This study revealed the characteristics of the respiratory microbiome and serum metabolites in pediatric patients with IAV, providing a new direction for exploring the pathogenesis of IAV in children.

Temperature variability and influenza incidence in China: Effect modification by ambient fine particulate matter

This study aims to examine the association between temperature variabilit (TV) exposure and influenza incidence in China, and the modification effect of PM2.5 levels. Data on daily influenza cases, weather conditions, and PM2.5 concentrations were collected from 339 cities across mainland China from 2014 to 2019. TV was computed as the standard deviation of daily maximum and minimum temperatures for the current day and the previous several days (i.e., TV0-1 to TV0-7). A space-time-stratified case-crossover design with conditional Poisson regression was employed. Overall, each 1 °C increase in TV0-6 was linked to 3.3 % (95 % CI: 3.1 %, 3.5 %) rise in influenza incidence, potentially attributing 14.73 % (95 % CI: 14.08 %, 15.37 %) of cases to this exposure. PM2.5 concentration showed substantial modification effect on the association, such that the relative risk (RR) of influenza incidence grew from 1.027 (95 % CI: 1.025, 1.029) to 1.040 (95 % CI: 1.038, 1.042) as PM2.5 levels increased from 15 to 75 μg/m³ . Females and individuals over 65 years old were more susceptible to TV exposure and the PM2.5 modification. Stronger effects were observed during cold season and in North region. The findings highlight the integrating considerations of TV and PM2.5 exposures into public health measures for influenza prevention and control.

A comparative analysis of influenza and COVID-19: Environmental-ecological impacts, socioeconomic implications, and future challenges

In the last century, global pandemics have been primarily driven by respiratory infections, which consistently rank among the top 20 causes of death worldwide. The coronavirus disease 2019 (COVID-19) pandemic has underscored the intricate nature of managing multiple health crises simultaneously. In recent years, climate change has emerged as a major biosafety and population health challenge. Global warming and extreme weather events have intensified outbreaks of climate-sensitive infectious diseases, especially respiratory diseases. Influenza and COVID-19 have emerged as two of the most significant respiratory pandemics, each with unique epidemic characteristics and far-reaching consequences. Our comparative analysis reveals that while both diseases exhibit high transmission rates, COVID-19's longer incubation period and higher severity have led to more profound and prolonged socioeconomic disruptions than influenza. Both pandemics have highlighted the exacerbating effects of climate change, with extreme weather events intensifying the spread and impact of these diseases. The COVID-19 pandemic exposed vulnerabilities in global healthcare systems and economies on an unprecedented scale, outstripping the strain caused by influenza outbreaks. Importantly, the COVID-19 pandemic has not only reshaped global public health strategies but also significantly impacted the epidemiology of influenza. Despite these differences and associations, both diseases underscore the urgent need for robust pandemic preparedness and adaptable public health strategies. This review delineates the overlaps and distinctions between influenza and COVID-19, offering insights into future challenges and the critical steps needed to enhance healthcare system resilience and improve global responses to pandemics.

Measures of Population Immunity Can Predict the Dominant Clade of Influenza A (H3N2) in the 2017-2018 Season and Reveal Age-Associated Differences in Susceptibility and Antibody-Binding Specificity

BACKGROUND

For antigenically variable pathogens such as influenza, strain fitness is partly determined by the relative availability of hosts susceptible to infection with that strain compared with others. Antibodies to the hemagglutinin (HA) and neuraminidase (NA) confer substantial protection against influenza infection. We asked if a cross-sectional antibody-derived estimate of population susceptibility to different clades of influenza A (H3N2) could predict the success of clades in the following season.

METHODS

We collected sera from 483 healthy individuals aged 1 to 90 years in the summer of 2017 and analyzed neutralizing responses to the HA and NA of representative strains using focus reduction neutralization tests (FNRT) and enzyme-linked lectin assays (ELLA). We estimated relative population-average and age-specific susceptibilities to circulating viral clades and compared those estimates to changes in clade frequencies in the following 2017-2018 season.

