Dynamic patterns of avian and human influenza in east and southeast Asia

Potential risk zones and climatic factors influencing the occurrence and persistence of avian influenza viruses in the environment of live bird markets in Bangladesh

Live bird markets (LBMs) are critical for poultry trade in many developing countries that are regarded as hotspots for the prevalence and contamination of avian influenza viruses (AIV). Therefore, we conducted weekly longitudinal environmental surveillance in LBMs to determine annual cyclic patterns of AIV subtypes, environmental risk zones, and the role of climatic factors on the AIV presence and persistence in the environment of LBM in Bangladesh. From January 2018 to March 2020, we collected weekly fecal and offal swab samples from each LBM and tested using rRT-PCR for the M gene and subtyped for H5, H7, and H9. We used Generalized Estimating Equations (GEE) approaches to account for repeated observations over time to correlate the AIV prevalence and potential risk factors and the negative binomial and Poisson model to investigate the role of climatic factors on environmental contamination of AIV at the LBM. Over the study period, 37.8% of samples tested AIV positive, 18.8% for A/H5, and A/H9 was, for 15.4%. We found the circulation of H5, H9, and co-circulation of H5 and H9 in the environmental surfaces year-round. The Generalized Estimating Equations (GEE) model reveals a distinct seasonal pattern in transmitting AIV and H5. Specifically, certain summer months exhibited a substantial reduction of risk up to 70-90% and 93-94% for AIV and H5 contamination, respectively. The slaughtering zone showed a significantly higher risk of contamination with H5, with a three-fold increase in risk compared to bird-holding zones. From the negative binomial model, we found that climatic factors like temperature and relative humidity were also significantly associated with weekly AIV circulation. An increase in temperature and relative humidity decreases the risk of AIV circulation. Our study underscores the significance of longitudinal environmental surveillance for identifying potential risk zones to detect H5 and H9 virus co-circulation and seasonal transmission, as well as the imperative for immediate interventions to reduce AIV at LBMs in Bangladesh. We recommend adopting a One Health approach to integrated AIV surveillance across animal, human, and environmental interfaces in order to prevent the epidemic and pandemic of AIV.

Mapping chicken production and distribution networks in Vietnam: An analysis of socio-economic factors and their epidemiological significances

The growing chicken industry in Viet Nam has an increasingly important contribution to the country's food security, but its development requires careful planning to prevent disease risks. This study characterizes the chicken production and distribution networks in Vietnam and identifies potential factors that could promote disease emergence and transmission. Qualitative data were collected from interviews with 29 key informants from five stakeholder groups representing the main nodes from chicken production and distribution networks (PDN). Three main networks were identified based on production type: a colored broiler and spent hen network, a white (or exotic) broiler network, and an egg network. Colored chickens and spent hens are the most preferred commodity by vietnamese consumers and their PDN is composed of production units differing in their scale and management and with long distribution chains involving numerous small-scale independent stakeholders. Live bird markets plays a central role in this network, which is driven by consumers' preference for live chickens. The white chicken network presents an important duality, as it is composed of both a large number of independent household farms and traders operating independently with little chain coordination, and of large farms contracted by vertically-integrated companies. The egg PDN was the most organized network, being mostly controlled by large vertically-integrated companies. High level specialization and diversification of stakeholders is found in all three networks. Stakeholders' perceptions of the main factors promoting disease risk along the PDN were the low biosecurity in household farms and live bird markets, mobile traders, the informal slaughter of birds and the management of sick birds. Findings from this study can be used to plan future studies to support food system planners in the development of safer poultry production and distribution in Vietnam.

Prevalence of respiratory viruses among paediatric patients in acute respiratory illnesses in Malaysia

Objectives

Acute respiratory infections (ARIs) are one of the leading causes of childhood morbidity and mortality worldwide. However, there is limited surveillance data on the epidemiological burden of respiratory pathogens in tropical countries like Malaysia. This study aims to estimate the prevalence of respiratory pathogens causing ARIs among children aged <18 years old in Malaysia and their epidemiological characteristics.

Methods

Nasopharyngeal swab specimens received at 12 laboratories located in different states of Malaysia from 2015–2019 were studied. Detection of 18 respiratory pathogens were performed using multiplex PCR.

Results

Data from a total of 23,306 paediatric patients who presented with ARI over a five-year period was studied. Of these, 18538 (79.5%) were tested positive. The most prevalent respiratory pathogens detected in this study were enterovirus/ rhinovirus (6837/ 23000; 29.7%), influenza virus (5176/ 23000; 22.5%) and respiratory syncytial virus (RSV) (3652/ 23000; 15.9%). Throughout the study period, RSV demonstrated the most pronounce seasonality; peak infection occurred during July to September. Whereas the influenza virus was detected year-round in Malaysia. No seasonal variation was noted in other respiratory pathogens. The risk of RSV hospitalisation was found to be significantly higher in children aged less than two years old, whereas hospitalisation rates for the influenza virus peaked at children aged between 3–6 years old.

Conclusion

This study provides insight into the epidemiology and the seasonality of the causative pathogens of ARI among the paediatric population in Malaysia. Knowledge of seasonal respiratory pathogens epidemiological dynamics will facilitate the identification of a target window for vaccination.

Spatiotemporal analysis of highly pathogenic avian influenza (H5N1) outbreaks in poultry in Egypt (2006 to 2017)

Background

In Egypt, the highly pathogenic avian influenza (HPAI) subtype H5N1 is endemic and possesses a severe impact on the poultry. To provide a better understanding of the distributional characteristics of HPAI H5N1 outbreaks in Egypt, this study aimed to explore the spatiotemporal pattern and identify clusters of HPAI H5N1 outbreaks in Egypt from 2006 to 2017.

Results

The Epidemic curve (EC) was constructed through time series analysis; in which six epidemic waves (EWs) were revealed. Outbreaks mainly started in winter peaked in March and ended in summer. However, newly emerged thermostable clades (2.2.1.1 and 2.2.1.2) during the 4th EW enabled the virus to survive and cause infection in warmer months with a clear alteration in the seasonality of the epidemic cycle in the 5th EW. The endemic situation became more complicated by the emergence of new serotypes. As a result, the EC ended up without any specific pattern since the 6th EW to now. The spatial analysis showed that the highest outbreak density was recorded in the Nile Delta considering it as the ‘Hot spot’ region. By the 6th EW, the outbreak extended to include the Nile valley. From spatiotemporal cluster epidemics, clustering in the Delta was a common feature in all EWs with primary clusters consistently detected in the hot-spot region, but the location and size varied with each EW. The highest Relative Risk (RR) regions in an EW were noticed to contain the primary clusters of the next EW and were found to include stopover sites for migratory wild birds. They were in Fayoum, Dakahlia, Qalyobiya, Sharkia, Kafr_Elsheikh, Giza, Behera, Menia, and BeniSuef governorates. Transmission of HPAI H5N1 occurred from one location to another directly resulted in a series of outbreaks forming neighboring secondary clusters. The absence of geographical borders between the governorates in addition to non-restricted movements of poultry and low vaccination and surveillance coverage contributed to the wider spread of infection all over Egypt and to look like one epidemiological unit.

Conclusion

Our findings can help in better understanding of the characteristics of HPAI H5N1 outbreaks and the distribution of outbreak risk, which can be used for effective disease control strategies.

