Characterising routes of H5N1 and H7N9 spread in China using Bayesian phylogeographical analysis

Multifaceted analysis of temporal and spatial distribution and risk factors of global poultry HPAI-H5N1, 2005-2023

The purpose of this study was to analyze the characteristics of occurrence and spread of highly pathogenic avian influenza H5N1 (HPAI-H5N1) globally, understand its spatiotemporal characteristics, investigate the risk factors influencing outbreaks, and identify high-risk areas for disease occurrence. We collected the data on global poultry HPAI-H5N1 outbreaks from January 2005 to April 2023, and conducted a thorough analysis of the spatial and temporal characteristics of the disease through time series decomposition and directional distribution analysis. Additionally, an ecological niche model was established to explore the major factors influencing the occurrence of HPAI-H5N1 and to pinpoint high-risk areas. Our findings revealed that HPAI-H5N1 outbreaks were cyclical, and seasonal, exhibiting a rising trend, with a predominant northwest-southeast transmission direction. The ecological niche model highlighted that species factors and economic trade factors are critical in influencing the outbreak of HPAI-H5N1. Variables such as chicken and duck density, population density, isothermality, and road density, contributed to importantly risk of outbreaks. High-risk areas for HPAI-H5N1 occurrence were primarily identified in Europe, West Africa, Southeast Asia, and Southeast China. This study provided valuable insights into the spatial and temporal distribution characteristics and risk factors of global poultry HPAI-H5N1 outbreaks. The identification of high-risk areas provides essential information that can be used to develop more effective prevention and control policies.

Investigating the Genetic Diversity of H5 Avian Influenza Viruses in the United Kingdom from 2020-2022

Since 2020, the United Kingdom and Europe have experienced annual epizootics of high-pathogenicity avian influenza virus (HPAIV). The first epizootic, during the autumn/winter of 2020-2021, involved six H5Nx subtypes, although H5N8 HPAIV dominated in the United Kingdom. While genetic assessments of the H5N8 HPAIVs within the United Kingdom demonstrated relative homogeneity, there was a background of other genotypes circulating at a lower degree with different neuraminidase and internal genes.  Following a small number of detections of H5N1 in wild birds over the summer of 2021, the autumn/winter of 2021-2022 saw another European H5 HPAIV epizootic that dwarfed the prior epizootic. This second epizootic was dominated almost exclusively by H5N1 HPAIV, although six distinct genotypes were defined. We have used genetic analysis to evaluate the emergence of different genotypes and proposed reassortment events that have been observed. The existing data suggest that the H5N1 viruses circulating in Europe during late 2020 continued to circulate in wild birds throughout 2021, with minimal adaptation, but then went on to reassort with AIVs in the wild bird population. We have undertaken an in-depth genetic assessment of H5 HPAIVs detected in the United Kingdom over two winter seasons and demonstrate the utility of in-depth genetic analyses in defining the diversity of H5 HPAIVs circulating in avian species, the potential for zoonotic risk, and whether incidents of lateral spread can be defined over independent incursions of infections from wild birds. This provides key supporting data for mitigation activities. IMPORTANCE High-pathogenicity avian influenza virus (HPAIV) outbreaks devastate avian species across all sectors, having both economic and ecological impacts through mortalities in poultry and wild birds, respectively. These viruses can also represent a significant zoonotic risk. Since 2020, the United Kingdom has experienced two successive outbreaks of H5 HPAIV. While H5N8 HPAIV was predominant during the 2020-2021 outbreak, other H5 subtypes were also detected. The following year, there was a shift in the subtype dominance to H5N1 HPAIV, but multiple H5N1 genotypes were detected. Through the thorough utilization of whole-genome sequencing, it was possible to track and characterize the genetic evolution of these H5 HPAIVs in United Kingdom poultry and wild birds. This enabled us to assess the risk posed by these viruses at the poultry-wild bird and the avian-human interfaces and to investigate the potential lateral spread between infected premises, a key factor in understanding the threat to the commercial sector.

A comprehensive method of source apportionment and ecological risk assessment of soil heavy metals: A case study in Qingyuan city, China

The study combined multiple models to provide a deeper understanding to soil heavy metal contamination and source information, which are essential for controlling pollution and reducing human health risks. In this study, the agricultural soils were collected from the Qingyuan City of China as an example. The multiple models (APCS/MLR, PMF, and GDM) were used to identify and quantitatively apportion the main sources of heavy metal pollution in the area. The results showed that Cu (56.4 %), Ni (70.9 %), B (44.5 %), and Cr (72.8 %) were associated with natural sources, such as soil parent material and soil-forming processes. However, Pb (41.2 %), Zn (61.8 %), Hg (67.0 %), and Cd (69.6 %) were associated with agricultural activities, atmospheric deposition, vehicle exhaust emissions, and vehicle tires, while Mo, Se, and Mn were possibly derived from natural sources, including rock weathering and soil parent materials. Additionally, the network of environmental analysis revealed that soil microbes are far more sensitive to soil heavy metal pollution than herbivores, vegetation, and carnivores. This study can serve as a guideline for reducing the ecological and health risks associated with heavy metals in soil by controlling their preferential sources. Environmental implication Combining multiple models is more effective approach to wide understanding of heavy metal contamination and source information, which is essential for controlling pollution and reducing human health risks. Based on multiple models (APCS/MLR, PMF, and GDM) and network environ analysis, a comprehensive method for apportioning soil heavy metal sources and assessing ecological risk had been provided. Further, the present study can be a guideline for reducing ecological and health risks by heavy metals in soil by controlling preferential sources.