RESULTS

The clade to which neutralizing antibody titers were lowest, indicating greater population susceptibility, dominated the next season. Titer correlations between viral strains varied by age, suggesting age-associated differences in epitope targeting driven by shared past exposures. Yet substantial unexplained variation remains within age groups.

CONCLUSIONS

This study indicates how representative measures of population immunity might improve evolutionary forecasts and inform selective pressures on influenza.

Study of the driving factors of the abnormal influenza A (H3N2) epidemic in 2022 and early predictions in Xiamen, China

BACKGROUND

Influenza outbreaks have occurred frequently these years, especially in the summer of 2022 when the number of influenza cases in southern provinces of China increased abnormally. However, the exact evidence of the driving factors involved in the prodrome period is unclear, posing great difficulties for early and accurate prediction in practical work.

METHODS

In order to avoid the serious interference of strict prevention and control measures on the analysis of influenza influencing factors during the COVID-19 epidemic period, only the impact of meteorological and air quality factors on influenza A (H3N2) in Xiamen during the non coronavirus disease 2019 (COVID-19) period (2013/01/01-202/01/24) was analyzed using the distribution lag non-linear model. Phylogenetic analysis of influenza A (H3N2) during 2013-2022 was also performed. Influenza A (H3N2) was predicted through a random forest and long short-term memory (RF-LSTM) model via actual and forecasted meteorological and influenza A (H3N2) values.

RESULTS

Twenty nine thousand four hundred thirty five influenza cases were reported in 2022, accounting for 58.54% of the total cases during 2013-2022. A (H3N2) dominated the 2022 summer epidemic season, accounting for 95.60%. The influenza cases in the summer of 2022 accounted for 83.72% of the year and 49.02% of all influenza reported from 2013 to 2022. Among them, the A (H3N2) cases in the summer of 2022 accounted for 83.90% of all A (H3N2) reported from 2013 to 2022. Daily precipitation(20-50 mm), relative humidity (70-78%), low (≤ 3 h) and high (≥ 7 h) sunshine duration, air temperature (≤ 21 °C) and O3 concentration (≤ 30 µg/m3, > 85 µg/m3) had significant cumulative effects on influenza A (H3N2) during the non-COVID-19 period. The daily values of PRE, RHU, SSD, and TEM in the prodrome period of the abnormal influenza A (H3N2) epidemic (19-22 weeks) in the summer of 2022 were significantly different from the average values of the same period from 2013 to 2019 (P < 0.05). The minimum RHU value was 70.5%, the lowest TEM value was 16.0 °C, and there was no sunlight exposure for 9 consecutive days. The highest O3 concentration reached 164 µg/m3. The range of these factors were consistent with the risk factor range of A (H3N2). The common influenza A (H3N2) variant genotype in 2022 was 3 C.2a1b.2a.1a. It was more accurate to predict influenza A (H3N2) with meteorological forecast values than with actual values only.

CONCLUSION

The extreme weather conditions of sustained low temperature and wet rain may have been important driving factors for the abnormal influenza A (H3N2) epidemic. A low vaccination rate, new mutated strains, and insufficient immune barriers formed by natural infections may have exacerbated this epidemic. Meteorological forecast values can aid in the early prediction of influenza outbreaks. This study can help relevant departments prepare for influenza outbreaks during extreme weather, provide a scientific basis for prevention strategies and risk warnings, better adapt to climate change, and improve public health.

Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States

Influenza viruses continually evolve new antigenic variants, through mutations in epitopes of their major surface proteins, hemagglutinin (HA) and neuraminidase (NA). Antigenic drift potentiates the reinfection of previously infected individuals, but the contribution of this process to variability in annual epidemics is not well understood. Here, we link influenza A(H3N2) virus evolution to regional epidemic dynamics in the United States during 1997-2019. We integrate phenotypic measures of HA antigenic drift and sequence-based measures of HA and NA fitness to infer antigenic and genetic distances between viruses circulating in successive seasons. We estimate the magnitude, severity, timing, transmission rate, age-specific patterns, and subtype dominance of each regional outbreak and find that genetic distance based on broad sets of epitope sites is the strongest evolutionary predictor of A(H3N2) virus epidemiology. Increased HA and NA epitope distance between seasons correlates with larger, more intense epidemics, higher transmission, greater A(H3N2) subtype dominance, and a greater proportion of cases in adults relative to children, consistent with increased population susceptibility. Based on random forest models, A(H1N1) incidence impacts A(H3N2) epidemics to a greater extent than viral evolution, suggesting that subtype interference is a major driver of influenza A virus infection ynamics, presumably via heterosubtypic cross-immunity.

