Evidence of influenza a virus RNA in siberian lake ice

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.

Historical RNA expression profiles from the extinct Tasmanian tiger

Paleogenomics continues to yield valuable insights into the evolution, population dynamics, and ecology of our ancestors and other extinct species. However, DNA sequencing cannot reveal tissue-specific gene expression, cellular identity, or gene regulation, which are only attainable at the transcriptional level. Pioneering studies have shown that useful RNA can be extracted from ancient specimens preserved in permafrost and historical skins from extant canids, but no attempts have been made so far on extinct species. We extract, sequence, and analyze historical RNA from muscle and skin tissue of a ∼130-year-old Tasmanian tiger (Thylacinus cynocephalus) preserved in desiccation at room temperature in a museum collection. The transcriptional profiles closely resemble those of extant species, revealing specific anatomical features such as slow muscle fibers or blood infiltration. Metatranscriptomic analysis, RNA damage, tissue-specific RNA profiles, and expression hotspots genome-wide further confirm the thylacine origin of the sequences. RNA sequences are used to improve protein-coding and noncoding annotations, evidencing missing exonic loci and the location of ribosomal RNA genes while increasing the number of annotated thylacine microRNAs from 62 to 325. We discover a thylacine-specific microRNA isoform that could not have been confirmed without RNA evidence. Finally, we detect traces of RNA viruses, suggesting the possibility of profiling viral evolution. Our results represent the first successful attempt to obtain transcriptional profiles from an extinct animal species, providing thought-to-be-lost information on gene expression dynamics. These findings hold promising implications for the study of RNA molecules across the vast collections of natural history museums and from well-preserved permafrost remains.

Beyond the state of the art of reverse vaccinology: predicting vaccine efficacy with the universal immune system simulator for influenza

When it was first introduced in 2000, reverse vaccinology was defined as an in silico approach that begins with the pathogen's genomic sequence. It concludes with a list of potential proteins with a possible, but not necessarily, list of peptide candidates that need to be experimentally confirmed for vaccine production. During the subsequent years, reverse vaccinology has dramatically changed: now it consists of a large number of bioinformatics tools and processes, namely subtractive proteomics, computational vaccinology, immunoinformatics, and in silico related procedures. However, the state of the art of reverse vaccinology still misses the ability to predict the efficacy of the proposed vaccine formulation. Here, we describe how to fill the gap by introducing an advanced immune system simulator that tests the efficacy of a vaccine formulation against the disease for which it has been designed. As a working example, we entirely apply this advanced reverse vaccinology approach to design and predict the efficacy of a potential vaccine formulation against influenza H5N1. Climate change and melting glaciers are critical due to reactivating frozen viruses and emerging new pandemics. H5N1 is one of the potential strains present in icy lakes that can raise a pandemic. Investigating structural antigen protein is the most profitable therapeutic pipeline to generate an effective vaccine against H5N1. In particular, we designed a multi-epitope vaccine based on predicted epitopes of hemagglutinin and neuraminidase proteins that potentially trigger B-cells, CD4, and CD8 T-cell immune responses. Antigenicity and toxicity of all predicted CTL, Helper T-lymphocytes, and B-cells epitopes were evaluated, and both antigenic and non-allergenic epitopes were selected. From the perspective of advanced reverse vaccinology, the Universal Immune System Simulator, an in silico trial computational framework, was applied to estimate vaccine efficacy using a cohort of 100 digital patients.

Monitoring of Avian Influenza Viruses and Paramyxoviruses in Ponds of Moscow and the Moscow Region

The ponds of the Moscow region during the autumn migration of birds are a place with large concentrations of mallard ducks, which are the main hosts of avulaviruses (avian paramyxoviruses) and influenza A viruses (IAV). The purpose of this study was the determination of the biological diversity of IAV and avulaviruses isolated from mallards in Moscow's ponds. A phylogenetic analysis of IAV was performed based on complete genome sequencing, and virus genomic reassortment in nature was studied. Almost all IAV genome segments clustered with apathogenic duck viruses according to phylogenetic analysis. The origin of the genes of Moscow isolates were different; some of them belong to European evolutionary branches, some to Asian ones. The majority of closely related viruses have been isolated in the Western Eurasian region. Much less frequently, closely related viruses have been isolated in Siberia, China, and Korea. The quantity and diversity of isolated viruses varied considerably depending on the year and have decreased since 2014, perhaps due to the increasing proportion of nesting and wintering ducks in Moscow.

Epidemiology and Ecology of Influenza A Viruses among Wildlife in the Arctic

Arctic regions are ecologically significant for the environmental persistence and geographic dissemination of influenza A viruses (IAVs) by avian hosts and other wildlife species. Data describing the epidemiology and ecology of IAVs among wildlife in the arctic are less frequently published compared to southern temperate regions, where prevalence and subtype diversity are more routinely documented. Following PRISMA guidelines, this systematic review addresses this gap by describing the prevalence, spatiotemporal distribution, and ecological characteristics of IAVs detected among wildlife and the environment in this understudied region of the globe. The literature search was performed in PubMed and Google Scholar using a set of pre-defined search terms to identify publications reporting on IAVs in Arctic regions between 1978 and February 2022. A total of 2125 articles were initially screened, 267 were assessed for eligibility, and 71 articles met inclusion criteria. IAVs have been detected in multiple wildlife species in all Arctic regions, including seabirds, shorebirds, waterfowl, seals, sea lions, whales, and terrestrial mammals, and in the environment. Isolates from wild birds comprise the majority of documented viruses derived from wildlife; however, among all animals and environmental matrices, 26 unique low and highly pathogenic subtypes have been characterized in the scientific literature from Arctic regions. Pooled prevalence across studies indicates 4.23% for wild birds, 3.42% among tested environmental matrices, and seroprevalences of 9.29% and 1.69% among marine and terrestrial mammals, respectively. Surveillance data are geographically biased, with most data from the Alaskan Arctic and many fewer reports from the Russian, Canadian, North Atlantic, and Western European Arctic. We highlight multiple important aspects of wildlife host, pathogen, and environmental ecology of IAVs in Arctic regions, including the role of avian migration and breeding cycles for the global spread of IAVs, evidence of inter-species and inter-continental reassortment at high latitudes, and how climate change-driven ecosystem shifts, including changes in the seasonal availability and distribution of dietary resources, have the potential to alter host–pathogen–environment dynamics in Arctic regions. We conclude by identifying gaps in knowledge and propose priorities for future research.

