Characterizing the transmission patterns of seasonal influenza in Italy: lessons from the last decade

Background Despite thousands of influenza cases annually recorded by surveillance systems around the globe, estimating the transmission patterns of seasonal influenza is challenging. Methods We develop an age-structured mathematical model to influenza transmission to analyze ten consecutive seasons (from 2010 to 2011 to 2019–2020) of influenza epidemiological and virological data reported to the Italian surveillance system. Results We estimate that 18.4–29.3% of influenza infections are detected by the surveillance system. Influenza infection attack rate varied between 12.7 and 30.5% and is generally larger for seasons characterized by the circulation of A/H3N2 and/or B types/subtypes. Individuals aged 14 years or less are the most affected age-segment of the population, with A viruses especially affecting children aged 0–4 years. For all influenza types/subtypes, the mean effective reproduction number is estimated to be generally in the range 1.09–1.33 (9 out of 10 seasons) and never exceeding 1.41. The age-specific susceptibility to infection appears to be a type/subtype-specific feature. Conclusions The results presented in this study provide insights on type/subtype-specific transmission patterns of seasonal influenza that could be instrumental to fine-tune immunization strategies and non-pharmaceutical interventions aimed at limiting seasonal influenza spread and burden.

The Effectiveness of Governmental Nonpharmaceutical Interventions Against COVID-19 On The Control of Seasonal Influenza Transmission: An Ecological Study

Background: A range of strict nonpharmaceutical interventions (NPIs) had been implemented in many countries to combat the COVID-19 pandemic. These NPIs might also be effective in controlling the seasonal influenza virus, which share the same transmission path with SARS-CoV-2. The aim of this study is to evaluate the effect of different NPIs for control of seasonal influenza.Methods: Data on 14 NPIs implemented in 33 countries and corresponding data on influenza virologic surveillance were collected. The influenza suppression index was calculated as the difference between the influenza-positive rate during its decline period from 2019 to 2020 and that during influenza epidemic seasons in the previous 9 years. A machine learning model was developed by using extreme gradient boosting tree (XGBoost) regressor to fit NPI data and influenza suppression index. SHapley Additive exPlanations (SHAP) was used to characterize NPIs in suppressing influenza.Results: Gathering limitation contributed the most (37.60%) among all NPIs in suppressing influenza transmission in the 2019-2020 influenza season. The top three effective NPIs were gathering limitation, international travel restriction, and school closure. Regarding the three NPIs, their intensity threshold to generate effect were restrictions on the size of gatherings less than 1000 people, travel bans on all regions or total border closure, and closing only some categories of schools, respectively. There was a strong positive interaction effect between mask wearing requirement and gathering limitation, whereas merely implementing mask wearing requirement but ignoring other NPIs would dilute mask wearing requirement’s effectiveness in suppressing influenza.Conclusions: Gathering limitation, travel bans on all regions or total border closure, and closing some levels of schools are the most effective NPIs to suppress influenza transmission. Mask wearing requirement is advised to be combined with gathering limitation and other NPIs. Our findings could facilitate the precise control of future influenza epidemics and potential pandemics.

Frequency and patterns of exposure to live poultry and the potential risk of avian influenza transmission to humans in urban Bangladesh

Avian influenza is endemic in Bangladesh, where greater than 90% of poultry are marketed through live poultry markets (LPMs). We conducted a population-based cross-sectional mobile telephone survey in urban Dhaka, Bangladesh to investigate the frequency and patterns of human exposure to live poultry in LPMs and at home. Among 1047 urban residents surveyed, 74.2% (95% CI 70.9–77.2) reported exposure to live poultry in the past year, with the majority of exposure occurring on a weekly basis. While visiting LPMs was less common amongst females (40.3%, 95% CI 35.0–45.8) than males (58.9%, 95% CI 54.0–63.5), females reported greater poultry exposure through food preparation, including defeathering (13.2%, 95% CI 9.5–17.9) and eviscerating (14.8%, 95% CI 11.2–19.4) (p < 0.001). A large proportion of the urban population is frequently exposed to live poultry in a setting where avian influenza viruses are endemic in LPMs. There is thus not only ample opportunity for spillover of avian influenza infections into humans in Dhaka, Bangladesh, but also greater potential for viral reassortment which could generate novel strains with pandemic potential.