Graphical abstract

Semi-Scavenging Poultry as Carriers of Avian Influenza Genes

Ducks are the natural reservoir of influenza A virus and the central host for the avian influenza virus (AIV) subtype H5N1, which is highly pathogenic. Semi-scavenging domestic ducks allow for the reemergence of new influenza subtypes which could be transmitted to humans. We collected 844 cloacal swabs from semi-scavenging ducks inhabiting seven migratory bird sanctuaries of Bangladesh for the molecular detection of avian influenza genes. We detected the matrix gene (M gene) using real-time RT-PCR (RT-qPCR). Subtyping of the AIV-positive samples was performed by RT-qPCR specific for H5, H7, and H9 genes. Out of 844 samples, 21 (2.488%) were positive for AIV. Subtyping of AIV positive samples (n = 21) revealed that nine samples (42.85%) were positive for the H9 subtype, five (23.80%) were positive for H5, and seven (33.33%) were negative for the three genes (H5, H7, and H9). We detected the same genes after propagating the virus in embryonated chicken eggs from positive samples. Semi-scavenging ducks could act as carriers of pathogenic AIV, including the less pathogenic H9 subtype. This can enhance the pathogenicity of the virus in ducks by reassortment. The large dataset presented in our study from seven areas should trigger further studies on AIV prevalence and ecology.

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.

Molecular evolution of the hemagglutinin gene and epidemiological insight into low-pathogenic avian influenza H9N2 viruses in Egypt

Despite the low pathogenicity of the H9N2 avian influenza viruses, they can induce severe economic losses in various poultry sectors in conjunction with other factors. In Egypt, low-pathogenic avian influenza (LPAI) H9N2 became endemic in 2011 and has undergone continuous genetic evolution since then. The regular monitoring of the evolution of the virus is necessary to control its spread. During 2017-2020, there were 44 positive samples isolated, and these viruses were genetically sequenced to determine the hemagglutinin (HA) gene circulating in Egypt. The molecular analysis revealed at least nine changes in amino acid residues in comparison with the reference Egyptian strain from the original introduction in 2011 (A/qu/Egypt/113413v/2011), with a similarity of 95%-96%. Amino acid residues 180 and 216 are the most important residues in terms of positive selection pressure. Phylogenetically, the new Egyptian H9N2 viruses in 2017-2020 belonged to a new subcluster related to the strains that had been circulating since 2015. Comparative analysis of the HA gene of LPAI H9N2 viruses in Egypt from 2011 to 2020 supports a continuous evolution through the years with persistent markers.

Disappearance of summer influenza in the Okinawa prefecture during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic

Since the Okinawan islands are located in the southernmost part of Japan, where the climate is subtropical, several episodes of influenza epidemics occur during the summer season. More recently, we have demonstrated that summer influenza epidemics occur every year. After the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began in January 2020, measures to avoid disease transmission have been widely promoted in Japan, such as the use of masks, handwashing, remote work, and cancellation of large events. These measures might also have reduced the spread of other infectious diseases, such as the seasonal influenza. Based on this background, we evaluated weekly influenza activity in the 2019/2020 season. After the SARS-CoV-2 pandemic, the summer influenza in the Okinawa prefecture disappeared in 2020. The reasons for the disappearance of summer influenza in Okinawa are discussed herein.

Dynamics of the occurrence of influenza in relation to seasonal variation in Chennai, Tamil Nadu: A 7 -year cumulative study

Background

Influenza viruses have emerged as virulent pathogens causing considerable burden across the world. A thorough understanding of the pattern in occurrence of influenza globally is the need of hour. The present study deals with analysis of the dynamics of Influenza virus, especially the influence of seasonal change on viral circulation and causation of epidemics/pandemics in the context of subtropical region.

Methods

During the 7 year (2009-2015) study, 36670 specimens were subjected to influenza analysis. Nasopharyngeal swabs collected from suspected patients from Chennai, Tamil Nadu, were tested and typed by real-time polymerase chain reaction assay.

Results

During 2009 pandemic, among influenza A positives 95.16% were Apdm09, indicating that there was a predominant circulation of Apdm09. During postpandemic period, there were waves in the occurrence of Apdm09 which indicates fall in immunity with buildup in the susceptible population.

Conclusion

In Chennai, Tamil Nadu, influenza positivity started with the onset of monsoon and peaks during the postmonsoon months throughout the study period. The assessment of meteorological factors compounding influenza activity can help in raising alerts to the public health officials of impending disaster which suggests that Influenza vaccination can be initiated before monsoon months in South India.

Prevalence of Avian Influenza A(H5) and A(H9) Viruses in Live Bird Markets, Bangladesh

We conducted a cross-sectional study in live bird markets (LBMs) in Dhaka and Chittagong, Bangladesh, to estimate the prevalence of avian influenza A(H5) and A(H9) viruses in different types of poultry and environmental areas by using Bayesian hierarchical logistic regression models. We detected these viruses in nearly all LBMs. Prevalence of A(H5) virus was higher in waterfowl than in chickens, whereas prevalence of A(H9) virus was higher in chickens than in waterfowl and, among chicken types, in industrial broilers than in cross-breeds and indigenous breeds. LBMs with >1 wholesaler were more frequently contaminated by A(H5) virus than retail-only LBMs. Prevalence of A(H9) virus in poultry and level of environmental contamination were also higher in LBMs with >1 wholesaler. We found a high level of circulation of both avian influenza viruses in surveyed LBMs. Prevalence was influenced by type of poultry, environmental site, and trading.

Biomedical and genetic characteristics of the Ryukyuans: demographic history, diseases and physical and physiological traits

Context: The Ryukyu Islands stretch across a southwestern area of the Japanese Archipelago. Because of their unique geographical and historical backgrounds, Ryukyuans have their own genetic and phenotypic characteristics, which have been disclosed in previous anthropological and biomedical studies. Objective: The history, peopling and biomedical and genetic characteristics of Ryukyuans are reviewed and future research directions are discussed. Conclusion: Morphological and genetic studies have suggested the complex demographic history of Ryukyuans and their relationships with other Asian populations. Knowledge of population formation processes is important to understand the distribution of pathogens. In viral infectious diseases, some strains that may be associated with disease symptoms are specific to Ryukyuans. Dramatic changes in diet have played an important role among Ryukyuans in terms of increases in lifestyle-related diseases and mortality risks. To achieve a better understanding of pathogenic disease factors, further integration of findings regarding the genetic and biomedical characteristics of the Ryukyuans is needed.

Inferring the global phylodynamics of influenza A/H3N2 viruses in Taiwan

BACKGROUND/PURPOSE

Influenza A/H3N2 viruses are characterized by highly mutated RNA genomes. In this study, we focused on tracing the phylodynamics of Taiwanese strains over the past four decades.

METHODS

All Taiwanese H3N2 HA1 sequences and references were downloaded from public database. A Bayesian skyline plot (BSP) and phylogenetic tree were used to analyze the evolutionary history, and Bayesian phylogeographic analysis was applied to predict the spatiotemporal migrations of influenza outbreaks.

RESULTS

Genetic diversity was found to have peaked near the summer of 2009 in BSP, in addition to the two earlier reported ones in summer of 2005 and 2007. We predicted their spatiotemporal migrations and found the summer epidemic of 2005 from Korea, and 2007 and 2009 from the Western United States. BSP also predicted an elevated genetic diversity in 2015-2017. Quasispecies were found over approximately 20% of the strains included in this time span. In addition, a first-time seen N31S mutation was noted in Taiwan in 2016-2017.

CONCLUSION

We comprehensively investigated the evolutionary history of Taiwanese strains in 1979-2017. An epidemic caution could thus be raised if genetic diversity was found to have peaked. An example showed a newly-discovered cluster in 2016-2017 strains featuring a mutation N31S together with HA-160 quasispecies. Phylogeographic analysis, moreover, provided useful insights in tracing the possible source and migrations of these epidemics around the world. We demonstrated that Asian destinations including Taiwan were the immediate followers, while U.S. continent was predicted the origin of two summer epidemics in 2007 and 2009.