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.

Climate change, melting cryosphere and frozen pathogens: Should we worry…?

Permanently frozen environments (glaciers, permafrost) are considered as natural reservoirs of huge amounts of microorganisms, mostly dormant, including human pathogens. Due to global warming, which increases the rate of ice-melting, approximately 4 × 1021 of these microorganisms are released annually from their frozen confinement and enter natural ecosystems, in close proximity to human settlements. Some years ago, the hypothesis was put forward that this massive release of potentially-pathogenic microbes-many of which disappeared from the face of the Earth thousands and even millions of years ago-could give rise to epidemics. The recent anthrax outbreaks that occurred in Siberia, and the presence of bacterial and viral pathogens in glaciers worldwide, seem to confirm this hypothesis. In that context, the present review summarizes the currently available scientific evidence that allows us to imagine a near future in which epidemic outbreaks, similar to the abovementioned, could occur as a consequence of the resurrection and release of microbes from glaciers and permafrost.

Supplementary Information

The online version of this article (10.1007/s42398-021-00184-8) contains supplementary material, which is available to authorized users.

Future threat from the past

Global warming is one of the major challenges facing humanity. The increase in the Earth's temperature and thawing of ancient ice release viable viruses, bacteria, fungi, and other microorganisms which were trapped for thousands and millions of years. Such microorganisms may belong to novel microbial species, unknown genotypes of present pathogens, already eradicated pathogens, or even known pathogens that gained extremely robust characteristics due to their subjection to long-term stress. These worries drew more attention following the death of a child by ancient anthrax spores in Siberian in 2016 and the reconstruction of smallpox and Spanish flu genomes from ancient frozen biological samples. The present review illustrates some examples of recently recovered pathogens after being buried for millions of years, including some identified viable ancient viruses, bacteria and even other forms of life. While some pathogens could be revived, genomes of other ancient pathogens which could not be revived were re-constructed. The present study aims to highlight and alarm the hidden aspect of global warming on the international public health, which represents future threats from the past for humanity.

Resurrection of inactive microbes and resistome present in the natural frozen world: Reality or myth?

The present world faces a new threat of ancient microbes and resistomes that are locked in the cryosphere and now releasing upon thawing due to climate change and anthropogenic activities. The cryosphere act as the best preserving place for these microbes and resistomes that stay alive for millions of years. Current reviews extensively discussed whether the resurrection of microbes and resistomes existing in these pristine environments is true or just a hype. Release of these ancient microorganisms and naked DNA is of great concern for society as these microbes can either cause infections directly or they can interact with contemporary microorganisms and affect their fitness, survival, and mutation rate. Moreover, the contemporary microorganisms may uptake the unlocked naked DNA, which might transform non-pathogenic microorganisms into deadly antibiotic-resistant microbes. Additionally, the resurrection of glacial microorganisms can cause adverse effects on ecosystems downstream. The release of glacial pathogens and naked DNA is real and can lead to fatal outbreaks; therefore, we must prepare ourselves for the possible reemergence of diseases caused by these microbes. This study provides a scientific base for the adoption of actions by international cooperation to develop preventive measures.

Using geospatial methods to measure the risk of environmental persistence of avian influenza virus in South Carolina

Avian influenza (AIV) is a highly contagious virus that can infect both wild birds and domestic poultry. This study aimed to define areas within the state of South Carolina (SC) at heightened risk for environmental persistence of AIV using geospatial methods. Environmental factors known to influence AIV survival were identified through the published literature and using a multi-criteria decision analysis with GIS was performed. Risk was defined using five categories following the World Organization for Animal Health Risk Assessment Guidelines. Less than 1% of 1km grid cells in SC showed a high risk of AIV persistence. Approximately 2% - 17% of counties with high or very high environmental risk also had medium to very high numbers of commercial poultry operations. Results can be used to improve surveillance activities and to inform biosecurity practices and emergency preparedness efforts.

Ancient RNA from Late Pleistocene permafrost and historical canids shows tissue-specific transcriptome survival

While sequencing ancient DNA (aDNA) from archaeological material is now commonplace, very few attempts to sequence ancient transcriptomes have been made, even from typically stable deposition environments such as permafrost. This is presumably due to assumptions that RNA completely degrades relatively quickly, particularly when dealing with autolytic, nuclease-rich mammalian tissues. However, given the recent successes in sequencing ancient RNA (aRNA) from various sources including plants and animals, we suspect that these assumptions may be incorrect or exaggerated. To challenge the underlying dogma, we generated shotgun RNA data from sources that might normally be dismissed for such study. Here, we present aRNA data generated from two historical wolf skins, and permafrost-preserved liver tissue of a 14,300-year-old Pleistocene canid. Not only is the latter the oldest RNA ever to be sequenced, but it also shows evidence of biologically relevant tissue specificity and close similarity to equivalent data derived from modern-day control tissue. Other hallmarks of RNA sequencing (RNA-seq) data such as exon-exon junction presence and high endogenous ribosomal RNA (rRNA) content confirms our data’s authenticity. By performing independent technical library replicates using two high-throughput sequencing platforms, we show not only that aRNA can survive for extended periods in mammalian tissues but also that it has potential for tissue identification. aRNA also has possible further potential, such as identifying in vivo genome activity and adaptation, when sequenced using this technology.