Increased urbanization reduced the effectiveness of school closures on seasonal influenza epidemics in China

Background School closure is a common mitigation strategy during severe influenza epidemics and pandemics. However, the effectiveness of this strategy remains controversial. In this study, we aimed to explore the effectiveness of school closure on seasonal influenza epidemics in provincial-level administrative divisions (PLADs) with varying urbanization rates in China. Methods This study analyzed influenza surveillance data between 2010 and 2019 provided by the Chinese National Influenza Center. Taking into consideration the climate, this study included a region with 3 adjacent PLADs in Northern China and another region with 4 adjacent PLADs in Southern China. The effect of school closure on influenza transmission was evaluated by the reduction of the effective reproductive number of seasonal influenza during school winter breaks compared with that before school winter breaks. An age-structured Susceptible-Infected-Recovered-Susceptible (SIRS) model was built to model influenza transmission in different levels of urbanization. Parameters were determined using the surveillance data via robust Bayesian method. Results Between 2010 and 2019, in the less urbanized provinces: Hebei, Zhejiang, Jiangsu and Anhui, during school winter breaks, the effective reproductive number of seasonal influenza epidemics reduced 14.6% [95% confidential interval (CI): 6.2–22.9%], 9.6% (95% CI: 2.5–16.6%), 7.3% (95% CI: 0.1–14.4%) and 8.2% (95% CI: 1.1–15.3%) respectively. However, in the highly urbanized cities: Beijing, Tianjin and Shanghai, it reduced only 5.2% (95% CI: -0.7–11.2%), 4.1% (95% CI: -0.9–9.1%) and 3.9% (95% CI: -1.6–9.4%) respectively. In China, urbanization is associated with decreased proportion of children and increased social contact. According to the SIRS model, both factors could reduce the impact of school closure on seasonal influenza epidemics, and the proportion of children in the population is thought to be the dominant influencing factor. Conclusions Effectiveness of school closure on the epidemics varies with the age structure in the population and social contact patterns. School closure should be recommended in the low urbanized regions in China in the influenza seasons. Graphical abstract

Avian influenza transmission risk along live poultry trading networks in Bangladesh

Live animal markets are known hotspots of zoonotic disease emergence. To mitigate those risks, we need to understand how networks shaped by trading practices influence disease spread. Yet, those practices are rarely recorded in high-risk settings. Through a large cross-sectional study, we assessed the potential impact of live poultry trading networks’ structures on avian influenza transmission dynamics in Bangladesh. Networks promoted mixing between chickens sourced from different farming systems and geographical locations, fostering co-circulation of viral strains of diverse origins in markets. Viral transmission models suggested that the observed rise in viral prevalence from farms to markets was unlikely explained by intra-market transmission alone, but substantially influenced by transmission occurring in upstream network nodes. Disease control interventions should therefore alter the entire network structures. However, as networks differed between chicken types and city supplied, standardised interventions are unlikely to be effective, and should be tailored to local structural characteristics.

Non-respiratory particles emitted by guinea pigs in airborne disease transmission experiments

Animal models are often used to assess the airborne transmissibility of various pathogens, which are typically assumed to be carried by expiratory droplets emitted directly from the respiratory tract of the infected animal. We recently established that influenza virus is also transmissible via “aerosolized fomites,” micron-scale dust particulates released from virus-contaminated surfaces (Asadi et al. in Nat Commun 11(1):4062, 2020). Here we expand on this observation, by counting and characterizing the particles emitted from guinea pig cages using an Aerodynamic Particle Sizer (APS) and an Interferometric Mie Imaging (IMI) system. Of over 9000 airborne particles emitted from guinea pig cages and directly imaged with IMI, none had an interference pattern indicative of a liquid droplet. Separate measurements of the particle count using the APS indicate that particle concentrations spike upwards immediately following animal motion, then decay exponentially with a time constant commensurate with the air exchange rate in the cage. Taken together, the results presented here raise the possibility that a non-negligible fraction of airborne influenza transmission events between guinea pigs occurs via aerosolized fomites rather than respiratory droplets, though the relative frequencies of these two routes have yet to be definitively determined.

