Isolation of non-cytopathic viruses implicated in the aetiology of nephritis and baby chick nephropathy and serologically related to avian nephritis virus

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.

The First Whole Genome Sequence and Characterisation of Avian Nephritis Virus Genotype 3

Avian nephritis virus (ANV) is classified in the Avastroviridae family with disease associations with nephritis, uneven flock growth and runting stunting syndrome (RSS) in chicken and turkey flocks, and other avian species. The whole genome of ANV genotype 3 (ANV-3) of 6959 nucleotides including the untranslated 5′ and 3′ regions and polyadenylated tail was detected in a metagenomic virome investigation of RSS-affected chicken broiler flocks. This report characterises the ANV-3 genome, identifying partially overlapping open reading frames (ORFs), ORF1a and ORF1b, and an opposing secondary pseudoknot prior to a ribosomal frameshift stemloop structure, with a separate ORF2, whilst observing conserved astrovirus motifs. Phylogenetic analysis of the Avastroviridae whole genome and ORF2 capsid polyprotein classified the first complete whole genome of ANV-3 within Avastroviridae genogroup 2.

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.

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.

Detection of astrovirus infection in pigeons (Columbia livia) during an outbreak of diarrhoea

Avian astrovirus infections are widespread in many countries, and infections have been linked to enteritis and increased mortality in young poultry. Although pigeons are treated as an important poultry product in some countries, their diseases are often poorly understood and astrovirus infection in pigeons has not been reported. In the present study, faecal samples were collected during an outbreak of gastrointestinal illness in a population of Shanghai pigeons. The samples were examined for astroviruses by reverse transcription-polymerase chain reaction. Eighty-nine per cent (40/45) and 4% (2/45) were found to be positive for avian nephritis virus (ANV) and chicken astrovirus, respectively. One positive sample indicated a co-infection with both ANV and chicken astrovirus. Phylogenetic analysis based on the partial polymerase gene sequence and full-length capsid protein from published avian astrovirus sequences in GenBank revealed that the pigeon viruses detected in this study were evolutionarily closely related to chicken ANV. The present study provided evidence for the presence of astrovirus in pigeons and suggests that cross-infection between pigeons and commercial chickens was likely. Whether the astroviruses in pigeons were responsible for the diarrhoea remains to be determined.

Segmentation expression of capsid protein as an antigen for the detection of avian nephritis virus infection in chicken flocks

Subclinical pathological changes in the kidneys of broiler chickens and suppression of growth caused by the avian nephritis virus (ANV) affect poultry flocks worldwide. A test for detection of virus-specific antibodies in serum would be useful for epidemiological investigations, however the poor propagation in cell cultures has restricted the development of serological tests based on the use of ANV particles as antigens. An enzyme-linked immunosorbent assay (ELISA) was developed for detection of ANV-specific antibodies in chicken serum, using a recombinant protein antigen prepared by segmentation expression of the capsid protein antigen epitope of ANV (HM029238) transfected into Escherichia coli. The expressed fusion protein was detected by Western blotting with ANV-positive serum, and the optimal immunoreactive fusion P1 protein was determined. Using the optimized P1-ELISA, ANV-specific antibodies were detected in commercial chicken flocks aged 10-25 days obtained from the Liaoning Province, China. Out of 960 serum samples, 459 (47.8%) were positive for infection with ANV. These results indicate that the P1-ELISA is helpful for preliminary serological diagnosis of ANV infection, and could be used to for screening in ANV infection and for determining antibodies against ANV.