Ancient DNA is known to survive in cold environments for tens of millennia, but it is assumed that ancient RNA could not persist in such a way due to its relative instability. However, this study shows that under permafrost conditions, ancient RNA can survive well enough to show tissue specificity even in mammalian soft tissues.

Glass Wool Concentration Optimization for the Detection of Enveloped and Non-enveloped Waterborne Viruses

An extremely affordable virus concentration method based on adsorption-elution to glass wool and subsequent reconcentration through polyethylene glycol 6000 (PEG) precipitation was optimized to recover not only non-enveloped viruses but also enveloped viruses. Hepatitis A virus (HAV) and transmissible gastroenteritis virus (TGEV) were employed as surrogates for naked and enveloped viruses, respectively, to set up the methodology. Initial experimentation in small-volume samples showed that both types of particles readily adsorbed to the positively charged glass wool but were poorly detached from it through standard elution with 0.05 M glycine with 3% of beef extract buffer, pH 9.5, with elution efficiencies of 7.2% and 2.6%, for HAV and TGEV, respectively. To improve the recovery of enveloped viruses, several modifications in the elution were assayed: increasing the elution pH, extending glass wool and eluent contact time, adding a detergent, or performing the elution by recirculation or under agitation. Considering practicability and performance, recircularization of the eluent at pH 11.0 for 20 min was the elution procedure of choice, with efficiencies of 25.7% and 18.8% for HAV and TGEV in 50 L of water. Additionally, employing 20% PEG instead of 10% for virus reconcentration improved recoveries up to 47% and 51%, respectively. The optimized procedure was applied to detect naturally occurring HAV and coronaviruses in surface water of Wadi Hanifa, Riyadh. HAV was detected in 38% of the samples, while one sample was positive for an alphacoronavirus. This cheap virus detection system enables the comprehensive surveillance of viruses present in water samples.

Influenza Virus Segment Composition Influences Viral Stability in the Environment

The transmission routes of Influenza A viruses (IAVs) submit virus particles to a wide range of environmental conditions that affect their transmission. In water, temperature, salinity, and pH are important factors modulating viral persistence in a strain-dependent manner, and the viral factors driving IAV persistence remain to be described. We used an innovative method based on a real-time cell system analysis to quantify viral decay in an environmental model. Thus, we identified the viral hemagglutinin (HA) and neuraminidase (NA) as the main proteins driving the environmental persistence by comparing the inactivation slopes of several reassortant viruses. We also introduced synonymous and non-synonymous mutations in the HA or in the NA that modulated IAV persistence. Our results demonstrate that HA stability and expression level, as well as calcium-binding sites of the NA protein, are molecular determinants of viral persistence. Finally, IAV particles could not trigger membrane fusion after environmental exposure, stressing the importance of the HA and the NA for environmental persistence.

Detection of Influenza A viruses at migratory bird stopover sites in Michigan, USA

Introduction: Influenza A viruses have the potential to cause devastating illness in humans and domestic poultry. Wild birds are the natural reservoirs of Influenza A viruses and migratory birds are implicated in their global dissemination. High concentrations of this virus are excreted in the faeces of infected birds and faecal contamination of shared aquatic habitats can lead to indirect transmission among birds via the faecal-oral route. The role of migratory birds in the spread of avian influenza has led to large-scale surveillance efforts of circulating avian influenza viruses through direct sampling of live and dead wild birds. Environmental monitoring of bird habitats using molecular detection methods may provide additional information on the persistence of influenza virus at migratory stopover sites distributed across large spatial scales.

Materials and methods: In the current study, faecal and water samples were collected at migratory stopover sites and evaluated for Influenza A by real-time quantitative reverse transcriptase PCR.

Results and Discussion: This study found that Influenza A was detected at 53% of the evaluated stopover sites, and 7% and 4.8% of the faecal and water samples, respectively, tested positive for Influenza A virus.

Conclusion: Environmental monitoring detected Influenza A at stopover sites used by migratory birds.

Effect of the epidemiological heterogeneity on the outbreak outcomes

Multi-host pathogens infect and are transmitted by different kinds of hosts and, therefore, the host heterogeneity may have a great impact on the outbreak outcome of the system. This paper deals with the following problem: consider the system of interacting and mixed populations of hosts epidemiologically different, what would be the outbreak outcome for each host population composing the system as a result of mixing in comparison to the situation with zero mixing? To address this issue we have characterized the epidemic response function for a single-host population and defined a heterogeneity index measuring how host systems are epidemiologically different in terms of generation time, basic reproduction number R0 and, therefore, epidemic response function. Based on the individual epidemiological characteristics of populations, with heterogeneities and mixing affinities, the response of subpopulations in a multi-host system is compared to that of a single-host system. The case of a two-host system, in which the infection transmission depends solely on the infection susceptibility of the receiver, is analyzed in detail. Three types of responses are observed: dilution, amplification or no effect, corresponding to lower, higher or equal attack rates, respectively, for a host population in an interacting multi-host system compared to the zero-mixing situation. We find that no effect is generally observed for zero heterogeneity. A dilution effect is always observed for all the host populations when their individual R0,i < 1. Whereas, when at least one of the individual R0,i > 1, then the hosts ''i'' with R0,i > R0,j undergo a dilution effect while the hosts ''j'' undergo an amplification effect.