VAKSIN FLU BURUNG DI MANUSIA SEBAGAI UPAYA ALTERNATIF PENCEGAHAN TERHADAP RE-EMERGING VIRUS H5N1

A total of 182 human cases of avian influenza have been reported in Indonesia in the period 2004-2011, with a case fatality rate (CFR) among them of 86%. Various risk factors for avian influenza transmission have also been identified, including a high population, having many types of poultry (broiler, layer, village chickens, etc), traditional poultry systems that promote close human relationships, and the presence of several areas in Indonesia which are strategic locations as a place to rest and meet various wild birds. Vaccination is one of the efforts to prevent the re-emergence of H5N1 avian influenza transmission. However, the avian influenza vaccine for the public is not yet available in Indonesia. The purpose of this review article is to examine the avian influenza vaccine in humans as a preventive measure against the re-emergence of avian influenza in Indonesia, and to determine the progress of developing avian influenza vaccines. The results of the review show that several avian influenza vaccine candidates have been approved by WHO, one of which is a vaccine candidate using an isolated virus from Indonesia. This information on the development of avian influenza vaccines for humans is useful and can be used as an avian influenza pre-pandemic preparedness in Indonesia. Abstrak Sebanyak 182 kasus flu burung pada manusia telah dilaporkan di Indonesia pada periode tahun 2004-2011, dengan case fatality rate (CFR) sebesar 86%. Berbagai faktor risiko penularan flu burung juga telah diidentifikasi, antara lain jumlah penduduk yang tinggi, memiliki banyak jenis unggas (ayam broiler, layer, kampong, dsb), sistem perunggasan tradisional yang membuat kedekatan hubungan antara manusia, dan adanya beberpa wilayah di Indonesia yang menjadi lokasi strategis sebagai tempat istirahat dan bertemunya berbagai unggas liar. Vaksinasi merupakan salah satu upaya untuk mencegah munculnya kembali penularan flu burung H5N1. Namun demikian, vaksin flu burung untuk masyarakat belum tersedia hingga saat ini. Tujuan dari review artikel ini adalah untuk mengkaji vaksin flu burung pada manusia sebagai tindakan pencegahan terhadap kemunculan kembali flu burung di Indonesia, dan untuk mengetahui kemajuan pengembangan vaksin flu burung. Hasil review menunjukkan beberapa kandidat vaksin flu burung telah disetujui oleh WHO, salah satunya adalah kandidat vaksin menggunakan isolat virus asal Indonesia. Informasi perkembangan vaksin flu burung bagi manusia ini bermanfaat dan dapat digunakan sebagai kesiapsiagaan prepandemi flu burung di Indonesia.

Masks in a Post COVID-19 World: A Better Alternative to Curtailing Influenza?

Over the course of the coronavirus pandemic, it has become apparent that non-pharmaceutical interventions such as masks and social distancing are of great help in mitigating the transmission of airborne infectious diseases. Additionally, data from respiratory specimen analysis from the past year show that current mask mandates established for COVID-19 have inadvertently reduced the rates of other respiratory diseases, including influenza. Thus, the question arises as to whether comparatively mild measures should be kept in place after the pandemic to reduce the impact of influenza. In this study, we employed a series of differential equations to simulate past influenza seasons, assuming people wore face masks. This was achieved by introducing a variable to account for the efficacy and prevalence of masks and then analyzing its impact on influenza transmission rate in an SEIR model fit to the actual past seasons. We then compared influenza rates in this hypothetical scenario with the actual rates over the seasons. Our results show that several combinations of mask efficacy and prevalence can significantly reduce the burden of seasonal influenza. Particularly, our simulations suggest that a minority of individuals wearing masks greatly reduce the number of influenza infections. Considering the efficacy rates of masks and the relatively insignificant monetary cost, we highlight that it may be a viable alternative or complement to influenza vaccinations. We conclude with a brief discussion of our results and other practical aspects.

High confidence identification of intra-host single nucleotide variants for person-to-person influenza transmission tracking in congregate settings

Influenza within-host viral populations are the source of all global influenza diversity and play an important role in driving the evolution and escape of the influenza virus from human immune responses, antiviral treatment, and vaccines, and have been used in precision tracking of influenza transmission chains. Next Generation Sequencing (NGS) has greatly improved our ability to study these populations, however, major challenges remain, such as accurate identification of intra-host single nucleotide variants (iSNVs) that represent within-host viral diversity of influenza virus. In order to investigate the sources and the frequency of called iSNVs in influenza samples, we used a set of longitudinal influenza patient samples collected within a University of Maryland (UMD) cohort of college students in a living learning community. Our results indicate that technical replicates aid in removal of random RT-PCR, PCR, and platform sequencing errors, while the use of clonal plasmids for removal of systematic errors is more important in samples of low RNA abundance. We show that the choice of reference for read mapping affects the frequency of called iSNVs, with the sample self-reference resulting in the lowest amount of iSNV noise. The importance of variant caller choice is also highlighted in our study, as we observe differential sensitivity of variant callers to the mapping reference choice, as well as the poor overlap of their called iSNVs. Based on this, we develop an approach for identification of highly probable iSNVs by removal of sequencing and bioinformatics algorithm-associated errors, which we implement in phylogenetic analyses of the UMD samples for a greater resolution of transmission links. In addition to identifying closely related transmission connections supported by the presence of highly confident shared iSNVs between patients, our results also indicate that the rate of minor variant turnover within a host may be a limiting factor for utilization of iSNVs to determine patient epidemiological links.