Astrovirus infections in humans and animals - molecular biology, genetic diversity, and interspecies transmissions

Astroviruses are small, non-enveloped, positive sense, single-stranded RNA viruses first identified in 1975 in children suffering from diarrhea and then described in a wide variety of animals. To date, the list of animal species susceptible to astrovirus infection has expanded to 22 animal species or families, including domestic, synantropic and wild animals, avian, and mammalian species in the terrestrial and aquatic environments. Astrovirus infections are considered among the most common cause of gastroenteritis in children, second only to rotavirus infections, but in animals their association with enteric diseases is not well documented, with the exception of turkey and mink astrovirus infection. Genetic variability has been described in almost all astrovirus species sufficiently examined infecting mammals and birds; however, antigenic variability has been demonstrated for human astroviruses but is far less investigated in animal viruses. Interestingly, there is an increasing evidence of recombination events occurring in astroviruses, which contributes to increase the genetic variability of this group of viruses. A wide variety of species infected, the evident virus genetic diversity and the occurrence of recombination events indicate or imply either cross-species transmission and subsequent virus adaptation to new hosts or the co-infection of the same host with different astroviruses. This can also favor the emergence of novel astroviruses infecting animals or with a zoonotic potential. After more than 30 years from their first description in humans, there are many exciting streams of research to be explored and intriguing questions that remain to be answered about the relatively under-studied Astroviridae family. In the present work, we will review the existing knowledge concerning astrovirus infections in humans and animals, with particular focus on the molecular biology, interspecies transmission and zoonotic potential of this group of viruses.

Detection and characterization of a new astrovirus in chicken and turkeys with enteric and locomotion disorders

In the present paper, we report the unexpected discovery of a new virus in samples from chicken and turkey flocks with clinical disorders such as tenosynovitis, enteric problems, or runting and/or stunting-like conditions. Since 1987, several virus isolation attempts on samples from these flocks resulted in the same macroscopic characteristic lesions in embryonated specific pathogen free eggs, being mortality with bright-red discolouration of legs and wing-tips, a swollen dark-red liver and oedema. Initial work suggested the presence of an agent with characteristics of a non-enveloped RNA virus. Further work, which is described in this paper, showed that the isolated strains formed a new group of avian nephritis viruses, which is genetically and antigenically distinct from known avian astroviruses. Inoculation of a representative strain (isolate 19) of this new group of avian nephritis viruses, provisionally named avian nephritis virus-3, in specific pathogen free layer chicks resulted in diarrhoea, runting and stunting, and even mortality.

Sequence analyses of the representative Chinese-prevalent strain of avian nephritis virus in healthy chicken flocks

Avian nephritis virus (ANV), which belongs to the Astroviridae family, has been associated with acute nephritis in chickens. Cases of ANV infection have been recorded in Japan and in several European countries. However, related studies have never been performed in China. Thus, this study isolated ANV in Chinese chicken flocks. ANV RNA was detected by reverse transcription-PCR in stool samples collected from healthy layer chickens in the Sichuan Province of China in 2009. Of the 192 stool specimens collected, 32.3% (62/192) were positive for ANV infection. The whole genome of ANV-Sichuan54, the first representative Chinese strain, was 6941 nucleotides in length, including the 5' untranslated region, three open reading frames (ORFs), a 3' UTR, and a poly-(A) tail. Comparative and phylogenetic analyses based on partial RNA-dependent RNA polymerase (ORF1b) demonstrated that the majority of ANV investigations were more closely related to the U.S. ANV strain (DQ324827-324836) than to the G-4260 (AB033998).

One-year molecular survey of astrovirus infection in turkeys in Poland

The presence of turkey astrovirus (TAstV) was monitored in meat-type turkey flocks in Poland in 2008. Clinical samples (10 individual faecal swabs/flock) from 77 flocks aged 1-19 weeks were collected from different regions of the country. RT-PCR experiments were performed for detection and molecular characterization of TAstV using four sets of primers within the RdRp gene (ORF1b). The prevalence of astrovirus was 34/77 (44.15%) in the flocks tested. TAstV type 2 was associated with 30 of 77 infections (38.9%), either alone or in mixed infections; TAstV type 1 was detected in 9 of 77 flocks (11.6%), either alone or in mixed infections; ANV was detected only in one flock (1.29%) by sequence analysis during this study. Phylogenetic analysis revealed genetic variability in the TAstV strains that were isolated. Some of Polish TAstV-2 strains were genetically related to the North American isolates; however, most of them formed a distinct subgroup of "European" isolates, suggesting their separate origin or evolution. Additionally, due to the high variability of the TAstV sequences, the most suitable method for TAstV typing seems to be sequencing.