Single-Stranded RNA Viruses

In this chapter, we describe 73 zoonotic viruses that were isolated in Northern Eurasia and that belong to the different families of viruses with a single-stranded RNA (ssRNA) genome. The family includes viruses with a segmented negative-sense ssRNA genome (families Bunyaviridae and Orthomyxoviridae) and viruses with a positive-sense ssRNA genome (families Togaviridae and Flaviviridae). Among them are viruses associated with sporadic cases or outbreaks of human disease, such as hemorrhagic fever with renal syndrome (viruses of the genus Hantavirus), Crimean–Congo hemorrhagic fever (CCHFV, Nairovirus), California encephalitis (INKV, TAHV, and KHATV; Orthobunyavirus), sandfly fever (SFCV and SFNV, Phlebovirus), Tick-borne encephalitis (TBEV, Flavivirus), Omsk hemorrhagic fever (OHFV, Flavivirus), West Nile fever (WNV, Flavivirus), Sindbis fever (SINV, Alphavirus) Chikungunya fever (CHIKV, Alphavirus) and others. Other viruses described in the chapter can cause epizootics in wild or domestic animals: Geta virus (GETV, Alphavirus), Influenza A virus (Influenzavirus A), Bhanja virus (BHAV, Phlebovirus) and more. The chapter also discusses both ecological peculiarities that promote the circulation of these viruses in natural foci and factors influencing the occurrence of epidemic and epizootic outbreaks

Virological evaluation of avian influenza virus persistence in natural and anthropic ecosystems of Western Siberia (Novosibirsk Region, summer 2012)

BACKGROUND

Wild aquatic birds, reservoir of low-pathogenicity (LP) avian influenza viruses (AIVs), congregate in huge numbers in Western Siberia wetlands, where major intra- and inter-continental bird flyways overlap. In 2005 and 2006, highly pathogenic (HP) AIV H5N1 epizootics affected wild and domestic birds in the Novosibirsk Region. In 2012, we evaluated AIV persistence in Siberian natural and anthropic ecosystems.

METHODOLOGY/PRINCIPAL FINDINGS

In Novosibirsk Region, 166 wild birds ecologically linked to aquatic environments and 152 domestic waterfowl were examined for AIV isolation in embryonating chicken eggs. Biological samples were obtained by integrating the conventional cloacal swab collection with the harvesting of samples from birds' plumage. Haemagglutinating allantoic fluids were further characterized by serological and molecular methods. In August-September 2012, 17 AIVs, including three H3N8, eight H4N6, two H4N?, one H2N?, one H?N2, and two unsubtyped LPAIVs, were isolated from 15 wild ducks. Whereas comparable proportions of wild Anseriformes (n.118) tested virus isolation (VI)-positive from cloaca and feathers (5.9% vs 8.5%) were detected, the overall prevalence of virus isolation, obtained from both sampling methods, was 2.4 times higher than that calculated on results from cloacal swab examination only (14.4% vs 5.9%). Unlike previously described in this area, the H4N6 antigenic subtype was found to be the prevalent one in 2012. Both cloacal and feather samples collected from domestic waterfowl tested VI-negative.

CONCLUSION/SIGNIFICANCE

We found lack of evidence for the H5N1 HPAIV circulation, explainable by the poor environmental fitness of HPAIVs in natural ecosystems. Our LPAIV isolation data emphasise the importance of Siberia wetlands in influenza A virus ecology, providing evidence of changes in circulation dynamics of HN antigenic subtypes harboured in wild bird reservoirs. Further studies of isolates, based on bioinformatic approaches to virus molecular evolution and phylogenesis, will be needed to better elucidate mechanisms involved in AIV perpetuation in this area.

Influenza A virus prevalence and its implications on survival in mallard

Avian influenza is an infectious viral disease of birds caused by type A strains of the influenza virus. Aquatic bird species have adapted to carry and transmit a wide range of influenza strains in nature. Here we report the results of a 4.5-year monitoring program forOrthomyxovirusprevalence in a population of wild mallard (Anas plathyrynchos) in northwestern Italy. To determine whetherOrthomyxovirusprevalence affects survival, we used MARK software to compare the survival of AIV-positive versus AIV-negative birds. Prevalence rates and variance were estimated using inverse sampling method. The prevalence rate of influenza A virus was 4.3% (SE 0.00116) and lifespan was shorter (29.8%) for the young infected birds than for the young non-infected birds.

A complete ancient RNA genome: identification, reconstruction and evolutionary history of archaeological Barley Stripe Mosaic Virus

The origins of many plant diseases appear to be recent and associated with the rise of domestication, the spread of agriculture or recent global movements of crops. Distinguishing between these possibilities is problematic because of the difficulty of determining rates of molecular evolution over short time frames. Heterochronous approaches using recent and historical samples show that plant viruses exhibit highly variable and often rapid rates of molecular evolution. The accuracy of estimated evolution rates and age of origin can be greatly improved with the inclusion of older molecular data from archaeological material. Here we present the first reconstruction of an archaeological RNA genome, which is of Barley Stripe Mosaic Virus (BSMV) isolated from barley grain ~750 years of age. Phylogenetic analysis of BSMV that includes this genome indicates the divergence of BSMV and its closest relative prior to this time, most likely around 2000 years ago. However, exclusion of the archaeological data results in an apparently much more recent origin of the virus that postdates even the archaeological sample. We conclude that this viral lineage originated in the Near East or North Africa, and spread to North America and East Asia with their hosts along historical trade routes.

