Environment: a potential source of animal and human infection with influenza A (H5N1) virus

A systematic review of influenza virus in water environments across human, poultry, and wild bird habitats

Influenza, a highly contagious acute respiratory disease, remains a major global health concern. This study aimed to comprehensively assess the prevalence of influenza virus in different aquatic environments. Using 43 articles from four databases, we thoroughly examined water matrices from wastewater treatment plants (WTPs) and other human environments, as well as poultry habitats and areas frequented by migratory wild birds. In WTP influents (10 studies), positivity rates for influenza A ranged from 0.0 % to 97.6 %. For influenza B (8 studies), most studies reported no positivity, except for three studies reporting detection in 0.8 %, 5.6 %, and 46.9 % of samples. Within poultry habitats (13 studies), the prevalence of influenza A ranged from 4.3 % to 76.4 %, while in environments frequented by migratory wild birds (11 studies), it ranged from 0.4 % to 69.8 %. Geographically, the studies were distributed as follows: 39.5 % from the Americas, 18.6 % from Europe, 2.3 % from South-East Asia and 39.5 % from the Western Pacific. Several influenza A subtypes were found in water matrices, including avian influenza (H3N6, H3N8, H4N1, H4N2, H4N6, H4N8, H5N1, H5N8, H6N2, H6N6, H7N9, H0N8, and H11N9) and seasonal human influenza (H1N1 and H3N2). The existing literature indicates a crucial requirement for more extensive future research on this topic. Specifically, it emphasizes the need for method harmonization and delves into areas deserving of in-depth research, such as water matrices pertaining to pig farming and prevalence studies in low-income countries.

Environmental Surveillance and Detection of Infectious Highly Pathogenic Avian Influenza Virus in Iowa Wetlands

Avian influenza viruses (AIVs) infect both wild birds and domestic poultry, resulting in economically costly outbreaks that have the potential to impact public health. Currently, a knowledge gap exists regarding the detection of infectious AIVs in the aquatic environment. In response to the 2021-2022 Eurasian strain highly pathogenic avian influenza (HPAI) A/goose/Guangdong/1/1996 clade 2.3.4.4 lineage H5 outbreak, an AIV environmental outbreak response study was conducted using a One Health approach. An optimized method was used to temporally sample (April and May 2022) and analyze (culture and molecular methods) surface water from five water bodies (four wetlands and one lake used as a comparison location) in areas near confirmed HPAI detections in wild bird or poultry operations. Avian influenza viruses were isolated from water samples collected in April from all four wetlands (not from the comparison lake sample); HPAI H5N1 was isolated from one wetland. No virus was isolated from the May samples. Several factors, including increased water temperatures, precipitation, biotic and abiotic factors, and absence of AIV-contaminated fecal material due to fewer waterfowl present, may have contributed to the lack of virus isolation from May samples. Results demonstrate surface water as a plausible medium for transmission of AIVs, including the HPAI virus.

A comprehensive review of highly pathogenic avian influenza (HPAI) H5N1: An imminent threat at doorstep

Avian influenza viruses (AIVs) are globally challenging due to widespread circulation and high mortality rates. Highly pathogenic avian influenza (HPAI) strains like H5N1 have caused significant outbreaks in birds. Since 2003 to 14 July 2023, the World Health Organization (WHO) has documented 878 cases of HPAI H5N1 infection in humans and 458 (52.16%) fatalities in 23 countries. Recent outbreaks in wild birds, domestic birds, sea lions, minks, and etc., and the occurrence of genetic variations among HPAI H5N1 strains raise concerns about potential transmission and public health risks. This paper aims to provide a comprehensive overview of the current understanding and new insights into HPAI H5N1. It begins with an introduction to the significance of studying this virus and highlighting the need for updated knowledge. The origin and evaluation of HPAI H5N1 are examined, shedding light on its emergence, and spread across different geographic regions. The genome organization and structural biology of the H5N1 virus are explored, providing insights into its molecular composition and key structural features. This manuscript also delves into the phylogeny, evolution, mutational trends, reservoirs, and transmission routes of HPAI H5N1. The immune response against HPAI H5N1 and its implications for vaccine development are analyzed, along with an exploration of the pathogenesis and clinical manifestations of HPAI H5N1 in human cases. Furthermore, diagnostic tools and preventive and therapeutic strategies are discussed, highlighting the current approaches and potential future directions for better management of the potential pandemic.

