Complete sequence and genetic characterization of pigeon avian nephritis virus, a member of the family Astroviridae

Isolation, Identification, and Pathogenicity of a Goose Astrovirus Genotype 1 Strain in Goslings in China

Goose astrovirus genotype 1 (GAstV-1) has emerged in goose farms in some provinces of China in recent years and is considered to be one of the pathogens of gout in goslings in China. However, few studies have been conducted on the dynamic distribution, tissue tropism, and pathogenesis of GAstV-1 in goslings. In 2022, an epidemiological investigation of goose astrovirus (GAstV) in goslings was conducted in seven provinces of China. During the investigation, a GAstV-1 designated as GAstV-JSXZ was identified in the kidney of an 8-day-old gosling and was successfully isolated from a goose embryo. The full genome sequence of GAstV-JSXZ was determined using the next-generation sequencing technique. The complete genome of GAstV-JSXZ was 7299-nt-long. Interestingly, the phylogenetic analysis revealed that Chinese GAstV-1 has formed two distinct subgroups based on the ORF 2 genomes, designated GAstV-1 1a and GAstV-1 1b. The GAstV-JSXZ shared the highest identity with GAstV-1 1a strain FLX and TZ03 in nucleotides (ORF1a: 98.3-98.4%; ORF1b: 92.3-99.1%; ORF2: 95.8-98.8%) and amino acid sequences (ORF1a: 99.4-99.5%; ORF1b: 98.2-98.8%; ORF2: 97.0-99.4%). To evaluate the pathogenicity of GAstV-1, 1-day-old goslings were inoculated with the virus by oral and subcutaneous injection routes, respectively. The results revealed that the virus causes extensive pathological organ damage, especially in the kidney, liver, and thymus. Virus-specific genomic RNA could be detected in the cloacal swabs and tissues of infected goslings throughout the experiment. The viral copy numbers examined in the kidney and intestine were the highest, followed by the liver and spleen. These results are likely to provide a new understanding of the pathogenicity of GAstV-1 in geese.

Identification and characterization of a novel avian nephritis virus variant in chickens with enteritis in Hunan province, China

Avian nephritis virus (ANV) infection is associated with diarrhea, uricosis, stunting, tubulonephrosis, interstitial nephritis, and mortality of chicken flocks, leading to economic losses in the poultry industry. In this study, an ANV strain designated as HNU-ANV-ML-2020 was identified in tissue samples collected from chickens with severe enteritis on a poultry farm in Hunan province, China, and analyzed. The genome of HNU-ANV-ML-2020 is 6943 nucleotides in length. It showed the highest sequence identity (88.1%) to ANV strain CHN/GXJL815/2017 (MN732559) from Guangxi province, China, while it showed less than 86% identity to other astrovirus (AstV) genome sequences available in the GenBank database. The capsid protein of this virus showed the highest sequence identity to ANV strains HQ330482 and HQ330498 from the UK (81.2% and 81.06%, respectively), while it showed only 73.9% identity to MN732559 and less than 80% identity to the capsid proteins of other AstVs available in GenBank. Further phylogenetic analysis demonstrated that HNU-ANV-ML-2020 belongs to group 4, together with ANV strains identified in Australia, Brazil, the UK, and the Netherlands. Furthermore, ANV strains identified in chickens in China were found to be separated into four distinct groups/genotypes, indicating substantial genetic divergence and a complex circulation pattern in China. The virus characterized in the present study is a novel ANV variant identified for the first time in Hunan province, China.

A Review of the Emerging Poultry Visceral Gout Disease Linked to Avian Astrovirus Infection

Avian astroviruses, including chicken astrovirus (CAstV), avian nephritisvirus (ANV), and goose astrovirus (GoAstV), are ubiquitous enteric RNA viruses associated with enteric disorders in avian species. Recent research has found that infection of these astroviruses usually cause visceral gout in chicken, duckling and gosling. However, the underlying mechanism remains unknown. In the current article, we review recent discoveries of genetic diversity and variation of these astroviruses, as well as pathogenesis after astrovirus infection. In addition, we discuss the relation between avian astrovirus infection and visceral gout in poultry. Our aim is to review recent discoveries about the prevention and control of the consequential visceral gout diseases in poultry, along with the attempt to reveal the possible producing process of visceral gout diseases in poultry.