Global lack of flyway structure in a cosmopolitan bird revealed by a genome wide survey of single nucleotide polymorphisms

Knowledge about population structure and connectivity of waterfowl species, especially mallards (Anas platyrhynchos), is a priority because of recent outbreaks of avian influenza. Ringing studies that trace large-scale movement patterns have to date been unable to detect clearly delineated mallard populations. We employed 363 single nucleotide polymorphism markers in combination with population genetics and phylogeographical approaches to conduct a population genomic test of panmixia in 801 mallards from 45 locations worldwide. Basic population genetic and phylogenetic methods suggest no or very little population structure on continental scales. Nor could individual-based structuring algorithms discern geographical structuring. Model-based coalescent analyses for testing models of population structure pointed to strong genetic connectivity among the world's mallard population. These diverse approaches all support the conclusion that there is a lack of clear population structure, suggesting that the world's mallards, perhaps with minor exceptions, form a single large, mainly interbreeding population.

Persistence of avian influenza viruses in various artificially frozen environmental water types

Background. This study investigates the viable persistence of avian influenza viruses (AIVs) in various types of artificially frozen environmental water and evaluates the feasibility of similar occurrence taking place in nature, and allowing for prolonged abiotic virus survival, with subsequent biotic viral recirculation. Methods. Fresh, brackish, and salty water, taken in Japan from aquatic biotopes regularly visited by migratory waterfowl, were seeded with AIVs. We monthly monitored the viability of the seeded viruses in the frozen state at -20°C and -30°C, for 12 months. We also monitored virus viability following repeatedly induced freezing and thawing. Results. The viruses exhibited considerable viable persistence all along that period of time, as well as during freezing-thawing cycles. Appreciable, yet noncrucial variances were observed in relation to some of the parameters examined. Conclusions. As typical waterborne pathogens of numerous northerly aquatic birds, AIVs are innately adapted to both the body temperature of their hosts (40°C to 42°C) and, presumably, to subzero temperatures of frozen lakes (down to -54°C in parts of Siberia) occupied and virus-seeded by subclinically infected birds, prior to freezing. Marked cryostability of AIVs appears to be evident. Preservation in environmental ice has significant ecophylogenetic and epidemiological implications, potentially, and could account for various unexplained phenomena.

Detection method for avian influenza viruses in water

Recent events have shown that humans may become infected with some pathogenic avian influenza A viruses (AIV). Since soil and water, including lakes, rivers, and seashores, may be contaminated by AIV excreted by birds, effective methods are needed for monitoring water for emerging viruses. Combining water filtration with molecular methods such as PCR is a fast and effective way for detecting viruses. The objective of this study was to apply a convenient method for the detection of AIV in natural water samples. Distilled water and lake, river, and seawater were artificially contaminated with AIV (H5N3) and passed through a filter system. AIV was detected from filter membrane by real-time RT-PCR. The performance of Zetapor, SMWP, and Sartobind D5F membranes in recovering influenza viruses was first evaluated using contaminated distilled water. SWMP, which gave the highest virus recoveries, was then compared with a pre-filter combined GF/F filter membrane in a trial using natural water samples. In this study, the cellulose membrane SMWP was found to be practical for recovery of AIVs in water. Viral yields varied between 62.1 and 65.9% in distilled water and between 1 and 16.7% in natural water samples. The borosilicate glass membrane GF/F combined with pre-filter was also feasible in filtering natural water samples with viral yields from 1.98 to 7.33%. The methods described can be used for monitoring fresh and seawater samples for the presence of AIV and to determine the source of AIV transmission in an outbreak situation.

Development and validation of a concentration method for the detection of influenza a viruses from large volumes of surface water

Contamination of lakes and ponds plays an essential role as a reservoir of avian influenza A virus (AIV) in the environment. A method to concentrate waterborne AIV is a prerequisite for the detection of virus present at low levels in water. The aim of this study was to develop and validate a method for the concentration and detection of infectious AIV from large volumes of surface water samples. Two filtration systems, glass wool and electropositive NanoCeram filter, were studied. The individual effects of filtration-elution and polyethylene glycol (PEG) concentration parameters on the recovery efficiency of the H1N1 strain from 10-liter surface water samples were assessed. An ultimate 1% recovery rate of infectious viruses was achieved with the optimal protocol, corresponding to filtration through glass wool, followed by a viral elution step and then a PEG concentration. This method was validated for the detection of highly pathogenic H5N1 strains from artificially contaminated larger water volumes, from 10 to up to 50 liters, from different sources. The viral recovery efficiencies ranged from 0.01% to 7.89% and from 3.63% to 13.79% with lake water and rainwater, respectively. A theoretical detection threshold of 2.25 × 10(2) TCID(50) (50% tissue culture infectious dose) in the filtered volume was obtained for seeded lake waters by M gene reverse transcriptase PCR (RT-PCR). Moreover, the method was used successfully in field studies for the detection of naturally occurring influenza A viruses in lake water in France.

Complementary monoclonal antibody-based dot ELISA for universal detection of H5 avian influenza virus

BACKGROUND

Rapid diagnosis and surveillance for H5 subtype viruses are critical for the control of H5N1 infection.