Aerosol exposure of live bird market workers to viable influenza A/H5N1 and A/H9N2 viruses, Cambodia

Live bird markets (LBMs) have been identified as key factors in the spread, persistence and evolution of avian influenza viruses (AIVs). In addition, these settings have been associated with human infections with AIVs of pandemic concern. Exposure to aerosolised AIVs by workers in a Cambodian LBM was assessed using aerosol impact samplers. LBM vendors were asked to wear an air sampler for 30 min per day for 1 week while continuing their usual activities in the LBM during a period of high AIV circulation (February) and a period of low circulation (May). During the period of high circulation, AIV RNA was detected from 100% of the air samplers using molecular methods and viable AIV (A/H5N1 and/or A/H9N2) was isolated from 50% of air samplers following inoculation into embryonated chicken eggs. In contrast, AIV was not detected by molecular methods or successfully isolated during the period of low circulation. This study demonstrates the increased risk of aerosol exposure of LBM workers to AIVs during periods of high circulation and highlights the need for interventions during these high-risk periods. Novel approaches, such as environmental sampling, should be further explored at key high-risk interfaces as a potentially cost-effective alternative for monitoring pandemic threats.

Exploring surface water as a transmission medium of avian influenza viruses - systematic infection studies in mallards

Mallards (Anas platyrhynchos) are an abundant anseriform migratory wild bird species worldwide and an important reservoir for the maintenance of low pathogenicity (LP) avian influenza viruses (AIV). They have also been implicated in the spread of high pathogenicity (HP) AIV after spill-over events from HPAIV-infected poultry. The spread of HPAIV within wild water bird populations may lead to viral contamination of natural habitats. The role of small shallow water bodies as a transmission medium of AIV among mallards is investigated here in three experimental settings. (i) Delayed onset but rapid progression of infection seeded by two mallards inoculated with either LP or HP AIV to each eight sentinel mallards was observed in groups with access to a small 100 L water pool. In contrast, groups with a bell drinker as the sole source of drinking water showed a rapid onset but lengthened course of infection. (ii) HPAIV infection also set off when virus was dispersed in the water pool; titres as low as 10² TCID₅₀ L^-1 (translating to 0.1 TCID₅₀ mL^-1) proved to be sufficient. (iii) Substantial loads of viral RNA (and infectivity) were also found on the surface of the birds' breast plumage. "Unloading" of virus infectivity from contaminated plumage into water bodies may be an efficient mechanism of virus spread by infected mallards. However, transposure of HPAIV via the plumage of an uninfected mallard failed. We conclude, surface water in small shallow water bodies may play an important role as a mediator of AIV infection of aquatic wild birds.

Simultaneous Detection of SARS-CoV-2 and Influenza Virus in Wastewater of Two Cities in Southeastern Germany, January to May 2022

Dependent on the excretion pattern, wastewater monitoring of viruses can be a valuable approach to characterizing their circulation in the human population. Using polyethylene glycol precipitation and reverse transcription-quantitative PCR, the occurrence of RNA of SARS-CoV-2 and influenza viruses A/B in the raw wastewater of two treatment plants in Germany between January and May 2022 was investigated. Due to the relatively high incidence in both exposal areas (plant 1 and plant 2), SARS-CoV-2-specific RNA was determined in all 273 composite samples analyzed (concentration of E gene: 1.3 × 10⁴ to 3.2 × 10⁶ gc/L). Despite a nation-wide low number of confirmed infections, influenza virus A was demonstrated in 5.2% (concentration: 9.8 × 10² to 8.4 × 10⁴ gc/L; plant 1) and in 41.6% (3.6 × 10³ to 3.0 × 10⁵ gc/L; plant 2) of samples. Influenza virus B was detected in 36.0% (7.2 × 10² to 8.5 × 10⁶ gc/L; plant 1) and 57.7% (9.6 × 10³ to 2.1 × 10⁷ gc/L; plant 2) of wastewater samples. The results of the study demonstrate the frequent detection of two primary respiratory viruses in wastewater and offer the possibility to track the epidemiology of influenza by wastewater-based monitoring.

Methods Evaluation for Rapid Concentration and Quantification of SARS-CoV-2 in Raw Wastewater Using Droplet Digital and Quantitative RT-PCR