The live poultry trade and the spread of highly pathogenic avian influenza: Regional differences between Europe, West Africa, and Southeast Asia

In the past two decades, avian influenzas have posed an increasing international threat to human and livestock health. In particular, highly pathogenic avian influenza H5N1 has spread across Asia, Africa, and Europe, leading to the deaths of millions of poultry and hundreds of people. The two main means of international spread are through migratory birds and the live poultry trade. We focus on the role played by the live poultry trade in the spread of H5N1 across three regions widely infected by the disease, which also correspond to three major trade blocs: the European Union (EU), the Economic Community of West African States (ECOWAS), and the Association of Southeast Asian Nations (ASEAN). Across all three regions, we found per-capita GDP (a proxy for modernization, general biosecurity, and value-at-risk) to be risk reducing. A more specific biosecurity measure-general surveillance-was also found to be mitigating at the all-regions level. However, there were important inter-regional differences. For the EU and ASEAN, intra-bloc live poultry imports were risk reducing while extra-bloc imports were risk increasing; for ECOWAS the reverse was true. This is likely due to the fact that while the EU and ASEAN have long-standing biosecurity standards and stringent enforcement (pursuant to the World Trade Organization's Agreement on the Application of Sanitary and Phytosanitary Measures), ECOWAS suffered from a lack of uniform standards and lax enforcement.

Genome-wide characterization of the seasonal H3N2 virus in Shanghai reveals natural temperature-sensitive strains conferred by the I668V mutation in the PA subunit

Seasonal H3N2 influenza viruses are recognized as major epidemic viruses, exhibiting complex seasonal patterns in regions with temperate climates. To investigate the influence of viral evolution and mutations on the seasonality of influenza, we performed a genome-wide analysis of samples collected from 62 influenza A/H3N2-infected patients in Shanghai during 2016-2017. Phylogenetic analysis of all eight segments of the influenza A virus revealed that there were two epidemic influenza virus strains circulating in the 2016-2017 winter season (2016-2017win) and 2017 summer season (2017sum). Replication of the two epidemic viral strains at different temperatures (33, 35, 37, and 39 °C) was measured, and the correlation of the mutations in the two epidemic viral strains with temperature sensitivity and viral replication was analyzed. Analysis of the replication kinetics showed that replication of the 2016-2017win strains was significantly restricted at 39 °C compared with that of the 2017sum strains. A polymerase activity assay and mutational analysis demonstrated that the PA I668V mutation of the 2016-2017win viruses suppressed polymerase activity in vitro at high temperatures. Taken together, these data suggest that the I668V mutation in the PA subunit of the 2016-2017win strains may confer temperature sensitivity and attenuate viral replication and polymerase activity; meanwhile, the 2017sum strains maintained virulence at high temperatures. These findings highlight the importance of certain mutations in viral adaptation and persistence in subsequent seasons.

Global dynamics of highly pathogenic avian influenza outbreaks in poultry between 2005 and 2016-Focus on distance and rate of spread

Highly pathogenic avian influenza (HPAI) is of major importance for human and animal health because of high morbidity and mortality in poultry and the potential for transmission of this zoonotic pathogen to humans. Knowledge of HPAI epidemiology in avian populations and practical information on the temporal and spatial spread of the disease after introduction into a country is important in order to enhance the capacity of predicting and managing epidemics to minimize the negative impacts on human and animal health. Using data reported to the World Organisation for Animal Health between 2005 and 2017 by 199 countries for 14,129 outbreaks in poultry, we used a spatial and time-series analysis to determine that: (a) During the last 12 years, there were two major global peaks in the number of countries affected by HPAI with 23% and 26% of countries affected in 2006 and 2016. (b) Based on the seasonality analysis, spread is the lowest in September, begins to rise in October, and peaks in February. (c) The median distance HPAI outbreaks spread from the index outbreak was 111 km, while the median apparent rate of spread of outbreaks was 1.9 km/day. (d) In 39% of HPAI events, the disease did not spread beyond the index outbreak and the median maximum spread from the index outbreak per event was 45 km. (e) The distance HPAI outbreaks spread from the index outbreak was significantly negatively correlated with the number of outbreaks during the same time period, indicating that the spread of HPAI was lower during global panzootics than during periods of low transmission. These findings are of major importance for veterinary services to design and implement surveillance measures for improving preparedness to minimize the impacts of this disease.

Structural Basis for the Broad, Antibody-Mediated Neutralization of H5N1 Influenza Virus

Human infection with highly pathogenic avian influenza A viruses causes severe disease and fatalities. We previously identified a potent and broadly neutralizing antibody (bnAb), 13D4, against the H5N1 virus. Here, we report the co-crystal structure of 13D4 in complex with the hemagglutinin (HA) of A/Vietnam/1194/2004 (H5N1). We show that heavy-chain complementarity-determining region 3 (HCDR3) of 13D4 confers broad yet specific neutralization against H5N1, undergoing conformational rearrangement to bind to the receptor binding site (RBS). Further, we show that mutating four critical residues within the RBS-Trp153, Lys156, Lys193, and Leu194-disrupts the binding between 13D4 and HA. Viruses bearing Asn193 instead of Lys/Arg can evade 13D4 neutralization, indicating that Lys193 polymorphism might be, at least in part, involved in the antigenicity of recent H5 genotypes (such as H5N6 and H5N8) as distinguished from H5N1. BnAb 13D4 may offers a template for therapeutic RBS inhibitor design and serve as an indicator of antigenic change for current H5 viruses.IMPORTANCE Infection by highly pathogenic avian influenza A virus remains a threat to public health. Our broadly neutralizing antibody, 13D4, is capable of neutralizing all representative H5N1 viruses and protecting mice against lethal challenge. Structural analysis revealed that 13D4 uses heavy-chain complementarity-determining region 3 (HCDR3) to fit the receptor binding site (RBS) via conformational rearrangement. Four conserved residues within the RBS are critical for the broad potency of 13D4. Importantly, polymorphism of Lys193 on the RBS may be associated with the antigenicity shift from H5N1 to other newly emerging viruses, such as H5N6 and H5N8. Our findings may pave the way for highly pathogenic avian influenza virus vaccine development and therapeutic RBS inhibitor design.

Avian influenza surveillance in domestic waterfowl and environment of live bird markets in Bangladesh, 2007-2012

Avian influenza viruses, including highly pathogenic strains, pose severe economic, animal and public health concerns. We implemented live bird market surveillance in Bangladesh to identify the subtypes of avian influenza A viruses in domestic waterfowl and market environments. We collected waterfowl samples monthly from 4 rural sites from 2007 to 2012 and environmental samples from 4 rural and 16 urban sites from 2009 to 2012. Samples were tested through real-time RT-PCR, virus culture, and sequencing to detect and characterize avian influenza A viruses. Among 4,308 waterfowl tested, 191 (4.4%) were positive for avian influenza A virus, including 74 (1.9%) avian influenza A/H5 subtype. The majority (99%, n = 73) of the influenza A/H5-positive samples were from healthy appearing waterfowl. Multiple subtypes, including H1N1, H1N3, H3N2, H3N6, H3N8, H4N1, H4N2, H4N6, H5N1 (clades 2.2.2, 2.3.2.1a, 2.3.4.2), H5N2, H6N1, H7N9, H9N2, H11N2 and H11N3, H11N6 were detected in waterfowl and environmental samples. Environmental samples tested positive for influenza A viruses throughout the year. Avian influenza viruses, including H5N1 and H9N2 subtypes were also identified in backyard and small-scale raised poultry. Live bird markets could be high-risk sites for harboring the viruses and have the potential to infect naive birds and humans exposed to them.