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

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.

Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States

Influenza viruses continually evolve new antigenic variants, through mutations in epitopes of their major surface proteins, hemagglutinin (HA) and neuraminidase (NA). Antigenic drift potentiates the reinfection of previously infected individuals, but the contribution of this process to variability in annual epidemics is not well understood. Here we link influenza A(H3N2) virus evolution to regional epidemic dynamics in the United States during 1997-2019. We integrate phenotypic measures of HA antigenic drift and sequence-based measures of HA and NA fitness to infer antigenic and genetic distances between viruses circulating in successive seasons. We estimate the magnitude, severity, timing, transmission rate, age-specific patterns, and subtype dominance of each regional outbreak and find that genetic distance based on broad sets of epitope sites is the strongest evolutionary predictor of A(H3N2) virus epidemiology. Increased HA and NA epitope distance between seasons correlates with larger, more intense epidemics, higher transmission, greater A(H3N2) subtype dominance, and a greater proportion of cases in adults relative to children, consistent with increased population susceptibility. Based on random forest models, A(H1N1) incidence impacts A(H3N2) epidemics to a greater extent than viral evolution, suggesting that subtype interference is a major driver of influenza A virus infection dynamics, presumably via heterosubtypic cross-immunity.

Ozone as an environmental driver of influenza

Under long-standing threat of seasonal influenza outbreaks, it remains imperative to understand the drivers of influenza dynamics which can guide mitigation measures. While the role of absolute humidity and temperature is extensively studied, the possibility of ambient ozone (O3) as an environmental driver of influenza has received scant attention. Here, using state-level data in the USA during 2010-2015, we examined such research hypothesis. For rigorous causal inference by evidence triangulation, we applied 3 distinct methods for data analysis: Convergent Cross Mapping from state-space reconstruction theory, Peter-Clark-momentary-conditional-independence plus as graphical modeling algorithms, and regression-based Generalised Linear Model. The negative impact of ambient O3 on influenza activity at 1-week lag is consistently demonstrated by those 3 methods. With O3 commonly known as air pollutant, the novel findings here on the inhibition effect of O3 on influenza activity warrant further investigations to inform environmental management and public health protection.

Intensity and drivers of subtypes interference between seasonal influenza viruses in mainland China: A modeling study

Subtype interference has a significant impact on the epidemiological patterns of seasonal influenza viruses (SIVs). We used attributable risk percent [the absolute value of the ratio of the effective reproduction number (Rₑ) of different subtypes minus one] to quantify interference intensity between A/H1N1 and A/H3N2, as well as B/Victoria and B/Yamagata. The interference intensity between A/H1N1 and A/H3N2 was higher in southern China 0.26 (IQR: 0.11-0.46) than in northern China 0.17 (IQR: 0.07-0.24). Similarly, interference intensity between B/Victoria and B/Yamagata was also higher in southern China 0.14 (IQR: 0.07-0.24) than in norther China 0.10 (IQR: 0.04-0.18). High relative humidity significantly increased subtype interference, with the highest relative risk reaching 20.59 (95% CI: 6.12-69.33) in southern China. Southern China exhibited higher levels of subtype interference, particularly between A/H1N1 and A/H3N2. Higher relative humidity has a more pronounced promoting effect on subtype interference.