Wastewater surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging public health tool to understand the spread of Coronavirus Disease 2019 (COVID-19) in communities. The performance of different virus concentration methods and PCR methods needs to be evaluated to ascertain their suitability for use in the detection of SARS-CoV-2 in wastewater. We evaluated ultrafiltration and polyethylene glycol (PEG) precipitation methods to concentrate SARS-CoV-2 from sewage in wastewater treatment plants and upstream in the wastewater network (e.g., manholes, lift stations). Recovery of viruses by different concentration methods was determined using Phi6 bacteriophage as a surrogate for enveloped viruses. Additionally, the presence of SARS-CoV-2 in all wastewater samples was determined using reverse transcription quantitative PCR (RT-qPCR) and reverse transcription droplet digital PCR (RT-ddPCR), targeting three genetic markers (N1, N2 and E). Using spiked samples, the Phi6 recoveries were estimated at 2.6-11.6% using ultrafiltration-based methods and 22.2-51.5% using PEG precipitation. There was no significant difference in recovery efficiencies (p < 0.05) between the PEG procedure with and without a 16 h overnight incubation, demonstrating the feasibility of obtaining same day results. The SARS-CoV-2 genetic markers were more often detected by RT-ddPCR than RT-qPCR with higher sensitivity and precision. While all three SARS-CoV-2 genetic markers were detected using RT-ddPCR, the levels of E gene were almost below the limit of detection using RT-qPCR. Collectively, our study suggested PEG precipitation is an effective low-cost procedure which allows a large number of samples to be processed simultaneously in a routine wastewater monitoring for SARS-CoV-2. RT-ddPCR can be implemented for the absolute quantification of SARS-CoV-2 genetic markers in different wastewater matrices.

A SYSTEMATIC REVIEW AND NARRATIVE SYNTHESIS OF THE USE OF ENVIRONMENTAL SAMPLES FOR THE SURVEILLANCE OF AVIAN INFLUENZA VIRUSES IN WILD WATERBIRDS

Wild waterbirds are reservoir hosts for avian influenza viruses (AIV), which can cause devastating outbreaks in multiple species, making them a focus for surveillance efforts. Traditional AIV surveillance involves direct sampling of live or dead birds, but environmental substrates present an alternative sample for surveillance. Environmental sampling analyzes AIV excreted by waterbirds into the environment and complements direct bird sampling by minimizing financial, logistic, permitting, and spatial-temporal constraints associated with traditional surveillance. Our objectives were to synthesize the literature on environmental AIV surveillance, to compare and contrast the different sample types, and to identify key themes and recommendations to aid in the implementation of AIV surveillance using environmental samples. The four main environmental substrates for AIV surveillance are feces, feathers, water, and sediment or soil. Feces were the most common environmental substrate collected. The laboratory analysis of water and sediment provided challenges, such as low AIV concentration, heterogenous AIV distribution, or presence of PCR inhibitors. There are a number of abiotic and biotic environmental factors, including temperature, pH, salinity, or presence of filter feeders, that can influence the presence and persistence of AIV in environmental substrates; however, the nature of this influence is poorly understood in field settings, and field data from southern, coastal, and tropical ecosystems are underrepresented. Similarly, there are few studies comparing the performance of environmental samples to each other and to samples collected in wild waterbirds, and environmental surveillance workflows have yet to be validated or optimized. Environmental samples, particularly when used in combination with new technology such as environmental DNA and next generation sequencing, provided information on trends in AIV detection rates and circulating subtypes that complemented traditional, direct waterbird sampling. The use of environmental samples for AIV surveillance also shows significant promise for programs whose goal is early warning of high-risk subtypes.

A literature review of the use of environmental sampling in the surveillance of avian influenza viruses

This literature review provides an overview of use of environmental samples (ES) such as faeces, water, air, mud and swabs of surfaces in avian influenza (AI) surveillance programs, focussing on effectiveness, advantages and gaps in knowledge. ES have been used effectively for AI surveillance since the 1970s. Results from ES have enhanced understanding of the biology of AI viruses in wild birds and in markets, of links between human and avian influenza, provided early warning of viral incursions, allowed assessment of effectiveness of control and preventive measures, and assisted epidemiological studies in outbreaks, both avian and human. Variation exists in the methods and protocols used, and no internationally recognized guidelines exist on the use of ES and data management. Few studies have performed direct comparisons of ES versus live bird samples (LBS). Results reported so far demonstrate reliance on ES will not be sufficient to detect virus in all cases when it is present, especially when the prevalence of infection/contamination is low. Multiple sample types should be collected. In live bird markets, ES from processing/selling areas are more likely to test positive than samples from bird holding areas. When compared to LBS, ES is considered a cost-effective, simple, rapid, flexible, convenient and acceptable way of achieving surveillance objectives. As a non-invasive technique, it can minimize effects on animal welfare and trade in markets and reduce impacts on wild bird communities. Some limitations of environmental sampling methods have been identified, such as the loss of species-specific or information on the source of virus, and taxonomic-level analyses, unless additional methods are applied. Some studies employing ES have not provided detailed methods. In others, where ES and LBS are collected from the same site, positive results have not been assigned to specific sample types. These gaps should be remedied in future studies.