Molecular characterization of avian astroviruses

Astroviruses are frequently associated with enteric diseases in poultry, being isolated from cases of runting-stunting syndrome (RSS) of broiler chickens, poult enteritis complex (PEC), and poult enteritis mortality syndrome (PEMS) of turkeys. Currently, five types of avian astrovirus have been identified: turkey astroviruses 1 and 2 (TAstV-1, TAstV-2), avian nephritis virus (ANV), chicken astrovirus (CAstV) and duck astrovirus (DAstV). The objective of this study was to molecularly characterize the different types of avian astroviruses circulating in commercial poultry. Sequence analysis of a region of ORF2, which encodes the capsid precursor protein associated with serotype and viral pathogenesis, revealed extensive variation in amino acid sequence within each subtype: TAstV-2 (81.5%-100%), ANV (69.9%-100%), and CAstV (85.3%-97.9%). However, this region was more conserved in TAstV-1's (96.2%-100%). Furthermore, a novel astrovirus was detected in chicken samples and found to be <64% similar to ANV and <30.6% similar to CAstV. The results of this study underline the great genetic variability of avian astroviruses and indicate that there are most likely multiple serotypes of each avian astrovirus circulating in commercial poultry.

Detection of avian nephritis virus in Australian chicken flocks

Avian nephritis virus (ANV) is thought to infect poultry flocks worldwide, but no confirmed case has been reported in Australia. The first such case is described in this study. Cases of young chickens with clinical signs of dehydration and diarrhea were submitted to our laboratory and histopathology detected interstitial nephritis. Vaccine strains of infectious bronchitis virus were detected in some of these cases but were not considered to be the causative agent. A total of seven fresh submissions from broiler chicken flocks were collected at 8-11 days of age. Degenerate PCR primers were designed based on published ANV polymerase gene sequences and used to analyze historic cases as well as the fresh submissions. Six of the seven fresh submissions, and one historic case, were positive for ANV with nucleotide sequencing confirming these results. These results establish ANV as an infectious pathogen circulating in Australian poultry.

Enteric viruses detected by molecular methods in commercial chicken and turkey flocks in the United States between 2005 and 2006

Intestinal samples collected from 43 commercial broiler and 33 commercial turkey flocks from all regions of the United States during 2005 and 2006 were examined for the presence of astrovirus, rotavirus, reovirus, and coronavirus by reverse transcription-polymerase chain reaction (PCR), and for the presence of groups 1 and 2 adenovirus by PCR. Phylogenetic analysis was performed to further characterize the viruses and to evaluate species association and geographic patterns. Astroviruses were identified in samples from 86% of the chicken flocks and from 100% of the turkey flocks. Both chicken astrovirus and avian nephritis virus (ANV) were identified in chicken samples, and often both viruses were detected in the same flock. Turkey astrovirus type-2 and turkey astrovirus type-1 were found in 100% and 15.4% of the turkey flocks, respectively. In addition, 12.5% of turkey flocks were positive for ANV. Rotaviruses were present in 46.5% of the chicken flocks tested and in 69.7% of the turkey flocks tested. Based upon the rotavirus NSP4 gene sequence, the chicken and turkey origin rotaviruses assorted in a species-specific manner. The turkey origin rotaviruses also assorted based upon geographical location. Reoviruses were identified in 62.8% and 45.5% of chicken and turkey flocks, respectively. Based on the reovirus S4 gene segment, the chicken and turkey origin viruses assorted separately, and they were distinct from all previously reported avian reoviruses. Coronaviruses were detected in the intestinal contents of chickens, but not turkeys. Adenoviruses were not detected in any chicken or turkeys flocks. Of the 76 total chicken and turkey flocks tested, only three chicken flocks were negative for all viruses targeted by this study. Most flocks were positive for two or more of the viruses, and overall no clear pattern of virus geographic distribution was evident. This study provides updated enteric virus prevalence data for the United States using molecular methods, and it reinforces that enteric viruses are widespread in poultry throughout the United States, although the clinical importance of most of these viruses remains unclear.