Determinants of epidemic size and the impacts of lulls in seasonal influenza virus circulation

During the COVID-19 pandemic, levels of seasonal influenza virus circulation were unprecedentedly low, leading to concerns that a lack of exposure to influenza viruses, combined with waning antibody titres, could result in larger and/or more severe post-pandemic seasonal influenza epidemics. However, in most countries the first post-pandemic influenza season was not unusually large and/or severe. Here, based on an analysis of historical influenza virus epidemic patterns from 2002 to 2019, we show that historic lulls in influenza virus circulation had relatively minor impacts on subsequent epidemic size and that epidemic size was more substantially impacted by season-specific effects unrelated to the magnitude of circulation in prior seasons. From measurements of antibody levels from serum samples collected each year from 2017 to 2021, we show that the rate of waning of antibody titres against influenza virus during the pandemic was smaller than assumed in predictive models. Taken together, these results partially explain why the re-emergence of seasonal influenza virus epidemics was less dramatic than anticipated and suggest that influenza virus epidemic dynamics are not currently amenable to multi-season prediction.

The impact of anthropogenic climate change on pediatric viral diseases

The adverse effects of climate change on human health are unfolding in real time. Environmental fragmentation is amplifying spillover of viruses from wildlife to humans. Increasing temperatures are expanding mosquito and tick habitats, introducing vector-borne viruses into immunologically susceptible populations. More frequent flooding is spreading water-borne viral pathogens, while prolonged droughts reduce regional capacity to prevent and respond to disease outbreaks with adequate water, sanitation, and hygiene resources. Worsening air quality and altered transmission seasons due to an increasingly volatile climate may exacerbate the impacts of respiratory viruses. Furthermore, both extreme weather events and long-term climate variation are causing the destruction of health systems and large-scale migrations, reshaping health care delivery in the face of an evolving global burden of viral disease. Because of their immunological immaturity, differences in physiology (e.g., size), dependence on caregivers, and behavioral traits, children are particularly vulnerable to climate change. This investigation into the unique pediatric viral threats posed by an increasingly inhospitable world elucidates potential avenues of targeted programming and uncovers future research questions to effect equitable, actionable change. IMPACT: A review of the effects of climate change on viral threats to pediatric health, including zoonotic, vector-borne, water-borne, and respiratory viruses, as well as distal threats related to climate-induced migration and health systems. A unique focus on viruses offers a more in-depth look at the effect of climate change on vector competence, viral particle survival, co-morbidities, and host behavior. An examination of children as a particularly vulnerable population provokes programming tailored to their unique set of vulnerabilities and encourages reflection on equitable climate adaptation frameworks.

The diverse roles of peroxisomes in the interplay between viruses and mammalian cells

Peroxisomes are ubiquitous organelles found in eukaryotic cells that play a critical role in the oxidative metabolism of lipids and detoxification of reactive oxygen species (ROS). Recently, the role of peroxisomes in viral infections has been extensively studied. Although several studies have reported that peroxisomes exert antiviral activity, evidence indicates that viruses have also evolved diverse strategies to evade peroxisomal antiviral signals. In this review, we summarize the multiple roles of peroxisomes in the interplay between viruses and mammalian cells. Focus is given on the peroxisomal regulation of innate immune response, lipid metabolism, ROS production, and viral regulation of peroxisomal biosynthesis and degradation. Understanding the interactions between peroxisomes and viruses provides novel insights for the development of new antiviral strategies.

Linking health to geology-a new assessment and zoning model based on the frame of medical geology

With the growing concerns about the Earth's environment and human health, there has been a surge in research focused on the intersection of health and geology. This study quantitatively assesses the relationship between human health and geological factors using a new framework. The framework considers four key geological environment indicators related to health: soil, water, geological landform, and atmosphere. Results indicate that the atmospheric and water resource indicators in the study area were generally favorable, while the scores of geological landforms varied based on topography. The study also found that the selenium content in the soil greatly exceeded the local background value. Our research underscores the importance of geological factors on human health, establishes a new health-geological assessment model, and provides a scientific foundation for local spatial planning, water resource development, and land resource management. However, due to varying geological conditions worldwide, the framework and indicators for health geology may need to be adjusted accordingly.