Detection of Low Pathogenic Avian Influenza Virus Subtype H10N7 in Poultry and Environmental Water Samples During a Clinical Outbreak in Commercial Free-Range Layers, Netherlands 2017

Wild birds are the natural reservoir of the avian influenza virus (AIV) and may transmit AIV to poultry via direct contact or indirectly through the environment. In the Netherlands, a clinically suspected free-range layer flock was reported to the veterinary authorities by the farmer. Increased mortality, a decreased feed intake, and a drop in egg production were observed. Subsequently, an infection with low pathogenic avian influenza virus was detected. This study describes the diagnostic procedures used for detection and subtyping of the virus. In addition to routine diagnostics, the potential of two different environmental diagnostic methods was investigated for detecting AIV in surface water. AIV was first detected using rRT-PCR and isolated from tracheal and cloacal swabs collected from the hens. The virus was subtyped as H10N7. Antibodies against the virus were detected in 28 of the 31 sera tested. An intravenous pathogenicity index (IVPI) experiment was performed, but no clinical signs (IVPI = 0) were observed. Post-mortem examination and histology confirmed the AIV infection. Multiple water samples were collected longitudinally from the free-range area and waterway near the farm. Both environmental diagnostic methods allowed the detection of the H10N7 virus, demonstrating the potential of these methods in detection of AIV. The described methods could be a useful additional procedure for AIV surveillance in water-rich areas with large concentrations of wild birds or in areas around poultry farms. In addition, these methods could be used as a tool to test if the environment or free-range area is virus-free again, at the end of an AIV epidemic.

The evolution and genetic diversity of avian influenza A(H9N2) viruses in Cambodia, 2015 - 2016

Low pathogenic A(H9N2) subtype avian influenza viruses (AIVs) were originally detected in Cambodian poultry in 2013, and now circulate endemically. We sequenced and characterised 64 A(H9N2) AIVs detected in Cambodian poultry (chickens and ducks) from January 2015 to May 2016. All A(H9) viruses collected in 2015 and 2016 belonged to a new BJ/94-like h9-4.2.5 sub-lineage that emerged in the region during or after 2013, and was distinct to previously detected Cambodian viruses. Overall, there was a reduction of genetic diversity of H9N2 since 2013, however two genotypes were detected in circulation, P and V, with extensive reassortment between the viruses. Phylogenetic analysis showed a close relationship between A(H9N2) AIVs detected in Cambodian and Vietnamese poultry, highlighting cross-border trade/movement of live, domestic poultry between the countries. Wild birds may also play a role in A(H9N2) transmission in the region. Some genes of the Cambodian isolates frequently clustered with zoonotic A(H7N9), A(H9N2) and A(H10N8) viruses, suggesting a common ecology. Molecular analysis showed 100% of viruses contained the hemagglutinin (HA) Q226L substitution, which favours mammalian receptor type binding. All viruses were susceptible to the neuraminidase inhibitor antivirals; however, 41% contained the matrix (M2) S31N substitution associated with resistance to adamantanes. Overall, Cambodian A(H9N2) viruses possessed factors known to increase zoonotic potential, and therefore their evolution should be continually monitored.

Evidence of exposure and human seroconversion during an outbreak of avian influenza A(H5N1) among poultry in Cameroon

From May 2016 to March 2017, 22 poultry outbreaks of avian influenza A(H5N1) were reported in Cameroon, mainly in poultry farms and live bird markets. No human cases were reported. In this study, we sought to describe the 2016 A(H5N1) outbreak strain and to investigate the risk of infection in exposed individuals. We find that highly pathogenic influenza subtype A(H5N1), clade 2.3.2.1c from Cameroon is closely related phylogenetically and antigenically to strains isolated in central and western Africa at the time. No molecular markers of increased human transmissibility were noted; however, seroconversion was detected in two poultry workers (1.5% of total screened). Therefore, the continued outbreaks of avian influenza in poultry and the risk of zoonotic human infection highlight the crucial need for continued and vigilant influenza surveillance and research in Africa, especially in areas of high poultry trade, such as Cameroon.

Genetic analysis identifies potential transmission of low pathogenic avian influenza viruses between poultry farms

Poultry can become infected with low pathogenic avian influenza (LPAI) viruses via (in)direct contact with infected wild birds or by transmission of the virus between farms. This study combines routinely collected surveillance data with genetic analysis to assess the contribution of between‐farm transmission to the overall incidence of LPAI virus infections in poultry. Over a 10‐year surveillance period, we identified 35 potential cases of between‐farm transmission in the Netherlands, of which 10 formed geographical clusters. A total of 21 LPAI viruses were isolated from nine potential between‐farm transmission cases, which were further studied by genetic and epidemiological analysis. Whole genome sequence analysis identified close genetic links between infected farms in seven cases. The presence of identical deletions in the neuraminidase stalk region and minority variants provided additional indications of between‐farm transmission. Spatiotemporal analysis demonstrated that genetically closely related viruses were detected within a median time interval of 8 days, and the median distance between the infected farms was significantly shorter compared to farms infected with genetically distinct viruses (6.3 versus 69.0 km; p < 0.05). The results further suggest that between‐farm transmission was not restricted to holdings of the same poultry type and not related to the housing system. Although separate introductions from the wild bird reservoir cannot be excluded, our study indicates that between‐farm transmission occurred in seven of nine virologically analysed cases. Based on these findings, it is likely that between‐farm transmission contributes considerably to the incidence of LPAI virus infections in poultry.