RESULTS

In this study, H5 Dot ELISA, a rapid test for the detection of avian H5N1 influenza virus, was developed with two complementary H5 monoclonal antibodies. HA sequencing of escape mutants followed by epitope mapping revealed that the two Mabs target the epitope component (189th amino acid) on the HA protein but are specific for different amino acids (189Lys or 189Arg). Gene alignment indicated that these two amino acids are the most frequent types on this position among all of the H5 AIV reported in GeneBank. These two H5 Mabs were used together in a dot ELISA to detect H5 viral antigen. The detection limit of the developed test for multiple clades of H5N1 viruses, including clades 0, 1, 2.1, 2.2, 2.3, 4, 7, and 8, was less than 0.5 hemagglutinin units. The specificity of the optimized dot ELISA was examined by using 100 H5 strains, including H5N1 HPAI strains from multiple clades, 36 non-H5N1 viruses, and 4 influenza B viruses. No cross-reactivity was observed for any of the non-H5N1 viruses tested. Among 200 random poultry samples, the test gave 100% positive results for all of the twelve RT-PCR-positive samples.

CONCLUSIONS

Considering that the test is convenient for field use, this H5 Dot ELISA can be used for on-site detection of H5N1 infection in clinical or environmental specimens and facilitate the investigation of H5N1 influenza outbreaks and surveillance in poultry.

Avian influenza: our current understanding

Avian influenza (AI) virus is one of the most important diseases of the poultry industry around the world. The virus has a broad host range in birds and mammals, although the natural reservoir is wild birds where it typically causes an asymptomatic to mild infection. The virus in poultry can cause a range of clinical diseases and is defined either as low pathogenic AI (LPAI) or highly pathogenic AI (HPAI) depending on the type of disease it causes in chickens. Viruses that replicate primarily on mucosal surfaces and cause mild disease with low mortality are termed LPAI. Viruses that replicate on mucosal surfaces and systemically and cause severe disease with a mortality rate of 75% or greater in experimentally infected chickens are referred to as HPAI. A virus that is highly pathogenic in chickens may infect but result in a completely different disease and replication pattern in other host species. Outbreaks of HPAI have been relatively uncommon around the world in the last 50 years and have had limited spread within a country or region with one major exception, Asian lineage H5N1 that was first identified in 1996. This lineage of virus has spread to over 60 countries and has become endemic in poultry in at least four countries. AI virus also represents a public health threat, with some infected humans having severe disease and with a high case fatality rate. AI remains a difficult disease to control because of the highly infectious nature of the virus and the interface of domestic and wild animals. A better understanding of the disease and its transmission is important for control.

Interspecies and intraspecies transmission of influenza A viruses: viral, host and environmental factors

Influenza A viruses are enveloped viruses belonging to the familyOrthomyxoviridaethat encompasses four more genera: Influenza B, Influenza C, Isavirus and Thogotovirus. Type A viruses belong to the only genus that is highly infectious to a variety of mammalian and avian species. They are divided into subtypes based on two surface glycoproteins, the hemagglutinin (HA) and neuraminidase (NA). So far, 16 HA and 9 NA subtypes have been identified worldwide, making a possible combination of 144 subtypes between both proteins. Generally, individual viruses are host-specific, however, interspecies transmission of influenza A viruses is not uncommon. All of the HA and NA subtypes have been isolated from wild birds; however, infections in humans and other mammalian species are limited to a few subtypes. The replication of individual influenza A virus in a specific host is dependent on many factors including, viral proteins, host system and environmental conditions. In this review, the key findings that contribute to the transmission of influenza A viruses amongst different species are summarized.

Spatial and temporal association of outbreaks of H5N1 influenza virus infection in wild birds with the 0 degrees C isotherm

Wild bird movements and aggregations following spells of cold weather may have resulted in the spread of highly pathogenic avian influenza virus (HPAIV) H5N1 in Europe during the winter of 2005–2006. Waterbirds are constrained in winter to areas where bodies of water remain unfrozen in order to feed. On the one hand, waterbirds may choose to winter as close as possible to their breeding grounds in order to conserve energy for subsequent reproduction, and may be displaced by cold fronts. On the other hand, waterbirds may choose to winter in regions where adverse weather conditions are rare, and may be slowed by cold fronts upon their journey back to the breeding grounds, which typically starts before the end of winter. Waterbirds will thus tend to aggregate along cold fronts close to the 0°C isotherm during winter, creating conditions that favour HPAIV H5N1 transmission and spread. We determined that the occurrence of outbreaks of HPAIV H5N1 infection in waterbirds in Europe during the winter of 2005–2006 was associated with temperatures close to 0°C. The analysis suggests a significant spatial and temporal association of outbreaks caused by HPAIV H5N1 in wild birds with maximum surface air temperatures of 0°C–2°C on the day of the outbreaks and the two preceding days. At locations where waterbird census data have been collected since 1990, maximum mallard counts occurred when average and maximum surface air temperatures were 0°C and 3°C, respectively. Overall, the abundance of mallards (Anas platyrhynchos) and common pochards (Aythya ferina) was highest when surface air temperatures were lower than the mean temperatures of the region investigated. The analysis implies that waterbird movements associated with cold weather, and congregation of waterbirds along the 0°C isotherm likely contributed to the spread and geographical distribution of outbreaks of HPAIV H5N1 infection in wild birds in Europe during the winter of 2005–2006.