Viral respiratory infections in a rapidly changing climate: the need to prepare for the next pandemic

Viral respiratory infections (VRIs) cause seasonal epidemics and pandemics, with their transmission influenced by climate conditions. Despite the risks posed by novel VRIs, the relationships between climate change and VRIs remain poorly understood. In this review, we synthesized existing literature to explore the connections between changes in meteorological conditions, extreme weather events, long-term climate warming, and seasonal outbreaks, epidemics, and pandemics of VRIs from an interdisciplinary perspective. We proposed a comprehensive conceptual framework highlighting the potential biological, socioeconomic, and ecological mechanisms underlying the impact of climate change on VRIs. Our findings suggested that climate change increases the risk of VRI emergence and transmission by affecting the biology of viruses, host susceptibility, human behavior, and environmental conditions of both society and ecosystems. Further interdisciplinary research is needed to address the dual challenge of climate change and pandemics.

Mechanisms for the circulation of influenza A(H3N2) in China: A spatiotemporal modelling study

Circulation of seasonal influenza is the product of complex interplay among multiple drivers, yet characterizing the underlying mechanism remains challenging. Leveraging the diverse seasonality of A(H3N2) virus and abundant climatic space across regions in China, we quantitatively investigated the relative importance of population susceptibility, climatic factors, and antigenic change on the dynamics of influenza A(H3N2) through an integrative modelling framework. Specifically, an absolute humidity driven multiscale transmission model was constructed for the 2013/2014, 2014/2015 and 2016/2017 influenza seasons that were dominated by influenza A(H3N2). We revealed the variable impact of absolute humidity on influenza transmission and differences in the occurring timing and magnitude of antigenic change for those three seasons. Overall, the initial population susceptibility, climatic factors, and antigenic change explained nearly 55% of variations in the dynamics of influenza A(H3N2). Specifically, the additional variation explained by the initial population susceptibility, climatic factors, and antigenic change were at 33%, 26%, and 48%, respectively. The vaccination program alone failed to fully eliminate the summer epidemics of influenza A(H3N2) and non-pharmacological interventions were needed to suppress the summer circulation. The quantitative understanding of the interplay among driving factors on the circulation of influenza A(H3N2) highlights the importance of simultaneous monitoring of fluctuations for related factors, which is crucial for precise and targeted prevention and control of seasonal influenza.

The Impact of Urbanization and Human Mobility on Seasonal Influenza in Northern China

The intensity of influenza epidemics varies significantly from year to year among regions with similar climatic conditions and populations. However, the underlying mechanisms of the temporal and spatial variations remain unclear. We investigated the impact of urbanization and public transportation size on influenza activity. We used 6-year weekly provincial-level surveillance data of influenza-like disease incidence (ILI) and viral activity in northern China. We derived the transmission potential of influenza for each epidemic season using the susceptible-exposed-infectious-removed-susceptible (SEIRS) model and estimated the transmissibility in the peak period via the instantaneous reproduction number (R_t). Public transport was found to explain approximately 28% of the variance in the seasonal transmission potential. Urbanization and public transportation size explained approximately 10% and 21% of the variance in maximum R_t in the peak period, respectively. For the mean R_t during the peak period, urbanization and public transportation accounted for 9% and 16% of the variance in R_t, respectively. Our results indicated that the differences in the intensity of influenza epidemics among the northern provinces of China were partially driven by urbanization and public transport size. These findings are beneficial for predicting influenza intensity and developing preparedness strategies for the early stages of epidemics.

Potential impacts of prolonged absence of influenza virus circulation on subsequent epidemics

Background

During the first two years of the COVID-19 pandemic, the circulation of seasonal influenza viruses was unprecedentedly low. This led to concerns that the lack of immune stimulation to influenza viruses combined with waning antibody titres could lead to increased susceptibility to influenza in subsequent seasons, resulting in larger and more severe epidemics.

Methods

We analyzed historical influenza virus epidemiological data from 2003-2019 to assess the historical frequency of near-absence of seasonal influenza virus circulation and its impact on the size and severity of subsequent epidemics. Additionally, we measured haemagglutination inhibition-based antibody titres against seasonal influenza viruses using longitudinal serum samples from 165 healthy adults, collected before and during the COVID-19 pandemic, and estimated how antibody titres against seasonal influenza waned during the first two years of the pandemic.