Co-circulation of Influenza A H5, H7, and H9 Viruses and Co-infected Poultry in Live Bird Markets, Cambodia

Longitudinal surveillance of 2 live bird markets in Cambodia revealed year-round, high co-circulation of H5, H7, and H9 influenza viruses. We detected influenza A viruses in 51.3% of ducks and 39.6% of chickens, and co-infections, mainly by H5 and H9 viruses, in 0.8% of ducks and 4.5% of chickens.

An epidemiological study of avian influenza A (H5) virus in nomadic ducks and their raising practices in northeastern Bangladesh, 2011-2012

BACKGROUND

In Bangladesh, nomadic duck flocks are groups of domestic ducks reared for egg production that are moved to access feeding sites beyond their owners' village boundaries and are housed overnight in portable enclosures in scavenging areas. The objectives of this study were to measure the prevalence of influenza A virus RNA and H5-specific antibodies in nomadic ducks and to characterize nomadic duck raising practices in northeastern Bangladesh.

METHODS

We tested duck egg yolk specimens by competitive ELISA to detect antibodies against avian influenza A (H5) and environmental fecal samples by real-time reverse-transcription polymerase chain reaction (rRT-PCR) to detect influenza A virus RNA and H5 subtype.

RESULTS

The median age of the ducks was 24 months (range: 8-36 months) and the median flock size was 300 ducks (range: 105-1100). Of 1860 egg yolk samples, 556 (30%, 95% confidence interval (CI): 28-32) were positive for antibodies against H5 and 58 flocks (94%) had at least one egg with H5-specific antibodies. Of 496 fecal samples, 121 (24%, 95% CI: 22-29) had detectable influenza A RNA. Thirty-three flocks (53%) had at least one fecal sample positive for influenza A RNA.

CONCLUSIONS

Nomadic ducks in Bangladesh are commonly infected with avian influenza A (H5) virus and may serve as a bridging host for transmission of avian influenza A (H5) virus or other avian influenza A viruses subtypes between wild waterfowl, backyard poultry, and humans in Bangladesh.

Risk factors for avian influenza virus contamination of live poultry markets in Zhejiang, China during the 2015-2016 human influenza season

Live bird markets (LBMs), being a potential source of avian influenza virus, require effective environmental surveillance management. In our study, a total of 2865 environmental samples were collected from 292 LBMs during the 2015–2016 human influenza season from 10 cities in Zhejiang province, China. The samples were tested by real-time quantitative polymerase chain reaction (RT-PCR). Field investigations were carried out to investigate probable risk factors. Of the environmental samples, 1519 (53.0%) were contaminated by A subtype. The highest prevalence of the H9 subtype was 30.2%, and the frequencies of the H5 and H7 subtype were 9.3% and 17.3%, respectively. Hangzhou and Jinhua cities were contaminated more seriously than the others. The prevalence of H5/H7/H9 in drinking water samples was highest, at 50.9%, and chopping board swabs ranked second, at 49.3%. Duration of sales per day, types of live poultry, LBM location and the number of live poultry were the main risk factors for environmental contamination, according to logistic regression analysis. In conclusion, LBMs in Zhejiang were contaminated by avian influenza. Our study has provided clues for avian influenza prevention and control during the human influenza season, especially in areas where LBMs are not closed.

The ecology and adaptive evolution of influenza A interspecies transmission

Since 2013, there have been several alarming influenza-related events; the spread of highly pathogenic avian influenza H5 viruses into North America, the detection of H10N8 and H5N6 zoonotic infections, the ongoing H7N9 infections in China and the continued zoonosis of H5N1 viruses in parts of Asia and the Middle East. The risk of a new influenza pandemic increases with the repeated interspecies transmission events that facilitate reassortment between animal influenza strains; thus, it is of utmost importance to understand the factors involved that promote or become a barrier to cross-species transmission of Influenza A viruses (IAVs). Here, we provide an overview of the ecology and evolutionary adaptations of IAVs, with a focus on a review of the molecular factors that enable interspecies transmission of the various virus gene segments.