Live bird markets in Bangladesh as a potentially important source for Avian Influenza Virus transmission

Live bird markets (LBM) are important for trading poultry in many developing countries where they are being considered hotspots of Avian Influenza Virus (AIV) prevalence and contamination. An active surveillance for Avian Influenza Virus (AIV) was conducted on four species of LBM birds (chickens, ducks, quails and pigeons) from 10 of the largest LBM in Chittagong, Bangladesh, and two species of peri-domestic wild birds (house crow and Asian pied starling) in their direct vicinity from November 2012 until September 2016. Our aim was to identify the scale and annual pattern of AIV circulation in both the LBM birds and the two per-domestic wild bird species living in close proximity of the LBM. In the latter two species, the annual pattern in AIV antibody prevalence was additionally investigated. A total of 4770 LBM birds and 1119 peri-domestic wild birds were sampled. We used rt-PCR for detection of the AIV M-gene and AIV subtypes H5, H7 and H9 from swab samples. We used c-ELISA for AIV antibody detection from serum samples of peri-domestic wild birds. Average AIV prevalence among the four LBM species varied between 16 and 28%, whereas no AIV was detected in peri-domestic wild birds by rt-PCR. In all LBM species we found significantly higher AIV prevalence in winter compared to summer. A similar pattern was found in AIV antibody prevalence in peri-domestic wild birds feeding in the direct vicinity of LBM. For the subtypes of AIV investigated, we found a significantly higher proportion of AIV H5 in LBM chickens and H9 in LBM ducks. No H7 was detected in any of the investigated samples. We conclude that AIV and notably AIV H5 and H9 were circulating in the investigated LBM of Bangladesh with clear seasonality that matched the prevalence of AIV antibodies of peri-domestic wild birds. These patterns show great resemblance to the annual outbreak patterns in Bangladeshi poultry industry. Our data suggest considerable exchange of AIV within and among the four LBM bird species and peri-domestic wild birds, which likely contributes to the maintenance of the AIV problems in Bangladesh. Increasing biosecurity and notably reducing the direct and indirect mixing of various domestic bird species and peri-domestic wild birds and developing all-in-all-out selling systems with regular use of disinfectant are likely to reduce the risk of transmission and spread of AIV, including HPAI.

Circulation of influenza in backyard productive systems in central Chile and evidence of spillover from wild birds

Backyard productive systems (BPS) are recognized as the most common form of animal production in the world. However, BPS frequently exhibit inherent biosecurity deficiencies, and could play a major role in the epidemiology of animal diseases and zoonoses. The aim of this study was to determine if influenza A viruses (IAV) were prevalent in backyard poultry and swine BPS in central Chile. Through active surveillance in Valparaiso and Metropolitan regions from 2012 - 2014, we found that influenza virus positivity by real-time RT-PCR (qRT-PCR) ranged from 0% during winter 2012-45.8% during fall 2014 at the farm level. We also obtained an H12 hemagglutinin (HA) sequence of wild bird origin from a domestic Muscovy duck (Cairina moschata), indicating spillover from wild birds into backyard poultry populations. Furthermore, a one-year sampling effort in 113 BPS in the Libertador Bernardo O'Higgins (LGB ÓHiggins) region showed that 12.6% of poultry and 2.4% of swine were positive for IAV by enzyme-linked immunosorbent assay (ELISA), indicative of previous exposure of farm animals to IAV. This study highlights the need for improved IAV surveillance in backyard populations given the close interaction between domestic animals, wild birds and people in these farms, particularly in an understudied region, like South America.

Global spatial risk pattern of highly pathogenic avian influenza H5N1 virus in wild birds: A knowledge-fusion based approach

Highly pathogenic avian influenza (HPAI) H5N1 viruses have continuously circulated throughout much of the world since 2003, resulting in huge economic losses and major public health problems. Wild birds have played an important role in the spread of H5N1 HPAI. To understand its spatial distribution, H5N1 HPAI have been studied by many disciplines from different perspectives, but only one kind of disciplinary knowledge was involved, which has provided limited progress in understanding. Combining risk information from different disciplines based on knowledge fusion can provide more accurate and detailed information. In this study, local k function, phylogenetic tree analysis, and logistic spatial autoregressive models were used to explore the global spatial pattern of H5N1 HPAI based on outbreak data in wild birds, genetic sequences, and risk factors, respectively. On this basis, Dempster-Shafer (D-S) evidence theory was further applied to study the spatial distribution of H5N1 HPAI. We found D-S evidence theory was more robust and reliable than the other three methods, providing technical and methodological support for application to the research of other diseases. The shortest distance to wild bird migration routes, roads and railways, elevation, the normalized difference vegetation index (NDVI), land use and land cover (LULC) and infant mortality rates (IMR) were significantly associated with the occurrence of H5N1 HPAI. The high-risk areas were mainly located in Northern and Central Europe, the eastern Mediterranean, and East and Southeast Asia. High-risk clusters were closely related to the social, economic and ecological environment of the region. Locations where the potential transmission risk remains high should be prioritized for control efforts.

Economic factors influencing zoonotic disease dynamics: demand for poultry meat and seasonal transmission of avian influenza in Vietnam

While climate is often presented as a key factor influencing the seasonality of diseases, the importance of anthropogenic factors is less commonly evaluated. Using a combination of methods - wavelet analysis, economic analysis, statistical and disease transmission modelling - we aimed to explore the influence of climatic and economic factors on the seasonality of H5N1 Highly Pathogenic Avian Influenza in the domestic poultry population of Vietnam. We found that while climatic variables are associated with seasonal variation in the incidence of avian influenza outbreaks in the North of the country, this is not the case in the Centre and the South. In contrast, temporal patterns of H5N1 incidence are similar across these 3 regions: periods of high H5N1 incidence coincide with Lunar New Year festival, occurring in January-February, in the 3 climatic regions for 5 out of the 8 study years. Yet, daily poultry meat consumption drastically increases during Lunar New Year festival throughout the country. To meet this rise in demand, poultry production and trade are expected to peak around the festival period, promoting viral spread, which we demonstrated using a stochastic disease transmission model. This study illustrates the way in which economic factors may influence the dynamics of livestock pathogens.

Interventions in live poultry markets for the control of avian influenza: a systematic review

Background

Live poultry markets (LPMs) pose a threat to public health by promoting the amplification and dissemination of avian influenza viruses (AIVs) and by providing the ideal setting for zoonotic influenza transmission.

Objective

This review assessed the impact of different interventions implemented in LPMs to control the emergence of zoonotic influenza.

Methods

Publications were identified through a systematic literature search in the PubMed, MEDLINE and Web of Science databases. Eligible studies assessed the impact of different interventions, such as temporary market closure or a ban on holding poultry overnight, in reducing i) AIV-detection rates in birds and the market environment or ii) influenza incidence in humans. Unpublished literature, reviews, editorials, cross-sectional studies, theoretical models and publications in languages other than English were excluded. Relevant findings were extracted and critically evaluated. For the comparative analysis of findings across studies, standardized outcome measures were computed as i) the relative risk reduction (RRR) of AIV-detection in LPMs and ii) incidence rate ratios (IRRs) of H7N9-incidence in humans.