Findings

Low country-level prevalence of influenza virus (sub)types over one or more years occurred frequently before the COVID-19 pandemic and had relatively small impacts on subsequent epidemic size and severity. Additionally, antibody titres against seasonal influenza viruses waned negligibly during the first two years of the pandemic.

Interpretation

The commonly held notion that lulls in influenza virus circulation, as observed during the COVID-19 pandemic, will lead to larger and/or more severe subsequent epidemics might not be fully warranted, and it is likely that post-lull seasons will be similar in size and severity to pre-lull seasons.

Funding

European Research Council, Netherlands Organization for Scientific Research, Royal Dutch Academy of Sciences, Public Health Service of Amsterdam.

Research in context

Evidence before this study: During the first years of the COVID-19 pandemic, the incidence of seasonal influenza was unusually low, leading to widespread concerns of exceptionally large and/or severe influenza epidemics in the coming years. We searched PubMed and Google Scholar using a combination of search terms (i.e., "seasonal influenza", "SARS-CoV-2", "COVID-19", "low incidence", "waning rates", "immune protection") and critically considered published articles and preprints that studied or reviewed the low incidence of seasonal influenza viruses since the start of the COVID-19 pandemic and its potential impact on future seasonal influenza epidemics. We found a substantial body of work describing how influenza virus circulation was reduced during the COVID-19 pandemic, and a number of studies projecting the size of future epidemics, each positing that post-pandemic epidemics are likely to be larger than those observed pre-pandemic. However, it remains unclear to what extent the assumed relationship between accumulated susceptibility and subsequent epidemic size holds, and it remains unknown to what extent antibody levels have waned during the COVID-19 pandemic. Both are potentially crucial for accurate prediction of post-pandemic epidemic sizes.Added value of this study: We find that the relationship between epidemic size and severity and the magnitude of circulation in the preceding season(s) is decidedly more complex than assumed, with the magnitude of influenza circulation in preceding seasons having only limited effects on subsequent epidemic size and severity. Rather, epidemic size and severity are dominated by season-specific effects unrelated to the magnitude of circulation in the preceding season(s). Similarly, we find that antibody levels waned only modestly during the COVID-19 pandemic.Implications of all the available evidence: The lack of changes observed in the patterns of measured antibody titres against seasonal influenza viruses in adults and nearly two decades of epidemiological data suggest that post-pandemic epidemic sizes will likely be similar to those observed pre-pandemic, and challenge the commonly held notion that the widespread concern that the near-absence of seasonal influenza virus circulation during the COVID-19 pandemic, or potential future lulls, are likely to result in larger influenza epidemics in subsequent years.

System Complexity in Influenza Infection and Vaccination: Effects upon Excess Winter Mortality

Unexpected outcomes are usually associated with interventions in complex systems. Excess winter mortality (EWM) is a measure of the net effect of all competing forces operating each winter, including influenza(s) and non-influenza pathogens. In this study over 2400 data points from 97 countries are used to look at the net effect of influenza vaccination rates in the elderly aged 65+ against excess winter mortality (EWM) each year from the winter of 1980/81 through to 2019/20. The observed international net effect of influenza vaccination ranges from a 7.8% reduction in EWM estimated at 100% elderly vaccination for the winter of 1989/90 down to a 9.3% increase in EWM for the winter of 2018/19. The average was only a 0.3% reduction in EWM for a 100% vaccinated elderly population. Such outcomes do not contradict the known protective effect of influenza vaccination against influenza mortality per se—they merely indicate that multiple complex interactions lie behind the observed net effect against all-causes (including all pathogen causes) of winter mortality. This range from net benefit to net disbenefit is proposed to arise from system complexity which includes environmental conditions (weather, solar cycles), the antigenic distance between constantly emerging circulating influenza clades and the influenza vaccine makeup, vaccination timing, pathogen interference, and human immune diversity (including individual history of host-virus, host-antigen interactions and immunosenescence) all interacting to give the observed outcomes each year. We propose that a narrow focus on influenza vaccine effectiveness misses the far wider complexity of winter mortality. Influenza vaccines may need to be formulated in different ways, and perhaps administered over a shorter timeframe to avoid the unanticipated adverse net outcomes seen in around 40% of years.