Highly pathogenic avian influenza virus of the H5N1 subtype emerged more than a decade ago in poultry in South-East Asia. In 2005, it spread outside Asia infecting both poultry and wild birds in the Middle East, Europe and Africa. Both trade of poultry and movements of wild birds were likely implicated in the spread of the infection; however, the ability of wild birds to carry the virus to novel geographical areas is still highly debated and remains obscure. In Europe, the virus mainly infected wild birds, and emergence coincided with a spell of cold weather, which is known to result in massive movements of wild waterbirds. In this paper, we demonstrate that movements of wild waterbirds associated with cold weather contributed to the spread and geographical distribution of outbreaks in Europe during the winter of 2005–2006. Higher density of wild waterbirds on bodies of water that remain unfrozen ahead of the freezing line likely favoured transmission of the virus and resulted in distinctive distribution of outbreaks at locations where surface air temperatures were 0°C–2°C. This has important implications for surveillance, which should target areas where temperatures are close to freezing in winter, especially in poultry-dense regions close to areas where waterfowl aggregate.

Detection and quantification of infectious avian influenza A (H5N1) virus in environmental water by using real-time reverse transcription-PCR

Routes of avian influenza virus (AIV) dispersal among aquatic birds involve direct (bird-to-bird) and indirect (waterborne) transmission. The environmental persistence of H5N1 virus in natural water reservoirs can be assessed by isolation of virus in embryonated chicken eggs. Here we describe development and evaluation of a real-time quantitative reverse transcription (RT)-PCR (qRT-PCR) method for detection of H5N1 AIV in environmental water. This method is based on adsorption of virus particles to formalin-fixed erythrocytes, followed by qRT-PCR detection. The numbers of hemagglutinin RNA copies from H5N1 highly pathogenic AIV particles adsorbed to erythrocytes detected correlated highly with the infectious doses of the virus that were determined for three different types of artificially inoculated environmental water over a 17-day incubation period. The advantages of this method include detection and quantification of infectious H5N1 AIVs with a high level of sensitivity, a wide dynamic range, and reproducibility, as well as increased biosecurity. The lowest concentration of H5N1 virus that could be reproducibly detected was 0.91 50% egg infective dose per ml. In addition, a virus with high virion stability (Tobacco mosaic virus) was used as an internal control to accurately monitor the efficiency of RNA purification, cDNA synthesis, and PCR amplification for each individual sample. This detection system could be useful for rapid high-throughput monitoring for the presence of H5N1 AIVs in environmental water and in studies designed to explore the viability and epidemiology of these viruses in different waterfowl ecosystems. The proposed method may also be adapted for detection of other AIVs and for assessment of their prevalence and distribution in environmental reservoirs.

Potential Impact of Climate Change on Pandemic Influenza Risk

Health problems related to the environment continue to be a major source of concern all over the world.  Society needs to develop measures that will eliminate or considerably reduce hazardous factors from the environment that can result in health risk to humans.

RNA viruses in the sea

Viruses are ubiquitous in the sea and appear to outnumber all other forms of marine life by at least an order of magnitude. Through selective infection, viruses influence nutrient cycling, community structure, and evolution in the ocean. Over the past 20 years we have learned a great deal about the diversity and ecology of the viruses that constitute the marine virioplankton, but until recently the emphasis has been on DNA viruses. Along with expanding knowledge about RNA viruses that infect important marine animals, recent isolations of RNA viruses that infect single-celled eukaryotes and molecular analyses of the RNA virioplankton have revealed that marine RNA viruses are novel, widespread, and genetically diverse. Discoveries in marine RNA virology are broadening our understanding of the biology, ecology, and evolution of viruses, and the epidemiology of viral diseases, but there is still much that we need to learn about the ecology and diversity of RNA viruses before we can fully appreciate their contributions to the dynamics of marine ecosystems. As a step toward making sense of how RNA viruses contribute to the extraordinary viral diversity in the sea, we summarize in this review what is currently known about RNA viruses that infect marine organisms.

Molecular surveillance for avian influenza A virus in king penguins (Aptenodytes patagonicus)

An investigation of the presence of influenza A virus has been conducted in king penguins (Aptenodytes patagonicus) at the Possession Island in the Crozet Archipelago, Antarctica, using a rapid molecular diagnostic method based on real-time polymerase chain reaction. No evidence of outbreak or positive viral infection of influenza A virus was found in this study. We however recommend the implementation of long-term surveillance in seabird populations of polar ecosystems to detect the potential introduction of exotic strains and potential existence of a local epidemiological cycle for avian influenza viruses.

Inactivation of influenza A viruses in the environment and modes of transmission: a critical review

Objectives

The relative importance of airborne, droplet and contact transmission of influenza A virus and the efficiency of control measures depends among other factors on the inactivation of viruses in different environmental media.

Methods

We systematically review available information on the environmental inactivation of influenza A viruses and employ information on infectious dose and results from mathematical models to assess transmission modes.

Results

Daily inactivation rate constants differ by several orders of magnitude: on inanimate surfaces and in aerosols daily inactivation rates are in the order of 1–10², on hands in the order of 10³. Influenza virus can survive in aerosols for several hours, on hands for a few minutes. Nasal infectious dose of influenza A is several orders of magnitude larger than airborne infectious dose.

Conclusions

The airborne route is a potentially important transmission pathway for influenza in indoor environments. The importance of droplet transmission has to be reassessed. Contact transmission can be limited by fast inactivation of influenza virus on hands and is more so than airborne transmission dependent on behavioral parameters. However, the potentially large inocula deposited in the environment through sneezing and the protective effect of nasal mucus on virus survival could make contact transmission a key transmission mode.

Climate change and avian influenza

This paper discusses impacts of climate change on the ecology of avian influenza viruses (AI viruses), which presumably co-evolved with migratory water birds, with virus also persisting outside the host in subarctic water bodies. Climate change would almost certainly alter bird migration, influence the AI virus transmission cycle and directly affect virus survival outside the host. The joint, net effects of these changes are rather unpredictable, but it is likely that AI virus circulation in water bird populations will continue with endless adaptation and evolution. In domestic poultry, too little is known about the direct effect of environmental factors on highly pathogenic avian influenza transmission and persistence to allow inference about the possible effect of climate change. However, possible indirect links through changes in the distribution of duck-crop farming are discussed.