Environmental contamination and risk factors for transmission of highly pathogenic avian influenza A(H5N1) to humans, Cambodia, 2006-2010

BACKGROUND

Highly pathogenic avian influenza A (H5N1) virus has been of public health concern since 2003. Probable risk factors for A(H5N1) transmission to human have been demonstrated in several studies or epidemiological reports. However, transmission patterns may differ according to demographic characteristics of the population and local practices. This article aggregates these data from three studies with data collected in the previous surveys in 2006 and 2007 to further examine the risks factors associated with presence of anti-A(H5) antibodies among villagers residing within outbreak areas.

METHODS

We aggregated 5-year data (2006-2010) from serology survey and matched case-control studies in Cambodia to further examine the risks factors associated with A(H5N1) infection among villagers in the outbreak areas.

RESULTS

Serotesting among villagers detected 35 (1.5 % [0-2.6]) positive cases suggesting recent exposure to A(H5N1) virus. Practices associated with A(H5N1) infection among all ages were: having poultry cage or nesting area under or adjacent to the house (OR: 6.7 [1.6-28.3]; p = 0.010) and transporting poultry to market (OR: 17.6 [1.6-193.7]; p = 0.019). Practices found as risk factors for the infection among age under 20 years were swimming/bathing in ponds also accessed by domestic poultry (OR: 4.6 [1.1-19.1]; p = 0.038). Association with consuming wild birds reached borderline significance (p = 0.066).

CONCLUSION

Our results suggest that swimming/bathing in contaminated pond water and close contact with poultry may present a risk of A(H5N1) transmission to human.

Intense circulation of A/H5N1 and other avian influenza viruses in Cambodian live-bird markets with serological evidence of sub-clinical human infections

Surveillance for avian influenza viruses (AIVs) in poultry and environmental samples was conducted in four live-bird markets in Cambodia from January through November 2013. Through real-time RT-PCR testing, AIVs were detected in 45% of 1048 samples collected throughout the year. Detection rates ranged from 32% and 18% in duck and chicken swabs, respectively, to 75% in carcass wash water samples. Influenza A/H5N1 virus was detected in 79% of samples positive for influenza A virus and 35% of all samples collected. Sequence analysis of full-length haemagglutinin (HA) and neuraminidase (NA) genes from A/H5N1 viruses, and full-genome analysis of six representative isolates, revealed that the clade 1.1.2 reassortant virus associated with Cambodian human cases during 2013 was the only A/H5N1 virus detected during the year. However, multiplex reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of HA and NA genes revealed co-circulation of at least nine low pathogenic AIVs from HA1, HA2, HA3, HA4, HA6, HA7, HA9, HA10 and HA11 subtypes. Four repeated serological surveys were conducted throughout the year in a cohort of 125 poultry workers. Serological testing found an overall prevalence of 4.5% and 1.8% for antibodies to A/H5N1 and A/H9N2, respectively. Seroconversion rates of 3.7 and 0.9 cases per 1000 person-months participation were detected for A/H5N1 and A/H9N2, respectively. Peak AIV circulation was associated with the Lunar New Year festival. Knowledge of periods of increased circulation of avian influenza in markets should inform intervention measures such as market cleaning and closures to reduce risk of human infections and emergence of novel AIVs.

Living with avian FLU--Persistence of the H5N1 highly pathogenic avian influenza virus in Egypt

H5N1 highly pathogenic avian influenza virus (HPAIV) continues to cause mortality in poultry and threaten human health at a panzootic scale in Egypt since it was reported in 2006. While the early focus has been in Asia, recent evidence suggests that Egypt is an emerging epicenter for the disease. Despite control measures, epizootic transmission of the disease continues. Here, we investigate the persistence of HPAIV across wild passerine birds and domestic poultry between 2009 and 2012 and the potential risk for continuous viral transmission in Egypt. We use a new weighted cross J-function to investigate the degree and spatial temporal nature of the clustering between sightings of infected birds of different types, and the risk of infection associated with direct contact with infected birds. While we found no infection in wild birds, outbreaks occurred year round between 2009 and 2012, with a positive interaction between chickens and ducks. The disease was more present in the years 2010 and 2011 coinciding with the political unrest in the country. Egypt thus continues to experience endemic outbreaks of avian influenza HPAIV in poultry and an increased potential risk of infection to other species including humans. With the current trends, the elimination of the HPAIV infection is highly unlikely without a complete revamp of current policies. The application of spatial statistics techniques to these types of data may help us to understand the characteristics of the disease and may subsequently allow practitioners to explore possible preventive solutions.