Phylogenetic diversity of avian nephritis virus in Hungarian chicken flocks

Avian nephritis virus (ANV) infection was detected in 4-day-old to 22-day-old chickens collected on Hungarian farms between 2002 and 2005. The animals suffered from diarrhoea, growth retardation, runting-stunting syndrome, and 2 to 6% mortality was reported. Tubulonephrosis, interstitial nephritis and uricosis (gout) was diagnosed. The presence of ANV RNA was detected in chicken carcasses using reverse transcriptase-polymerase chain reaction. The virus was demonstrated in 69% of the investigated farms. The nucleotide sequence of the amplification products (corresponding to part of the genome that encodes the GP1 protein) was determined and phylogenetic analysis was performed. The nucleotide sequences showed 76 to 86% identity to the reference strain isolated in 1976 in Japan. The constructed phlyogenetic tree indicates high diversity of the Hungarian ANV sequences, regardless of their origin and year of sample collection. Analysis of the putative amino acid sequences encoded by the partial GP1 sequences also revealed high diversity of the virus. Even samples collected at the same farm, at the same time but from different flocks, differed in nucleotide and putative amino acid sequences. The possible effects of the sequence diversity on the pathogenicity, antigenicity and diagnostics of ANV are discussed.

Molecular characterization and typing of chicken and turkey astroviruses circulating in the United States: implications for diagnostics

Avian astroviruses were detected by reverse transcriptase and polymerase chain reaction in intestinal contents collected from commercial chickens and turkeys from throughout the United States from 2003 through 2005. Astroviruses were detected in birds from both healthy and poorly performing flocks with or without enteric disease. Phylogenetic analysis was performed with sequence data from the polymerase (ORF-1b) genes of 41 turkey-origin astroviruses and 23 chicken-origin astroviruses. All currently available avian astrovirus sequence data and selected mammalian astrovirus sequence data were included in the analysis. Four groups of avian astroviruses were observed by phylogenetic analysis: turkey astrovirus type 1 (TAstV-1)-like viruses, turkey astrovirus type 2 (TAstV-2)-like viruses, both detected in turkeys; avian nephritis virus (ANV)-like viruses, detected in both chickens and turkeys; and a novel group of chicken-origin astroviruses (CAstV). Among these four groups, amino acid identity was between 50.1% and 73.8%, and was a maximum of 49.4% for all avian isolates when compared with the mammalian astroviruses. There were multiple phylogenetic subgroups within the TAstV-2, ANV, and CAstV groups based on 9% nucleotide sequence divergence. Phylogenetic analysis revealed no clear assortment by geographic region or isolation date. Furthermore, no correlation was observed between the detection of a particular astrovirus and the presence of enteric disease or poor performance. Based on these data, a revision of the present taxonomic classification for avian astroviruses within the genus Avastrovirus is warranted.

Molecular diagnosis of avian nephritis: preliminary report

Kidney samples from chickens diagnosed with acute nephritis and gout were subjected to histological and electron microscopic examination. The investigations revealed cytoplasmic inclusion bodies in the tubular epithelial cells containing round virions of about 30 nm in diameter. Since avian nephritis virus (ANV) is known as a potential causative agent of the so-called baby chick nephropathy, an RT-PCR assay was developed for the molecular detection of ANV-specific nucleic acid in the specimen. The specificity of the assay was confirmed by direct sequencing of the amplicon obtained in the reaction. The nucleotide sequence of the PCR product showed 92% identity with the reference ANV sequence deposited in the GenBank database. After having been validated on some other suspicious cases of avian nephritis, the PCR method described in this study can be a potential tool for routine diagnostic examination of samples submitted from cases of gout and nephropathy in chickens.