New tools for the study and direct surveillance of viral pathogens in water

Half a century ago scientists attempted the detection of poliovirus in water. Since then other enteric viruses responsible for gastroenteritis and hepatitis have replaced enteroviruses as the main target for detection. However, most viral outbreaks are restricted to norovirus and hepatitis A virus, making them the main targets in water. The inclusion of virus analysis in regulatory standards for viruses in water samples must overcome several shortcomings such as the technical difficulties and high costs of virus monitoring, the lack of harmonised and standardised assays and the challenge posed by the ever-changing nature of viruses. However, new tools are nowadays available for the study and direct surveillance of viral pathogens in water that may contribute to fulfil these requirements.

Ecology of avian influenza virus in birds

Avian influenza A virus (an orthomyxovirus) is a zoonotic pathogen with a natural reservoir entirely in birds. The influenza virus genome is an 8-segment single-stranded RNA with high potential for in situ recombination. Two segments code for the hemagglutinin (H) and neuraminidase (N) antigens used for host-cell entry. At present, 16 H and 9 N subtypes are known, for a total of 144 possible different influenza subtypes, each with potentially different host susceptibility. With >10,000 species of birds found in nearly every terrestrial and aquatic habitat, there are few places on earth where birds cannot be found. The avian immune system differs from that of humans in several important features, including asynchronous B and T lymphocyte systems and a polymorphic multigene immune complex, but little is known about the immunogenetics of pathogenic response. Postbreeding dispersal and migration and a naturally high degree of environmental vagility mean that wild birds have the potential to be vectors that transmit highly pathogenic variants great distances from the original sources of infection.

Prevalence and diversity of avian influenza viruses in environmental reservoirs

Little is known about the ecology and evolution of avian influenza in the natural environment, despite how these affect the potential for transmission. Most work has focused on characterizing viruses isolated from hosts such as waterfowl, and there have also been several instances of isolation and detection from abiotic sources such as water and ice. We used RT-PCR to amplify and characterize the influenza virus sequences present in sediments of ponds that are used heavily by waterfowl. The detection rate of influenza virus was high (>50%). Characterization of the viruses present by sequencing part of the haemagglutinin (HA) gene showed that there is a diverse collection of viruses in these sediments. We sequenced 117 partial HA gene clones from 11 samples and detected four different HA subtypes (H3, H8, H11 and H12), with approximately 65% of clone sequences being unique. This culture-independent approach was also able to detect a virus subtype that was not found by sampling of birds in the same geographical region in the same year. Viruses were detected readily in the winter when the ponds were frozen, indicating that these sediments could be a year-to-year reservoir of viruses to infect birds using the ponds, although we have not shown that these viruses are viable. We demonstrate that this approach is a feasible and valuable way to assess the prevalence and diversity of viruses present in the environment, and can be a valuable complement to more difficult viral culturing in attempting to understand the ecology of influenza viruses.

Phylogenetic evidence against evolutionary stasis and natural abiotic reservoirs of influenza A virus

Zhang et al. (G. Zhang, D. Shoham, D. Gilichinsky, S. Davydov, J. D. Castello, and S. O. Rogers, J. Virol. 80:12229-12235, 2006) have claimed to have recovered influenza A virus RNA from Siberian lake ice, postulating that ice might represent an important abiotic reservoir for the persistence and reemergence of this medically important pathogen. A rigorous phylogenetic analysis of these influenza A virus hemagglutinin gene sequences, however, indicates that they originated from a laboratory reference strain derived from the earliest human influenza A virus isolate, WS/33. Contrary to Zhang et al.'s assertions that the Siberian "ice viruses" are most closely related either to avian influenza virus or to human influenza virus strains from Asia from the 1960s (Zhang et al., J. Virol. 81:2538 [erratum], 2007), they are clearly contaminants from the WS/33 positive control used in their laboratory. There is thus no credible evidence that environmental ice acts as a biologically relevant reservoir for influenza viruses. Several additional cases with findings that seem at odds with the biology of influenza virus, including modern-looking avian influenza virus RNA sequences from an archival goose specimen collected in 1917 (T. G. Fanning, R. D. Slemons, A. H. Reid, T. A. Janczewski, J. Dean, and J. K. Taubenberger, J. Virol. 76:7860-7862, 2002), can also be explained by laboratory contamination or other experimental errors. Many putative examples of evolutionary stasis in influenza A virus appear to be due to laboratory artifacts.

History of Influenza Pandemics

Influenza pandemics have been amongst the largest and the deadliest epidemics in the history of man, and were observed already in ancient times. For example, records from the fifth century B.C. suggest that influenza pandemics were observed in ancient Greece. In Europe, during the Middle Ages and the Renaissance, numerous concordant reports from different countries describe epidemics of respiratory infections that resemble influenza pandemics. However, it is not possible to be certain that these epidemics were due to influenza. In the twentieth century, three influenza pandemics have occurred, including the deadly Spanish flu pandemic. Modern virology has unravelled the mechanisms of emergence of pandemic viruses, and considerable knowledge on influenza viruses has been accumulated. The picture is now clear: influenza A is a zoonotic virus whose reservoir is in wild birds. In rare cases, these avian viruses are introduced into man and, eventually, become pandemic viruses. Although these mechanisms are now understood, the time frame required for adaptation of the avian virus to its new host remains unknown. Maybe the next pandemic will show us how rapid this adaptation can be.