Proteomic Analysis Reveals Zinc-finger CCHC-type Containing Protein 3 as a Factor Inhibiting Virus Infection by Promoting Innate Signaling

Influenza a virus exploits host machinery to benefit its replication in host cells. Knowledge of host factors reveals the complicated interaction and provides potential targets for antiviral treatment. Here, instead of the traditional proteomic analysis, we employed a 4D label free proteomic method to identify cellular factors in A549 cells treated with avian H9N2 virus. We observed that 425 proteins were upregulated and 502 proteins were downregulated. Western blotting and quantitative real-time PCR results showed that the zinc-finger CCHC-type containing protein 3 (ZCCHC3) levels were markedly induced by H9N2 infection. Transient expression assay showed that ZCCHC3 expression decreased NP protein levels and viral titers, whereas knockdown of ZCCHC3 enhanced viral growth. Specifically, ZCCHC3 promoted the expression of IFN-β, leading to the increased transcription of IFN downstream antiviral factors. Surprisingly, viral NS1 protein was able to antagonize the antiviral effect of ZCCHC3 by downregulating IFN-β. Eventually, we observed that chicken finger CCCH-type containing protein 3, named ZC3H3, could also suppress the replication of H9N2 virus and the coronavirus-infectious bronchitis virus (IBV) in DF-1 cells. Together, our results showed the cellular proteomic response to H9N2 infection and identified ZCCHC3 as a novel antiviral factor against H9N2 infection, contributing to the understanding of host-virus interaction.

Emergence of a young case infected with avian influenza A (H5N6) in Anhui Province, East China during the COVID-19 pandemic

In the context of the coronavirus disease 2019 pandemic, we investigated the epidemiological and clinical characteristics of a young patient infected by avian influenza A (H5N6) virus in Anhui Province, East China, and analyzed genomic features of the pathogen in 2020. Through the cross‐sectional investigation of external environment monitoring (December 29–31, 2020), 1909 samples were collected from Fuyang City. It was found that the positive rate of H5N6 was higher than other areas obviously in Tianma poultry market, where the case appeared. In addition, dual coinfections were detected with a 0.057% polymerase chain reaction positive rate the surveillance years. The virus was the clade 2.3.4.4, which was most likely formed by genetic reassortment between H5N6 and H9N2 viruses. This study found that the evolution rates of the hemagglutinin and neuraminidase genes of the virus were higher than those of common seasonal influenza viruses. The virus was still highly pathogenic to poultry and had a preference for avian receptor binding.

Various avian influenza virus (AIV) subtypes naturally have caused zoonotic infections, but the subtypes H5N1 and H7N9 have caused a prominent impact.

At present, the outbreak of novel coronavirus pneumonia (coronavirus disease 2019 [COVID‐19]) has caused a worldwide pandemic.

To our knowledge, this is the youngest child infected with H5N6 subtype avian influenza in Anhui Province.

Herein, we analyzed the epidemiology of the case and the characteristics of the pathogen genome, to find out the possible evolution of the virus.

Transport of Moving Duck Flocks in Indonesia and Vietnam: Management Practices That Potentially Impact Avian Pathogen Dissemination

Highly pathogenic avian influenza (HPAI) virus is endemic in Indonesia and Vietnam, where “moving” duck production is commonly practiced. Questionnaire surveys were conducted with transporters of “moving” duck flocks in Indonesia (N = 55) and Vietnam (N = 43). The main purpose of transportation was to transport duck flocks between rice paddies used for scavenging. Trucks were commonly utilized for transport in both countries (Indonesia: 98.2%, 54/55; Vietnam: 37.2%, 16/43), while boats were only used in Vietnam (62.8%, 27/43). Transporters in Vietnam moved larger flocks and traveled over longer distances. Deaths of ducks due to diseases were reported in both countries (Indonesia: 16.4%, 9/55; Vietnam: 4.7%, 2/43; p = 0.11). Throwing away of carcasses was the primary method of disposal of dead birds in Indonesia (60.0%, 33/55), but was not practiced in Vietnam (p < 0.001), while more transporters in Vietnam (34.9%, 15/43) buried carcasses compared to Indonesia (6.8%, 4/55; p = 0.001). Consumption of carcasses (20.9%, 9/43), sale of dead ducks (14.0%, 6/43) and processing of ducks for fish feed (9.3%, 4/43) was conducted in Vietnam, but not in Indonesia. Vehicles were predominantly cleaned in rivers and stored outside in Vietnam, while cleaning and storage was usually conducted in houses/garages in Indonesia. In conclusion, we identified management practices that potentially impact transmission of avian pathogens, such as HPAI virus. In Indonesia, unsafe management practices were related to multipurpose usage of transport vehicles and disposal of birds in the environment, while in Vietnam, they were related to the mixing of birds during transport, the processing of dead carcasses and the storage and cleaning of transport vehicles.