Results

A total of 16 publications were identified and reviewed. Collectively, the data suggest that AIV-circulation can be significantly reduced in the LPM-environment and among market-birds through (i) temporary LPM closure, (ii) periodic rest days (iii) market depopulation overnight and (iv) improved hygiene and disinfection. Overall, the findings indicate that the length of stay of poultry in the market is a critical control point to interrupt the AIV-replication cycle within LPMs. In addition, temporary LPM closure was associated with a significant reduction of the incidence of zoonotic influenza. The interpretation of these findings is limited by variations in the implementation of interventions. In addition, some of the included studies were of ecologic nature or lacked an inferential framework, which might have lead to cosiderable confounding and bias.

Conclusions

The evidence collected in this review endorses permanent LPM-closure as a long-term objective to reduce the zoonotic risk of avian influenza, although its economic and socio-political implications favour less drastic interventions, e.g. weekly rest days, for implementation in the short-term.

•Avian influenza viruses (AIVs) can infect humans. Bird-to-human transmission is particularly intense in live poultry markets. •Periodic rest days, overnight depopulation or sale bans of certain species significantly reduce AIV-circulation in the markets. •Market closure would lastingly reduce the risk of animal and human infection.

Comparative epidemiology of influenza A and B viral infection in a subtropical region: a 7-year surveillance in Okinawa, Japan

BACKGROUND

The epidemic patterns of influenza B infection and their association with climate conditions are not well understood. Influenza surveillance in Okinawa is important for clarifying transmission patterns in both temperate and tropical regions. Using surveillance data, collected over 7 years in the subtropical region of Japan, this study aims to characterize the epidemic patterns of influenza B infection and its association with ambient temperature and relative humidity, in a parallel comparison with influenza A.

METHODS

From January 2007 until March 2014, two individual influenza surveillance datasets were collected from external sources. The first dataset, included weekly rapid antigen test (RAT) results from four representative general hospitals, located in the capital city of Okinawa. A nation-wide surveillance of influenza, diagnosed by RAT results and/or influenza-like illness symptoms, included the age distribution of affected patients and was used as the second dataset. To analyze the association between infection and local climate conditions, ambient temperature and relative humidity during the study period were retrieved from the Japanese Meteorological Agency website.

RESULTS

Although influenza A maintained high number of infections from December through March, epidemics of influenza B infection were observed annually from March through July. The only observed exception was 2010, when the pandemic strain of 2009 dominated. During influenza B outbreaks, influenza patients aged 5 to 9 years old and 10 to 14 years old more frequently visited sentinel sites. Although both ambient temperature and relative humidity are inversely associated with influenza A infection, influenza B infection was found to be directly associated with high relative humidity.

CONCLUSION

Further studies are needed to elucidate the complex epidemiology of influenza B and its relationship with influenza A. In the subtropical setting of Okinawa, epidemics of influenza B infection occur from March to July following the influenza A epidemic, and primarily affect school-age children. These findings help to define unknown aspects of influenza B and can inform healthcare decisions for patients located outside temperate regions.

Presence of influenza viruses in backyard poultry and swine in El Yali wetland, Chile

In South America little is known regarding influenza virus circulating in backyard poultry and swine populations. Backyard productive systems (BPS) that breed swine and poultry are widely distributed throughout Chile with high density in the central zone, and several BPS are located within the "El Yali" (EY) ecosystem, which is one of the most important wetlands in South America. Here, 130 different wild bird species have been described, of them, at least 22 species migrate yearly from North America for nesting. For this reason, EY is considered as a high-risk zone for avian influenza virus. This study aims to identify if backyard poultry and swine bred in the EY ecosystem have been exposed to influenza A virus and if so, to identify influenza virus subtypes. A biosecurity and handling survey was applied and samples were collected from BPS in two seasons (spring 2013 and fall 2014) for influenza seroprevalence, and in one season (fall 2014) for virus presence. Seroprevalence at BPS level was 42% (95% CI:22-49) during spring 2013 and 60% (95% CI 43-72) in fall 2014. rRT-PCR for the influenza A matrix gene indicated a viral prevalence of 27% (95% CI:14-39) at BPS level in fall 2014. Eight farms (73% of rRT-PCR positive farms) were also positive to the Elisa test at the same time. One BPS was simultaneously positive (rRT-PCR) in multiple species (poultry, swine and geese) and a H1N2 virus was identified from swine, exemplifying the risk that these BPS may pose for generation of novel influenza viruses.

Surveillance, epidemiological, and virological detection of highly pathogenic H5N1 avian influenza viruses in duck and poultry from Bangladesh

Avian influenza viruses (AIVs) continue to pose a global threat. Waterfowl are the main reservoir and are responsible for the spillover of AIVs to other hosts. This study was conducted as part of routine surveillance activities in Bangladesh and it reports on the serological and molecular detection of H5N1 AIV subtype. A total of 2169 cloacal and 2191 oropharyngeal swabs as well as 1725 sera samples were collected from live birds including duck and chicken in different locations in Bangladesh between the years of 2013 and 2014. Samples were tested using virus isolation, serological tests and molecular methods of RT-PCR. Influenza A viruses were detected using reverse transcription PCR targeting the virus matrix (M) gene in 41/4360 (0.94%) samples including both cloacal and oropharyngeal swab samples, 31 of which were subtyped as H5N1 using subtype-specific primers. Twenty-one live H5N1 virus isolates were recovered from those 31 samples. Screening of 1,868 blood samples collected from the same birds using H5-specific ELISA identified 545/1603 (34%) positive samples. Disconcertingly, an analysis of 221 serum samples collected from vaccinated layer chicken in four districts revealed that only 18 samples (8.1%) were seropositive for anti H5 antibodies, compared to unvaccinated birds (n=105), where 8 samples (7.6%) were seropositive. Our result indicates that the vaccination program as currently implemented should be reviewed and updated. In addition, surveillance programs are crucial for monitoring the efficacy of the current poultry vaccinations programs, and to monitor the circulating AIV strains and emergence of AIV subtypes in Bangladesh.

Surveillance of acute respiratory infections in Mumbai during 2011-12

PURPOSE

Acute respiratory infections (ARIs) are a leading cause of morbidity and mortality in individuals aged less than 5 years. ARI often leads to hospitalisation, and it has been indicated that causative viral and bacterial infections go undetermined and results in the occurrence of resistant strains. The objective of the study was to assess the prevalence of various viral and bacterial infections in patients with ARIs.

MATERIALS AND METHODS

Two hundred samples were collected from July 2011 to July 2012 with patients suffering from ARI. Viral and bacterial infections were determined by real time reverse transcriptase polymerase chain reaction.

RESULTS

Influenza-like illness (ILI) consisted of 109 patients and ARI consisted of 91 patients. Pandemic influenza A H1N1 was the major viral infection with 21 (19.2%) patients in ILI as compared with 16 (17.4%) patients in ARI. Respiratory syncytial virus (RSV) was found to be 1 (0.9%) in ILI and ARI. Viral co-infections were 16 (14.4%) in ILI and 4 (4.37%) in ARI where pandemic influenza A H1N1 and influenza type B were major contributors. In bacterial infections, Streptococcus pneumoniae with 11 (10.9%) cases were predominant in both the groups. Bacterial co-infection accounted for only 1 (1.09%) case in both the groups but the most significant finding was the viral-bacterial co-infection in which Haemophilus influenzae was the major co-infecting bacteria with the influenza viruses with 4 (4.36%) cases as compared with Streptotoccus pneumoniae.

CONCLUSION

This data indicate the need to undertake continued surveillance that will help to better define the circulation of respiratory viruses along with the bacterial infections.