Characterization and pathogenicity of a novel avian nephritis virus isolated in China

AbstractAvian nephritis virus (ANV) infections of chicken flocks cause enteric and kidney disease, uneven growth, and runting stunting syndrome, leading to economic losses in the poultry industry. In this study, one ANV strain, designated as AH202017, was isolated from a diseased broiler flock in Anhui province, China, in 2020. Virus production in LMH cell culture was confirmed by real-time RT-PCR and immunofluorescence assay. The complete genome sequencing analysis indicated that AH202017 shares 77.5%-85.5% identity with 12 reference strains in GenBank. Phylogenetic analysis of the capsid protein revealed that AH202017 is more closely related to VIC-6a/Australia/2014 belonging to ANV genotype 2. However, the phylogenetic tree, based on the ORF1a protein and ORF1b protein, indicated that AH202017 manifests a close relationship with GXJL815/China/2017 belonging to genotype 8. In infection experiments, four infected chickens showed depression and one chicken died at 6 days post-infection, corresponding to 5% mortality. The virus was shed daily in the feces of infected chickens, and was found distributed in multiple organs. Macroscopic and microscopic lesions in the kidneys were observed. This is the first paper that describes the genomic characteristics and pathogenicity of a novel ANV strain in China.

Isolation and characterization of a goose astrovirus 1 strain causing fatal gout in goslings, China

In recent years, goose gout, a severe infectious disease, has affected the development of the goose industry in China. Two different genotypes of goose astrovirus (GAstV), named as GAstV-1 and GAstV-2, were identified. GAstV-2 viruses are known to be the causative agent of goose gout; however, GAstV-1 has not been isolated, and the relationship between GAstV-1 and goose gout is unknown. One full genome sequence, designated as GAstV/CHN/TZ03/2019 (TZ03), was determined from the clinical tissue samples of a diseased gosling using next-generation sequencing. The complete genome of TZ03 was 7,262 nucleotides in length with typical genomic characteristics of avastroviruses. The TZ03 strain shares the highest identity (96.6%) with the GAstV-1 strain FLX, but only 51.5 to 61.3% identity with other astroviruses in Avastrovirus. Phylogenetic analysis revealed that the TZ03 strain clustered together with the GAstV-1 strains FLX and AHDY and was highly divergent from GAstV-2 viruses. The TZ03 strain was successfully isolated from goose embryos and caused 100% mortality of goose embryos after 5 passages. Electron microscopy showed that the virus particles were spherical with a diameter of ∼22 nm. The clinical symptoms were reproduced by experimental infection of healthy goslings, which were similar to those caused by GAstV-2 strains. Our data show that GAstV-1 is one of the causative agents of the ongoing goose gout disease in China. These findings enrich our understanding of the evolution of GAstVs that cause gout and provide potential options for developing biological products to treat goose gout.

Intra- and Cross-Species Transmission of Astroviruses

Astroviruses are non-enveloped, single-stranded RNA viruses that infect mammalian and avian species. In humans, astrovirus infections are one of the most common causes of gastroenteritis in children. Infection has also been linked to serious neurological complications, especially in immunocompromised individuals. More extensive disease has also been characterized in non-human mammalian and avian species. To date, astroviruses have been detected in over 80 different avian and mammalian hosts. As the number of hosts continues to rise, the need to understand how astroviruses transmit within a given species as well as to new host species becomes increasingly important. Here, we review the current understanding of astrovirus transmission, the factors that influence viral spread, and the potential for cross-species transmission. Additionally, we highlight the current gaps in knowledge and areas of future research that will be key to understanding astrovirus transmission and zoonotic potential.

Analysis of astrovirus transmission pathways in a free-ranging fission-fusion colony of Natterer’s bats (Myotis nattereri)

Abstract

Bats are a diverse and widespread order of mammals. They fulfill critical ecosystem roles but may also act as reservoirs and spreaders for zoonotic agents. Consequently, many recent studies have focused on the potential of bats to spread diseases to other animals and to humans. However, virus transmission networks within bat colonies remain largely unexplored. We studied the detection rate and transmission pathway of astroviruses in a free-ranging Natterer’s bat colony (Myotis nattereri) that exhibits a high fission-fusion dynamic. Based on automatic roost monitoring data of radio-frequency identification tagged bats, we assessed the impact of the strength of an individual’s roosting associations with all other colony members (weighted degree), and the number of roost sites (bat boxes) an individual used—both being proxies for individual exposure risk—on the detected presence of astrovirus-related nucleic acid in individual swab samples. Moreover, we tested to which degree astrovirus sequence types were shared between individuals that frequently roosted together, as proxy for direct transmission risk, and between bats sharing the same roost sites in close temporal succession, as proxy for indirect transmission risk. Neither roosting associations nor the number of different roost sites had an effect on detected virus presence in individual bats. Transmission network data suggest that astroviruses are transmitted both via direct and indirect contact, implying that roost sites pose a risk of astrovirus infection for several days after the bats leave them. Our study offers novel insights in the presence and transmission of viruses within social networks of bat colonies.