Fine-scale heterogeneity in population density predicts wave dynamics in dengue epidemics

The spread of dengue and other arboviruses constitutes an expanding global health threat. The extensive heterogeneity in population distribution and potential complexity of movement in megacities of low and middle-income countries challenges predictive modeling, even as its importance to disease spread is clearer than ever. Using surveillance data at fine resolution from Rio de Janeiro, we document a scale-invariant pattern in the size of successive epidemics following DENV4 emergence. Using surveillance data at fine resolution following the emergence of the DENV4 dengue serotype in Rio de Janeiro, we document a pattern in the size of successive epidemics that is invariant to the scale of spatial aggregation. This pattern emerges from the combined effect of herd immunity and seasonal transmission, and is strongly driven by variation in population density at sub-kilometer scales. It is apparent only when the landscape is stratified by population density and not by spatial proximity as has been common practice. Models that exploit this emergent simplicity should afford improved predictions of the local size of successive epidemic waves.

Mixed-charge modification as a robust method to realize the antiviral ability of gold nanoparticles in a high protein environment

Pandemics caused by viruses have resulted in incalculable losses to human beings, which are exacerbated due to the lack of antiviral drugs. Sulfonic group modified nanomedicine has been proved to possess a broad-spectrum antiviral ability. However, it is very challenging to maintain the antiviral activity in a high protein environment in vivo. To improve the tolerance to the complex biological environment, sulfonic mixed-charge modified gold nanoparticles (MC_AuNPs) were prepared in this research by introducing positively charged ligands into sulfonic ligand modified gold nanoparticles. The MC_AuNPs showed excellent non-fouling ability while retaining comparable antiviral ability to single sulfonic ligand modified gold nanoparticles (MDS_AuNPs). The MC_AuNPs maintained their antiviral ability in 10 mg mL^-1 protein solutions, but the MDS_AuNPs completely lost their antiviral capability in 1 mg mL^-1 protein medium. The mixed-charge modification strategy provides a practical avenue to maintain the antiviral capability of HSPG mimicking nanoparticles in high protein environments.

Human Influenza Epidemiology

Influenza virus infections are common in people of all ages. Epidemics occur in the winter months in temperate locations and at varying times of the year in subtropical and tropical locations. Most influenza virus infections cause mild and self-limiting disease, and around one-half of all infections occur with a fever. Only a small minority of infections lead to serious disease requiring hospitalization. During epidemics, the rates of influenza virus infections are typically highest in school-age children. The clinical severity of infections tends to increase at the extremes of age and with the presence of underlying medical conditions, and impact of epidemics is greatest in these groups. Vaccination is the most effective measure to prevent infections, and in recent years influenza vaccines have become the most frequently used vaccines in the world. Nonpharmaceutical public health measures can also be effective in reducing transmission, allowing suppression or mitigation of influenza epidemics and pandemics.

Innate Immune Responses to Influenza Virus Infections in the Upper Respiratory Tract

The innate immune system is the host's first line of immune defence against any invading pathogen. To establish an infection in a human host the influenza virus must replicate in epithelial cells of the upper respiratory tract. However, there are several innate immune mechanisms in place to stop the virus from reaching epithelial cells. In addition to limiting viral replication and dissemination, the innate immune system also activates the adaptive immune system leading to viral clearance, enabling the respiratory system to return to normal homeostasis. However, an overzealous innate immune system or adaptive immune response can be associated with immunopathology and aid secondary bacterial infections of the lower respiratory tract leading to pneumonia. In this review, we discuss the mechanisms utilised by the innate immune system to limit influenza virus replication and the damage caused by influenza viruses on the respiratory tissues and how these very same protective immune responses can cause immunopathology.