Avian influenza infection dynamics under variable climatic conditions, viral prevalence is rainfall driven in waterfowl from temperate, south-east Australia

Understanding Avian Influenza Virus (AIV) infection dynamics in wildlife is crucial because of possible virus spill over to livestock and humans. Studies from the northern hemisphere have suggested several ecological and environmental drivers of AIV prevalence in wild birds. To determine if the same drivers apply in the southern hemisphere, where more irregular environmental conditions prevail, we investigated AIV prevalence in ducks in relation to biotic and abiotic factors in south-eastern Australia. We sampled duck faeces for AIV and tested for an effect of bird numbers, rainfall anomaly, temperature anomaly and long-term ENSO (El-Niño Southern Oscillation) patterns on AIV prevalence. We demonstrate a positive long term effect of ENSO-related rainfall on AIV prevalence. We also found a more immediate response to rainfall where AIV prevalence was positively related to rainfall in the preceding 3-7 months. Additionally, for one duck species we found a positive relationship between their numbers and AIV prevalence, while prevalence was negatively or not affected by duck numbers in the remaining four species studied. In Australia largely non-seasonal rainfall patterns determine breeding opportunities and thereby influence bird numbers. Based on our findings we suggest that rainfall influences age structures within populations, producing an influx of immunologically naïve juveniles within the population, which may subsequently affect AIV infection dynamics. Our study suggests that drivers of AIV dynamics in the northern hemisphere do not have the same influence at our south-east Australian field site in the southern hemisphere due to more erratic climatological conditions.

An Epidemiological Analysis of Summer Influenza Epidemics in Okinawa

Objective This study evaluates the difference between winter influenza and summer influenza in Okinawa. Methods From January 2007 to June 2014, weekly rapid antigen test (RAT) results performed in four acute care hospitals were collected for the surveillance of regional influenza prevalence in the Naha region of the Okinawa Islands. Results An antigenic data analysis revealed that multiple H1N1 and H3N2 viruses consistently co-circulate in Okinawa, creating synchronized seasonal patterns and a high genetic diversity of influenza A. Additionally, influenza B viruses play a significant role in summer epidemics, almost every year. To further understand influenza epidemics during the summer in Okinawa, we evaluated the full genome sequences of some representative human influenza A and influenza B viruses isolated in Okinawa. Phylogenetic data analysis also revealed that multiple H1N1 and H3N2 viruses consistently co-circulate in Okinawa. Conclusion This surveillance revealed a distinct epidemic pattern of seasonal and pandemic influenza in this subtropical region.

Identification of climate factors related to human infection with avian influenza A H7N9 and H5N1 viruses in China

Human influenza infections display a strongly seasonal pattern. However, whether H7N9 and H5N1 infections correlate with climate factors has not been examined. Here, we analyzed 350 cases of H7N9 infection and 47 cases of H5N1 infection. The spatial characteristics of these cases revealed that H5N1 infections mainly occurred in the South, Middle, and Northwest of China, while the occurrence of H7N9 was concentrated in coastal areas of East and South of China. Aside from spatial-temporal characteristics, the most adaptive meteorological conditions for the occurrence of human infections by these two viral subtypes were different. We found that H7N9 infections correlate with climate factors, especially temperature (TEM) and relative humidity (RHU), while H5N1 infections correlate with TEM and atmospheric pressure (PRS). Hence, we propose a risky window (TEM 4–14 °C and RHU 65–95%) for H7N9 infection and (TEM 2–22 °C and PRS 980-1025 kPa) for H5N1 infection. Our results represent the first step in determining the effects of climate factors on two different virus infections in China and provide warning guidelines for the future when provinces fall into the risky windows. These findings revealed integrated predictive meteorological factors rooted in statistic data that enable the establishment of preventive actions and precautionary measures against future outbreaks.

Highly pathogenic Avian Influenza A(H5N1) virus infection among workers at live bird markets, Bangladesh, 2009-2010

Evidence of infection was low despite frequent exposure to infected poultry and low use of personal protective equipment.

The risk for influenza A(H5N1) virus infection is unclear among poultry workers in countries where the virus is endemic. To assess H5N1 seroprevalence and seroconversion among workers at live bird markets (LBMs) in Bangladesh, we followed a cohort of workers from 12 LBMs with existing avian influenza surveillance. Serum samples from workers were tested for H5N1 antibodies at the end of the study or when LBM samples first had H5N1 virus–positive test results. Of 404 workers, 9 (2%) were seropositive at baseline. Of 284 workers who completed the study and were seronegative at baseline, 6 (2%) seroconverted (7 cases/100 poultry worker–years). Workers who frequently fed poultry, cleaned feces from pens, cleaned food/water containers, and did not wash hands after touching sick poultry had a 7.6 times higher risk for infection compared with workers who infrequently performed these behaviors. Despite frequent exposure to H5N1 virus, LBM workers showed evidence of only sporadic infection.

Comprehensive analysis of antibody recognition in convalescent humans from highly pathogenic avian influenza H5N1 infection

Understanding the mechanism of protective antibody recognition against highly pathogenic avian influenza A virus H5N1 in humans is critical for the development of effective therapies and vaccines. Here we report the crystal structure of three H5-specific human monoclonal antibodies bound to the globular head of hemagglutinin (HA) with distinct epitope specificities, neutralization potencies and breadth. A structural and functional analysis of these epitopes combined with those reported elsewhere identifies four major vulnerable sites on the globular head of H5N1 HA. Chimeric and vulnerable site-specific mutant pseudoviruses are generated to delineate broad neutralization specificities of convalescent sera from two individuals who recovered from the infection with H5N1 virus. Our results show that the four vulnerable sites on the globular head rather than the stem region are the major neutralizing targets, suggesting that during natural H5N1 infection neutralizing antibodies against the globular head work in concert to provide protective antibody-mediated immunity.

Timing of influenza A(H5N1) in poultry and humans and seasonal influenza activity worldwide, 2004-2013

Co-circulation of H5N1 in poultry and humans during seasonal influenza epidemic periods signals the need for enhanced surveillance and biosafety measures.

Co-circulation of influenza A(H5N1) and seasonal influenza viruses among humans and animals could lead to co-infections, reassortment, and emergence of novel viruses with pandemic potential. We assessed the timing of subtype H5N1 outbreaks among poultry, human H5N1 cases, and human seasonal influenza in 8 countries that reported 97% of all human H5N1 cases and 90% of all poultry H5N1 outbreaks. In these countries, most outbreaks among poultry (7,001/11,331, 62%) and half of human cases (313/625, 50%) occurred during January–March. Human H5N1 cases occurred in 167 (45%) of 372 months during which outbreaks among poultry occurred, compared with 59 (10%) of 574 months that had no outbreaks among poultry. Human H5N1 cases also occurred in 59 (22%) of 267 months during seasonal influenza periods. To reduce risk for co-infection, surveillance and control of H5N1 should be enhanced during January–March, when H5N1 outbreaks typically occur and overlap with seasonal influenza virus circulation.

Avian influenza A (H5N1) infection with respiratory failure and meningoencephalitis in a Canadian traveller

Since 1997, more than 600 individuals worldwide have been infected with the poultry-originating influenza, H5N1. This report describes the first case of avian influenza A (H5N1) in the Western hemisphere in a 28-year-old woman who had just returned from a trip to Beijing, China. The typical manifestations of H5N1 are described, and signs and symptoms are discussed.

In an urban centre in Alberta, an otherwise healthy 28-year-old woman presented to hospital with pleuritic chest and abdominal pain after returning from Beijing, China. After several days, this was followed by headache, confusion and, ultimately, respiratory failure, coma and death. Microbiology yielded influenza A subtype H5N1 from various body sites and neuroimaging was consistent with meningoencephalitis. While H5N1 infections in humans have been reported in Asia since 1997, this is the first documented case of H5N1 influenza in the Western Hemisphere. The present case demonstrated the typical manifestation of H5N1 influenza but, for the first time, also confirmed previous suggestions from human and animal studies that H5N1 is neurotropic and can manifest with neurological symptoms and meningoencephalitis.