Significance statement

Bats provide many ecosystem services but have moved into the focus of virological research as potential carriers of zoonotic disease agents. However, the sparse information available about virus transmission within bat colonies is solely based on simulated transmission data. In this field study, we examined the daily roosting behavior in a wild bat colony in relation to the presence of viruses in individual colony members. Our findings suggest that astroviruses are transmitted by direct contact and via contaminated roost sites. Bats typically defecate in their roost sites, and astroviruses can remain infectious in feces for several days. The here observed virus diversity and roosting behavior suggest that bats can contract astroviruses even if they use contaminated roost sites days after infected individuals have left. This study provides first-time insights in the transmission of astroviruses within bat colonies in the wild.

A novel group of avian Avastrovirus in domestic geese, China

Using an ORF1b-based astrovirus-specfic reverse transcription (RT)-PCR assay, a novel astrovirus-like was detected from domestic geese in China. Pairwise comparisons and phylogenetic analyzes suggested that a novel group of goose astrovirus, different with previously known astroviruses in the genus Avastrovirus, was found circulating in geese. This study has expanded our understanding about the role of domestic waterfowls as reservoirs for diverse astroviruses.

The Broad Host Range and Genetic Diversity of Mammalian and Avian Astroviruses

Astroviruses are a diverse family of viruses that infect a wide range of mammalian and avian hosts. Here we describe the phylogenetic diversity and current classification methodology of astroviruses based on the ORF1b and ORF2 genes, highlighting the propensity of astroviruses to undergo interspecies transmission and genetic recombination which greatly increase diversity and complicate attempts at a unified and comprehensive classification strategy.

Complete genome sequence analysis of chicken astrovirus isolate from India

Objective

Chicken astroviruses have been known to cause severe disease in chickens leading to increased mortality and “white chicks” condition. Here we aim to characterize the causative agent of visceral gout suspected for astrovirus infection in broiler breeder chickens.

Methods

Total RNA isolated from allantoic fluid of SPF embryo passaged with infected chicken sample was sequenced by whole genome shotgun sequencing using ion-torrent PGM platform. The sequence was analysed for the presence of coding and non-coding features, its similarity with reported isolates and epitope analysis of capsid structural protein.

Results

The consensus length of 7513 bp genome sequence of Indian isolate of chicken astrovirus was obtained after assembly of 14,121 high quality reads. The genome was comprised of 13 bp 5′-UTR, three open reading frames (ORFs) including ORF1a encoding serine protease, ORF1b encoding RNA dependent RNA polymerase (RdRp) and ORF2 encoding capsid protein, and 298 bp of 3′-UTR which harboured two corona virus stem loop II like “s2m” motifs and a poly A stretch of 19 nucleotides. The genetic analysis of CAstV/INDIA/ANAND/2016 suggested highest sequence similarity of 86.94% with the chicken astrovirus isolate CAstV/GA2011 followed by 84.76% with CAstV/4175 and 74.48%% with CAstV/Poland/G059/2014 isolates. The capsid structural protein of CAstV/INDIA/ANAND/2016 showed 84.67% similarity with chicken astrovirus isolate CAstV/GA2011, 81.06% with CAstV/4175 and 41.18% with CAstV/Poland/G059/2014 isolates. However, the capsid protein sequence showed high degree of sequence identity at nucleotide level (98.64-99.32%) and at amino acids level (97.74–98.69%) with reported sequences of Indian isolates suggesting their common origin and limited sequence divergence. The epitope analysis by SVMTriP identified two unique epitopes in our isolate, seven shared epitopes among Indian isolates and two shared epitopes among all isolates except Poland isolate which carried all distinct epitopes.

Electronic supplementary material

The online version of this article (doi:10.1007/s11259-016-9673-6) contains supplementary material, which is available to authorized users.