Wind-Mediated Spread of Low-Pathogenic Avian Influenza Virus into the Environment during Outbreaks at Commercial Poultry Farms

Avian influenza virus-infected poultry can release a large amount of virus-contaminated droppings that serve as sources of infection for susceptible birds. Much research so far has focused on virus spread within flocks. However, as fecal material or manure is a major constituent of airborne poultry dust, virus-contaminated particulate matter from infected flocks may be dispersed into the environment. We collected samples of suspended particulate matter, or the inhalable dust fraction, inside, upwind and downwind of buildings holding poultry infected with low-pathogenic avian influenza virus, and tested them for the presence of endotoxins and influenza virus to characterize the potential impact of airborne influenza virus transmission during outbreaks at commercial poultry farms. Influenza viruses were detected by RT-PCR in filter-rinse fluids collected up to 60 meters downwind from the barns, but virus isolation did not yield any isolates. Viral loads in the air samples were low and beyond the limit of RT-PCR quantification except for one in-barn measurement showing a virus concentration of 8.48 x 10(4) genome copies/m(3). Air samples taken outside poultry barns had endotoxin concentrations of ~50 EU/m(3) that declined with increasing distance from the barn. Atmospheric dispersion modeling of particulate matter, using location-specific meteorological data for the sampling days, demonstrated a positive correlation between endotoxin measurements and modeled particulate matter concentrations, with an R(2) varying from 0.59 to 0.88. Our data suggest that areas at high risk for human or animal exposure to airborne influenza viruses can be modeled during an outbreak to allow directed interventions following targeted surveillance.

In vitro inactivation of two Egyptian A/H5N1 viruses by four commercial chemical disinfectants

The highly pathogenic H5N1 avian influenza virus (A/H5N1) devastated the poultry industry and posed a serious health threat. Cleaning and disinfection are essential parts of preventative and postoutbreak management of A/H5N1 infections in poultry. In this preliminary study, we used suspension and carrier tests to evaluate the impact of concentration, time of exposure, surface porosity, and organic matter on the ability of four commercial chemical disinfectants to inactivate two A/H5N1 viruses of clade 2.2.1 isolated in 2006 and 2010 from broiler flocks in Egypt. Viruses were incubated with 0.5%, 1%, and 2% of formalin, glutaraldehyde, TH4, and Virkon S for 15, 30, 60, and 120 min at room temperature (22 +/- 2 C). In suspension tests, in the absence of organic matter, all disinfectants, at each concentration, except Virkon S 0.5%, effectively inactivated virus suspensions after a 15-min exposure time. In the presence of organic matter, the use of low concentrations of formalin (0.5%), glutaraldehyde (0.5%), or Virkon S (0.5%) was not sufficient to inactivate the viruses after 15 min. In gauze carrier tests, only formalin at any concentration for 15 min was sufficient to inactivate the viruses, whereas different concentrations or exposure times were required for glutaraldehyde (0.5% for 60 min), TH4 (0.5% for 30 min), and Virkon S (0.5% for 60 min or 1% for 30 min). In wood carrier tests, total inactivation of the virus was obtained at concentrations of 0.5% for 30 min (formalin and TH4) or 60 min (glutaraldehyde and Virkon S). This study emphasizes the need to use high concentrations of and/or extended time of exposure to disinfectants for efficient inactivation of A/H5N1, particularly in the presence of organic matter or different surfaces, which are common in poultry operations. In addition, it seemed that the virus isolated in 2010 was more resistant to disinfectants than the isolate from 2006 when wood was used as a carrier.

Poultry slaughtering practices in rural communities of Bangladesh and risk of avian influenza transmission: a qualitative study

Slaughtering sick poultry is a risk factor for human infection with highly pathogenic avian influenza and is a common practice in Bangladesh. This paper describes human exposures to poultry during slaughtering process and the customs and rituals influencing these practices in two Bangladeshi rural communities. In 2009, we conducted 30 observations to observe slaughtering practices and 110 in-depth and short interviews and 36 group discussions to explore reasons behind those practices. The villagers reported slaughtering 103 poultry, including 20 sick poultry during 2 months. During different stages of slaughtering, humans, the environment, healthy poultry, and other animals were exposed to poultry blood and body parts. Women performed most of the slaughtering tasks, including evisceration. Defeathering required the most time and involved several persons. During festivals, ceremonies, and rituals, many people gathered and participated in the slaughtering of poultry. Exposure to poultry slaughtering created numerous opportunities for potential avian influenza transmission. Strategies that can be further tested to determine if they reduce the risk of transmission include skinning the carcasses of sick poultry, using hot water for defeathering and cleaning, using a bucket to contain slaughtering blood and carcass, burying the offal and encouraging handwashing.