Differences in influenza seasonality by latitude, northern India

The seasonality of influenza in the tropics complicates vaccination timing. We investigated influenza seasonality in northern India and found influenza positivity peaked in Srinagar (34.09°N) in January–March but peaked in New Delhi (28.66°N) in July–September. Srinagar should consider influenza vaccination in October–November, but New Delhi should vaccinate in May–June.

Highly Pathogenic Avian Influenza H5N1 in Mainland China

Highly pathogenic avian influenza (HPAI) H5N1 has posed a significant threat to both humans and birds, and it has spanned large geographic areas and various ecological systems throughout Asia, Europe and Africa, but especially in mainland China. Great efforts in control and prevention of the disease, including universal vaccination campaigns in poultry and active serological and virological surveillance, have been undertaken in mainland China since the beginning of 2006. In this study, we aim to characterize the spatial and temporal patterns of HPAI H5N1, and identify influencing factors favoring the occurrence of HPAI H5N1 outbreaks in poultry in mainland China. Our study shows that HPAI H5N1 outbreaks took place sporadically after vaccination campaigns in poultry, and mostly occurred in the cold season. The positive tests in routine virological surveillance of HPAI H5N1 virus in chicken, duck, goose as well as environmental samples were mapped to display the potential risk distribution of the virus. Southern China had a higher positive rate than northern China, and positive samples were mostly detected from chickens in the north, while the majority were from duck in the south, and a negative correlation with monthly vaccination rates in domestic poultry was found (R = -0.19, p value = 0.005). Multivariate panel logistic regression identified vaccination rate, interaction between distance to the nearest city and national highway, interaction between distance to the nearest lake and wetland, and density of human population, as well as the autoregressive term in space and time as independent risk factors in the occurrence of HPAI H5N1 outbreaks, based on which a predicted risk map of the disease was derived. Our findings could provide new understanding of the distribution and transmission of HPAI H5N1 in mainland China and could be used to inform targeted surveillance and control efforts in both human and poultry populations to reduce the risk of future infections.

Dynamics of influenza seasonality at sub-regional levels in India and implications for vaccination timing

BACKGROUND

Influenza surveillance is an important tool to identify emerging/reemerging strains, and defining seasonality. We describe the distinct patterns of circulating strains of the virus in different areas in India from 2009 to 2013.

METHODS

Patients in ten cities presenting with influenza like illness in out-patient departments of dispensaries/hospitals and hospitalized patients with severe acute respiratory infections were enrolled. Nasopharangeal swabs were tested for influenza viruses by real-time RT-PCR, and subtyping; antigenic and genetic analysis were carried out using standard assays.

RESULTS

Of the 44,127 ILI/SARI cases, 6,193 (14.0%) were positive for influenza virus. Peaks of influenza were observed during July-September coinciding with monsoon in cities Delhi and Lucknow (north), Pune (west), Allaphuza (southwest), Nagpur (central), Kolkata (east) and Dibrugarh (northeast), whereas Chennai and Vellore (southeast) revealed peaks in October-November, coinciding with the monsoon months in these cities. In Srinagar (Northern most city at 34°N latitude) influenza circulation peaked in January-March in winter months. The patterns of circulating strains varied over the years: whereas A/H1N1pdm09 and type B co-circulated in 2009 and 2010, H3N2 was the predominant circulating strain in 2011, followed by circulation of A/H1N1pdm09 and influenza B in 2012 and return of A/H3N2 in 2013. Antigenic analysis revealed that most circulating viruses were close to vaccine selected viral strains.

CONCLUSIONS

Our data shows that India, though physically located in northern hemisphere, has distinct seasonality that might be related to latitude and environmental factors. While cities with temperate seasonality will benefit from vaccination in September-October, cities with peaks in the monsoon season in July-September will benefit from vaccination in April-May. Continued surveillance is critical to understand regional differences in influenza seasonality at regional and sub-regional level, especially in countries with large latitude span.

Seasonal patterns in human A (H5N1) virus infection: analysis of global cases

Background

Human cases of highly pathogenic avian influenza (HPAI) A (H5N1) have high mortality. Despite abundant data on seasonal patterns in influenza epidemics, it is unknown whether similar patterns exist for human HPAI H5N1 cases worldwide. Such knowledge could help decrease avian-to-human transmission through increased prevention and control activities during peak periods.

Methods

We performed a systematic search of published human HPAI H5N1 cases to date, collecting month, year, country, season, hemisphere, and climate data. We used negative binomial regression to predict changes in case incidence as a function of season. To investigate hemisphere as a potential moderator, we used AIC and the likelihood-ratio test to compare the season-only model to nested models including a main effect or interaction with hemisphere. Finally, we visually assessed replication of seasonal patterns across climate groups based on the Köppen-Geiger climate classification.

Findings

We identified 617 human cases (611 with complete seasonal data) occurring in 15 countries in Southeast Asia, Africa, and the Middle East. Case occurrence was much higher in winter (n = 285, p = 0.03) than summer (n = 64), and the winter peak occurred across diverse climate groups. There was no significant interaction between hemisphere and season.

Interpretation

Across diverse climates, HPAI H5N1 virus infection in humans increases significantly in winter. This is consistent with increased poultry outbreaks and HPAI H5N1 virus transmission during cold and dry conditions. Prioritizing prevention and control activities among poultry and focusing public health messaging to reduce poultry exposures during winter months may help to reduce zoonotic transmission of HPAI H5N1 virus in resource-limited settings.

Spatio-temporal epidemiology of highly pathogenic avian influenza (subtype H5N1) in poultry in eastern India

In India, majority outbreaks of highly pathogenic avian influenza (HPAI) H5N1 have occurred in eastern states of West Bengal, Assam and Tripura. This study aimed to identify disease clusters and risk factors of HPAI H5N1 in these states, for targeted surveillance and disease control. A spatial scan statistic identified two significant disease clusters in West Bengal and Assam, occurring during January and November-December 2008, respectively. Key risk factors were identified at sub-district level using bootstrapped logistic regression and boosted regression trees model. With both methods, HPAI H5N1 outbreaks in backyard poultry were associated with accessibility in terms of time taken to access a city with >50,000 persons, human population density and duck density (P<0.005). In addition, areas at lower elevation were also identified as high risk by BRT model. It is recommended that risk-based surveillance should be implemented in high duck density areas and all live-bird markets in high-throughput locations.

Global distribution patterns of highly pathogenic H5N1 avian influenza: environmental vs. socioeconomic factors

In this report, we quantitatively analyzed the essential ecological factors that were strongly correlated with the global outbreak of highly pathogenic H5N1 avian influenza. The ecological niche modeling (ENM) was used to reveal the potential outbreak hotspots of H5N1. A two-step modeling procedure has been proposed: we first used BioClim model to obtain the coarse suitable areas of H5N1, and then those suitable areas with very high probabilities were retained as the inputs of multiple-variable autologistic regression analysis (MAR) for model refinement. MAR was implemented taking spatial autocorrelation into account. The final performance of ENM was evaluated using the areas under the curve (AUC) of receiver-operating characteristic. In addition, principal component analysis (PCA) was employed to reveal the most important variables and relevant ecological gradients of H5N1 outbreak. Niche visualization was used to identify potential spreading trend of H5N1 along important ecological gradients. For the first time, we combined socioeconomic and environmental variables as joint predictors in developing ecological niche modeling. Environmental variables represented the natural element related to H5N1 outbreak, whereas socioeconomic ones represented the anthropogenic element. Our results indicated that: (1) the high-risk hotspots are mainly located in temperate zones (indicated by ENM)-correspondingly, we argued that the "ecoregions hypothesis" was reasonable to some extent; (2) evaporation, humidity, human population density, livestock population density were the first four important factors (in descending order) that were associated with the H5N1 global outbreak (indicated by PCA); (3) influenza had a tendency to expand into areas with low evaporation (indicated by niche visualization). In conclusion, our study substantiates that both the environmental and socioeconomic variables jointly determined the global spreading trend of H5N1, but environmental variables played a more important role. Consequently, our study is consistent with the assumption that the natural element is more important than the anthropogenic element as the underlying ecological mechanisms explaining global H5N1 transmission.