High-resolution melt curve analysis to confirm the presence of co-circulating isolates of avian nephritis virus in commercial chicken flocks

Avian Nephritis Virus (ANV) has been implicated in poor growth and renal disease of young chickens. This paper describes the development of a reverse-transcriptase polymerase chain reaction for the detection of ANV in commercial meat chickens and the use of high-resolution melt curves to detect the presence of genetically different ANVs. Pooled cloacal swabs from both healthy and ill commercial chicken broiler flocks were tested for the presence of ANV using a combination of polymerase chain reaction, molecular cloning, high-resolution melt curve analysis and sequencing. Except for one, all specimens were found to contain two genetically different ANVs. Phylogenetic analysis of the capsid amino acid sequences revealed the presence of four of six groups of ANV identified previously in other countries as well as in two novel groups of ANV. Phylogenetic analysis of nucleotide sequences of partial polymerase, capsid and 3' untranslated regions reveal that the genes of individual ANV virus isolates have different ancestors. This was shown to be due to a template-switching event in the capsid gene that resulted in the 3' end of the capsid gene and the 3' untranslated region of one ANV isolate being transferred to another ANV. These results reveal that infection of chicken flocks with multiple ANV isolates is common and this needs to be taken into consideration in diagnosis of ANV using molecular techniques and in future epidemiological investigations.

Detection of a novel astrovirus from a black-naped monarch (Hypothymis azurea) in Cambodia

BACKGROUND

Astroviruses are comprised of two genera with Avastrovirus infecting birds and Mamastrovirus infecting mammals. Avastroviruses have primarily been associated with infections of poultry, especially chicken, turkey, duck, and guineafowl production systems, but also infect wading birds and doves. Outcomes result in a spectrum of disease, ranging from asymptomatic shedding to gastroenteritis with diarrhea, stunting, failure to thrive and death.

FINDINGS

Virological surveillance was conducted in birds from two sites in Cambodia in 2010. Samples were screened for influenza, astroviruses, coronaviruses, flaviviruses, and paramyxoviruses. A total of 199 birds were tested and an astrovirus was detected in a black-naped monarch (Hypothymis azurea).

CONCLUSIONS

This is the first astrovirus detection in a passerine bird. Phylogenetic analysis and nucleotide distances suggest that this avastrovirus forms a distinct lineage and may constitute a fourth avastrovirus group.

Human astroviruses

Human astroviruses (HAtVs) are positive-sense single-stranded RNA viruses that were discovered in 1975. Astroviruses infecting other species, particularly mammalian and avian, were identified and classified into the genera Mamastrovirus and Avastrovirus. Through next-generation sequencing, many new astroviruses infecting different species, including humans, have been described, and the Astroviridae family shows a high diversity and zoonotic potential. Three divergent groups of HAstVs are recognized: the classic (MAstV 1), HAstV-MLB (MAstV 6), and HAstV-VA/HMO (MAstV 8 and MAstV 9) groups. Classic HAstVs contain 8 serotypes and account for 2 to 9% of all acute nonbacterial gastroenteritis in children worldwide. Infections are usually self-limiting but can also spread systemically and cause severe infections in immunocompromised patients. The other groups have also been identified in children with gastroenteritis, but extraintestinal pathologies have been suggested for them as well. Classic HAstVs may be grown in cells, allowing the study of their cell cycle, which is similar to that of caliciviruses. The continuous emergence of new astroviruses with a potential zoonotic transmission highlights the need to gain insights on their biology in order to prevent future health threats. This review focuses on the basic virology, pathogenesis, host response, epidemiology, diagnostic assays, and prevention strategies for HAstVs.

Novel coronavirus and astrovirus in Delaware Bay shorebirds

BACKGROUND

Wild birds are an important but to some extent under-studied reservoir for emerging pathogens. We used unbiased sequencing methods for virus discovery in shorebird samples from the Delaware Bay, USA; an important feeding ground for thousands of migratory birds.

FINDINGS

Analysis of shorebird fecal samples indicated the presence of a novel astrovirus and coronavirus. A sanderling sample yielded sequences with distant homology to avian nephritis virus 1, an astrovirus associated with acute nephritis in poultry. A ruddy turnstone sample yielded sequences with homology to deltacoronaviruses.

CONCLUSIONS

Our findings highlight shorebirds as a virus reservoir and the need to closely monitor wild bird populations for the emergence of novel virus variants.