Genetic diversity, phylogeography, and evolutionary dynamics of highly pathogenic avian influenza A (H5N6) viruses

From 2013 onwards, the spread of novel H5N6 highly pathogenic avian influenza (HPAI) viruses in China has posed great threats to not only poultry industry but also human health. Since late-2016 in particular, frequent outbreaks of clade 2.3.4.4 H5N6 HPAI viruses among wild birds have promoted viral dissemination in South Korea, Japan, and European countries. In response to those trends, we conducted molecular genetic analysis of global clade 2.3.4.4 H5N6 viruses in order to characterize spatio-temporal patterns of viral diffusion and genetic diversity among wild birds and poultry. The clade 2.3.4.4 H5N6 viruses were classified into three groups (Group B, C, and D). During the cocirculation of Group C/D H5N6 viruses from 2013 to 2017, viral movements occurred between close or adjacent regions of China, Vietnam, South Korea, and Japan. In addition, viral migration rates from Guangdong and Hunan to multiple adjacent provinces seemed to have been highly supported by transmission routes (Bayes factors >100), suggesting that southern China was an epicenter for the spread of H5N6 viruses in poultry during that period. Since the introduction of H5N6 viruses originating in wild birds in late-2016, evolving H5N6 viruses have lost most previous genotypes (e.g. G1, G2, and G1.2), whereas some prevailing genotypes (e.g. G1.1, G1.1.b, and G3) in aquatic birds have been dominated, and in particular, the effective population size of H5N6 originating in wild birds dramatically increased; however, the population size of poultry-origin H5N6 viruses declined during the same period, indicating that wild bird migration might accelerate the genetic diversity of H5N6 viruses. Phylogeographic approaches revealed that two independent paths of H5N6 viruses into South Korea and Japan from 2016 to 2018 and provided evidence of Group B and Group C H5N6 viruses were originated from Europe and China, respectively, as regions located in the East Asia-Australian migration flyway, which accelerated the genetic variability and dissemination. Altogether, our study provides insights to examine time of origin, evolutionary rate, diversification patterns, and phylogeographical approach of global clade 2.3.4.4 H5N6 HPAI viruses for assessing their evolutionary process and dissemination pathways.

Truncation or Deglycosylation of the Neuraminidase Stalk Enhances the Pathogenicity of the H5N1 Subtype Avian Influenza Virus in Mallard Ducks

H5N1 subtype avian influenza virus (AIV) with a deletion of 20 amino acids at residues 49–68 in the stalk region of neuraminidase (NA) became a major epidemic virus. To determine the effect of truncation or deglycosylation of the NA stalk on virulence, we used site-directed mutagenesis to insert 20 amino acids in the short-stalk virus A/mallard/Huadong/S/2005 (SY) to recover the long-stalk virus (rSNA+). A series of short-stalk or deglycosylated-stalk viruses were also constructed basing on the long-stalk virus, and then the characteristics and pathogenicity of the resulting viruses were evaluated. The results showed that most of the short-stalk or deglycosylated-stalk viruses had smaller plaques, and increased thermal and low-pH stability, and a decreased neuraminidase activity when compared with the virus rSNA+. In a mallard ducks challenge study, most of the short-stalk or deglycosylated-stalk viruses showed increased pathological lesions and virus titers in the organ tissues and increased virus shedding in the oropharynx and cloaca when compared with the rSNA+ virus, while most of the short-stalk viruses, especially rSNA-20, showed higher pathogenicity than the deglycosylated-stalk virus. In addition, the short-stalk viruses showed a significantly upregulated expression of the immune-related factors in the lungs of the infected mallard ducks, including IFN-α, Mx1, and IL-8. The results suggested that NA stalk truncation or deglycosylation increases the pathogenicity of H5N1 subtype AIV in mallard ducks, which will provide a pre-warning for prevention and control of H5N1 subtype avian influenza in the waterfowl.

Origin and cross-species transmission of bat coronaviruses in China

Bats are presumed reservoirs of diverse coronaviruses (CoVs) including progenitors of Severe Acute Respiratory Syndrome (SARS)-CoV and SARS-CoV-2, the causative agent of COVID-19. However, the evolution and diversification of these coronaviruses remains poorly understood. Here we use a Bayesian statistical framework and a large sequence data set from bat-CoVs (including 630 novel CoV sequences) in China to study their macroevolution, cross-species transmission and dispersal. We find that host-switching occurs more frequently and across more distantly related host taxa in alpha- than beta-CoVs, and is more highly constrained by phylogenetic distance for beta-CoVs. We show that inter-family and -genus switching is most common in Rhinolophidae and the genus Rhinolophus. Our analyses identify the host taxa and geographic regions that define hotspots of CoV evolutionary diversity in China that could help target bat-CoV discovery for proactive zoonotic disease surveillance. Finally, we present a phylogenetic analysis suggesting a likely origin for SARS-CoV-2 in Rhinolophus spp. bats.