Influenza vaccination in India: position paper of Indian Academy of Pediatrics, 2013

Burden of Influenza is significantly higher in developing countries as compared to developed countries, but the data on the disease burden is less well defined in most of the developing countries including India, and consequently, constraints evolving strategies for prioritization of measures to prevent and control it. The swine flu or A(H1N1) pandemic is on the wane but the virus continues to circulate causing sporadic outbreaks even in 2013. The A(H1N1)pdm09 has replaced the previous circulating seasonal A (H1N1) virus and acquired the status of a seasonal virus. Limited influenza activity is usually seen throughout the year in India with a clear peaking during the rainy season. The rainy season in the country lasts from June to August in all the regions except Tamil Nadu where it occurs from October to December. IAP recommends the ideal time for offering influenza vaccines is just before the onset of rainy season. The efficacy/effectiveness data of trivalent inactivated influenza vaccines are also presented in different age groups and different categories of individuals. The IAP maintains its earlier recommendations of using the current trivalent inactivated influenza vaccine in all children with risk factors but not as a universal measure. IAP has now prioritized different target groups for influenza vaccination based on contribution of the group to the overall influenza burden, disease severity, and vaccine effectiveness in different age groups and categories. The current trivalent inactivated influenza vaccines incorporate the 2009 pandemic strain also, hence avert the need of a separate A (H1N1) vaccine. IAP stresses the need of more refined surveillance; large scale studies on effectiveness of seasonal influenza vaccines in Indian children, and more effective, properly matched, higher-valent influenza vaccines.

Modeling and roles of meteorological factors in outbreaks of highly pathogenic avian influenza H5N1

The highly pathogenic avian influenza A virus subtype H5N1 (HPAI H5N1) is a deadly zoonotic pathogen. Its persistence in poultry in several countries is a potential threat: a mutant or genetically reassorted progenitor might cause a human pandemic. Its world-wide eradication from poultry is important to protect public health. The global trend of outbreaks of influenza attributable to HPAI H5N1 shows a clear seasonality. Meteorological factors might be associated with such trend but have not been studied. For the first time, we analyze the role of meteorological factors in the occurrences of HPAI outbreaks in Bangladesh. We employed autoregressive integrated moving average (ARIMA) and multiplicative seasonal autoregressive integrated moving average (SARIMA) to assess the roles of different meteorological factors in outbreaks of HPAI. Outbreaks were modeled best when multiplicative seasonality was incorporated. Incorporation of any meteorological variable(s) as inputs did not improve the performance of any multivariable models, but relative humidity (RH) was a significant covariate in several ARIMA and SARIMA models with different autoregressive and moving average orders. The variable cloud cover was also a significant covariate in two SARIMA models, but air temperature along with RH might be a predictor when moving average (MA) order at lag 1 month is considered.

Global spatiotemporal and genetic footprint of the H5N1 avian influenza virus

Background

Since 2005, the Qinghai-like lineage of the highly pathogenic avian influenza A virus H5N1 has rapidly spread westward to Europe, the Middle East and Africa, reaching a dominant level at a global scale in 2006.

Methods

Based on a combination of genetic sequence data and H5N1 outbreak information from 2005 to 2011, we use an interdisciplinary approach to improve our understanding of the transmission pattern of this particular clade 2.2, and present cartography of global spatiotemporal transmission footprints with genetic characteristics.

Results

Four major viral transmission routes were derived with three sources— Russia, Mongolia, and the Middle East (Kuwait and Saudi Arabia)—in the three consecutive years 2005, 2006 and 2007. With spatiotemporal transmission along each route, genetic distances to isolate A/goose/Guangdong/1996 are becoming significantly larger, leading to a more challenging situation in certain regions like Korea, India, France, Germany, Nigeria and Sudan. Europe and India have had at least two incursions along multiple routes, causing a mixed virus situation. In addition, spatiotemporal distribution along the routes showed that 2007/2008 was a temporal separation point for the infection of different host species; specifically, wild birds were the main host in 2005–2007/2008 and poultry was responsible for the genetic mutation in 2009–2011. “Global-to-local” and “high-to-low latitude” transmission footprints have been observed.

Conclusions

Our results suggest that both wild birds and poultry play important roles in the transmission of the H5N1 virus clade, but with different spatial, temporal, and genetic dominance. These characteristics necessitate that special attention be paid to countries along the transmission routes.

Influenza seasonality and vaccination timing in tropical and subtropical areas of southern and south-eastern Asia

OBJECTIVE

To characterize influenza seasonality and identify the best time of the year for vaccination against influenza in tropical and subtropical countries of southern and south-eastern Asia that lie north of the equator.

METHODS

Weekly influenza surveillance data for 2006 to 2011 were obtained from Bangladesh, Cambodia, India, Indonesia, the Lao People's Democratic Republic, Malaysia, the Philippines, Singapore, Thailand and Viet Nam. Weekly rates of influenza activity were based on the percentage of all nasopharyngeal samples collected during the year that tested positive for influenza virus or viral nucleic acid on any given week. Monthly positivity rates were then calculated to define annual peaks of influenza activity in each country and across countries.

FINDINGS

Influenza activity peaked between June/July and October in seven countries, three of which showed a second peak in December to February. Countries closer to the equator had year-round circulation without discrete peaks. Viral types and subtypes varied from year to year but not across countries in a given year. The cumulative proportion of specimens that tested positive from June to November was > 60% in Bangladesh, Cambodia, India, the Lao People's Democratic Republic, the Philippines, Thailand and Viet Nam. Thus, these tropical and subtropical countries exhibited earlier influenza activity peaks than temperate climate countries north of the equator.

CONCLUSION

Most southern and south-eastern Asian countries lying north of the equator should consider vaccinating against influenza from April to June; countries near the equator without a distinct peak in influenza activity can base vaccination timing on local factors.

MODELING SEASONALITY IN AVIAN INFLUENZA H5N1

The number of cases of H5N1 avian influenza in birds and humans exhibit seasonality which peaks during the winter months. What causes the seasonality in H5N1 cases is still being investigated. This article addresses the question of modeling the periodicity in cumulative number of human cases of H5N1. Three potential drivers of influenza seasonality are investigated: (1) seasonality in bird-to-bird transmission; (2) seasonality caused by wild bird migration or seasonal fluctuation of avian influenza in wild birds; (3) seasonality caused by environmental transmission. A framework of seven models is composed. The seven models involve these three mechanisms and combinations of the mechanisms. Each of the models in the framework is fitted to the cumulative number of humans cases of H5N1. The corrected akaike information criterion (AICc) is used to compare the models and it is found that the model with periodic bird-to-bird transmission rate best explains the data. The best fitted model with the best fitted parameters gives a reproduction number of highly pathogenic avian influenza [Formula: see text]. The best fitted model is a simple SI epidemic model with periodic transmission rate and disease-induced mortality, however, this model is capable of very complex dynamical behavior such as period doubling and chaos.