Crystal structure of the avian astrovirus capsid spike

Astroviruses are small, nonenveloped, single-stranded RNA viruses that cause diarrhea in a wide variety of mammals and birds. On the surface of the viral capsid are globular spikes that are thought to be involved in attachment to host cells. To understand the basis of species specificity, we investigated the structure of an avian astrovirus capsid spike and compared it to a previously reported human astrovirus capsid spike structure. Here we report the crystal structure of the turkey astrovirus 2 (TAstV-2) capsid surface spike domain, determined to 1.5-Å resolution, and identify three conserved patches on the surface of the spike that are candidate avian receptor-binding sites. Surprisingly, the overall TAstV-2 capsid spike structure is unique, with only distant structural similarities to the human astrovirus capsid spike and other viral capsid spikes. There is an absence of conserved putative receptor-binding sites between the human and avian spikes. However, there is evidence for carbohydrate-binding sites in both human and avian spikes, and studies with human astrovirus 1 (HAstV-1) suggest a minor role in infection for chondroitin sulfate but not heparin. Overall, our structural and functional studies provide new insights into astrovirus host cell entry, species specificity, and evolution.

Porcine astrovirus viremia and high genetic variability in pigs on large holdings in Croatia

Astroviruses are emerging viral agents, primarily enteropathogenic in mammals, but recently have been acknowledged to have extra-intestinal implications in humans and mink. Porcine astrovirus is thought to be widely distributed and highly prevalent among pigs, nevertheless its clinical significance remains doubtful as it can be detected in diarrheic as well as in healthy pigs. Recent reports imply the immense genetic variability among porcine astrovirus strains with five distinct lineages being characterized so far. Herein, we report porcine astrovirus circulation in the blood of healthy pigs in different age categories bred on two large industrial holdings in Croatia, with viral RNA seroprevalence of 3.89%. These are the first extra-intestinal findings of astrovirus in pigs, indicating a more complex pathogenesis than previously thought. Partial polymerase sequences of serum-derived strains provisionally clustered into porcine astrovirus lineages 2 and 4, sharing high genetic identity with previously described porcine astrovirus strains. The results were supported by detecting porcine astrovirus strains in composite fecal samples, regardless of pig category or holding tested. Phylogenetic analysis of derived strains suggested the presence of porcine astrovirus lineages previously detected in pig sera with an additional highly genetically divergent lineage 5, reported for the first time in Europe. Moreover, the existence of possible sub lineages should not be excluded. The results obtained in the present study, contribute to knowledge of porcine astrovirus pathogenesis; even though it's possible clinical significance remains unclear. High fecal prevalence accompanied with vast genetic diversity on a relatively confined area, underscores the importance of pigs as porcine astrovirus reservoirs with eventual recombination events as a possible outcome.

Avian Astroviruses

Avian astroviruses comprise a diverse group of viruses affecting many avian species and causing enteritis, hepatitis, and nephritis. To date, six different astroviruses have been identified in avian species based on the species of origin and viral genome characteristics: two turkey-origin astroviruses [Turkey Astrovirus type 1 (TAstV-1) and type 2 (TAstV-2)]; two chicken-origin astroviruses [Avian Nephritis Virus (ANV) and Chicken Astrovirus (CAstV)]; and two duck-origin astrovirus [Duck Astrovirus type 1 (DAstV-1) and type 2 (DAstV-2)]. ANV has also been detected in turkeys, ducklings, pigeons, and guinea fowl; and TAstrovirus-2-like viruses have also been found in guinea fowl. Astroviruses are commonly associated with enteric disease syndromes in poultry including runting-stunting syndrome of broilers (RSS), poult enteritis complex or syndrome (PEC or PES), poult enteritis mortality syndrome (PEMS), and enteritis in guinea fowl. The molecular characterization of the different avian astroviruses shows great genetic variability among each type, and this variability influences the ability to detect these viruses by molecular and serological techniques. In this chapter, we review the different aspects related to avian astroviruses, including molecular biology, pathogenesis, diagnosis, and control.

Experimental infection of poults and guinea fowl with genetically distinct avian astroviruses

Avian astroviruses, of the genus Avastrovirus, are recognized as being the cause of enteritis in different bird species worldwide. In particular, turkeys are very susceptible and can be severely affected by this viral agent. More recently, astroviruses were detected in diseased guinea fowl in Italy but whether or not they were the causative agents of the clinical disease was not established. Despite the distribution and relevance of Avastrovirus infection, very little information on pathogenesis or factors influencing the pathogenicity of astroviruses is available. To increase available data on the pathogenesis of these viruses and to test the hypothesis of possible interspecies transmission, experimental infections were carried out in turkeys and guinea fowl with two genetically distinct avian astroviruses, namely TK-6363 and GF-5497, originating respectively from diseased turkey poults and guinea fowl. Data obtained in our study show that both of the viruses selected were able to infect young birds of the species in which they were originally detected. Additionally, these viruses were able to infect young birds of different species causing clinical signs, thus providing experimental evidence for the infection of distinct avian astroviruses in different avian species.