Seroprevalence of antibodies to highly pathogenic avian influenza A (H5N1) virus among close contacts exposed to H5N1 cases, China, 2005-2008

To assess the extent of highly pathogenic avian influenza (HPAI) A (H5N1) virus transmission, we conducted sero-epidemiologic studies among close contacts exposed to H5N1 cases in mainland China during 2005-2008. Blood specimens were collected from 87 household members and 332 social contacts of 23 H5N1 index cases for HPAI H5N1 serological testing by modified horse red-blood-cell hemagglutinin inhibition and microneutralization assays. All participants were interviewed with a standardized questionnaire to collect information about the use of personal protective equipment, illness symptoms, exposure to an H5N1 case during the infectious period, and poultry exposures. Two (2.3%) household contacts tested positive for HPAI H5N1 virus antibody, and all social contacts tested negative. Both seropositive cases had prolonged, unprotected, close contact with a different H5N1 index case, including days of bed-care or sleeping together during the index case's infectious period, and did not develop any illness. None of the 419 close contacts used appropriate personal protective equipment including 17% who reported providing bedside care or having physical contact with an H5N1 case for at least 12 hours. Our findings suggest that HPAI H5N1 viruses that circulated among poultry in mainland China from 2005-2008 were not easily transmitted to close contacts of H5N1 cases.

Influenza A(H5N1) virus surveillance at live poultry markets, Cambodia, 2011

In Cambodia, influenza A(H5N1) virus surveillance at live poultry markets (LPMs) relies on virus isolation from poultry specimens; however, virus is rarely detected by this method. We tested 502 environmental LPM samples: 90 were positive by PCR, 10 by virus isolation. Virus circulation could be better monitored by environmental sampling of LPMs.

Connecting the study of wild influenza with the potential for pandemic disease

Continuing outbreaks of pathogenic (H5N1) and pandemic (SOIVH1N1) influenza have underscored the need to understand the origin, characteristics, and evolution of novel influenza A virus (IAV) variants that pose a threat to human health. In the last 4-5years, focus has been placed on the organization of large-scale surveillance programs to examine the phylogenetics of avian influenza virus (AIV) and host-virus relationships in domestic and wild animals. Here we review the current gaps in wild animal and environmental surveillance and the current understanding of genetic signatures in potentially pandemic strains.

Pathogen-host-environment interplay and disease emergence

Gaining insight in likely disease emergence scenarios is critical to preventing such events from happening. Recent focus has been on emerging zoonoses and on identifying common patterns and drivers of emerging diseases. However, no overarching framework exists to integrate knowledge on all emerging infectious disease events. Here, we propose such a conceptual framework based on changes in the interplay of pathogens, hosts and environment that lead to the formation of novel disease patterns and pathogen genetic adjustment. We categorize infectious disease emergence events into three groups: (i) pathogens showing up in a novel host, ranging from spill-over, including zoonoses, to complete species jumps; (ii) mutant pathogens displaying novel traits in the same host, including an increase in virulence, antimicrobial resistance and host immune escape; and (iii) disease complexes emerging in a new geographic area, either through range expansion or through long distance jumps. Each of these categories is characterized by a typical set of drivers of emergence, matching pathogen trait profiles, disease ecology and transmission dynamics. Our framework may assist in disentangling and structuring the rapidly growing amount of available information on infectious diseases. Moreover, it may contribute to a better understanding of how human action changes disease landscapes globally.

Highly pathogenic influenza A(H5N1) virus survival in complex artificial aquatic biotopes

Background

Very little is known regarding the persistence of Highly Pathogenic Avian Influenza (HPAI) H5N1 viruses in aquatic environments in tropical countries, although environmental materials have been suggested to play a role as reservoirs and sources of transmission for H5N1 viruses.

Methodology/Principal Findings

The survival of HPAI H5N1 viruses in experimental aquatic biotopes (water, mud, aquatic flora and fauna) relevant to field conditions in Cambodia was investigated. Artificial aquatic biotopes, including simple ones containing only mud and water, and complex biotopes involving the presence of aquatic flora and fauna, were set up. They were experimentally contaminated with H5N1 virus. The persistence of HPAI H5N1 virus (local avian and human isolates) was determined by virus isolation in embryonated chicken eggs and by real-time reverse-polymerase chain reaction. Persistence of infectious virus did not exceed 4 days, and was only identified in rain water. No infectious virus particles were detected in pond and lake water or mud even when high inoculum doses were used. However, viral RNA persisted up to 20 days in rain water and 7 days in pond or lake water. Viral RNA was also detected in mud samples, up to 14 days post-contamination in several cases. Infectious virus and viral RNA was detected in few cases in the aquatic fauna and flora, especially in bivalves and labyrinth fish, although these organisms seemed to be mostly passive carriers of the virus rather than host allowing virus replication.

Conclusions/Significance

Although several factors for the survival and persistence of HPAI viruses in the environment are still to be elucidated, and are particularly hard to control in laboratory conditions, our results, along with previous data, support the idea that environmental surveillance is of major relevance for avian influenza control programs.