Avian nephritis virus (ANV) as a new member of the family Astroviridae and construction of infectious ANV cDNA

The complete RNA genome of the avian nephritis virus (ANV) associated with acute nephritis in chickens has been molecularly cloned and sequenced. Excluding the poly(A) tail, the genome comprises 6,927 nucleotides and contains three sequential open reading frames (ORFs). The first ORF (ORF 1a) contains a sequence encoding a serine protease motif, and the second ORF (ORF 1b) has a sequence encoding an RNA-dependent RNA polymerase. ORF 1a may be linked to the second ORF by a ribosomal frameshifting mechanism. The third ORF (ORF 2) may encode the virion structural proteins as a polyprotein precursor. Two RNAs, probably genonic and subgenonic RNA (7.5 and 3.0 kb), were detected in the cytoplasm of ANV-infected cells. ANV and human astroviruses have the same genonic organization, and both are characterized by the presence of two RNA bands. The amino acid homologies of the products of ORF 1a, 1b, and 2 were 20.3, 41.9, and 25.8% to products of the corresponding ORFs of human astrovirus serotype 1 (A/88 Newcastle strain). We have constructed a genonic-length cDNA clone of ANV to test whether the in vitro transcript is infectious. When a chicken kidney cell culture was transfected with RNA transcribed in vitro and the cDNA clone, infectious virus was produced with cytopathic effects in the absence of trypsin. These observations suggested that the ANV (G-4260 strain) is a new genus of the family Astroviridae.

A comparison of three serological methods to detect chicken and turkey antibodies to avian nephritis virus and the use of virus-specific monoclonal antibodies

Avian nephritis virus (ANV) strain G-4260 was inoculated orally in to 1-day-old and 3-week-old chickens and the sequential antibody response to the virus was monitored by serum neutralization, ELISA and immunofluorescence tests. The order of sensitivity of the serological tests was in the sequence given above, with the neutralization test being by far the most sensitive. There was no obvious difference in the antibody titres produced by either age group. Virus was recovered from kidney tissue, the highest titres being obtained 3 to 5 days post-inoculation. Histological examination revealed mainly lymphocytic infiltration of the interstitium and degenerative changes in the tubular epithelium of the kidney. The G-4260 strain of ANV was given orally to 1-day-old turkey poults, but no serological response was induced. Virus was not recovered from the kidneys and no histological lesions were produced in this organ. Monoclonal antibodies were produced which neutralized the infectivity of ANV. An antigen trap ELISA was developed using a monoclonal antibody and infected chicken kidney tissue cultures. However, this assay did not detect ANV in kidney samples taken directly from infected chickens, with the exception of one sample which was shown to contain the highest concentration of infectious virus.

A survey of the viral flora of two commercial Pekin duck flocks

Ducklings on a problem farm which showed persistent and unacceptably high mortality yielded a larger range and greater number of viruses than did ducklings from a second flock, in which mortality was of a power and acceptable level. Reoviruses were the viruses most frequently isolated from young birds from both farms, but for longer at the problem site. ELAs (Embryo Lethal Agents), named since they caused high mortality in chick embryos, but could not otherwise be characterized, were recovered frequently and throughout the growth cycle of the problem flock, but not at all in the other flock. Lentogenic Newcastle disease virus was detected at all ages on the problem farm but less often than ELAs. The faeces of birds on the problem farm yielded rota-like viruses, corona-like viruses and adeno-like viruses, and on the farm with normal mortality, Egg Drop Syndrome-76 virus and adenovirus. Detection techniques included culture on chick embryos and chick embryo liver cells, and electron microscopy (EM). Inoculation of whole eggs was particularly valuable and more successful than cell culture for virus recovery. EM was most useful for direct examination of faecal preparations and confirmation of the viral type.

Recent advances in avian virology

Selected, recent research on the following avian diseases, and their causative viruses, has been reviewed: chicken anaemia, infectious bursal disease, turkey rhinotracheitis, avian nephritis, fowlpox, influenza, infectious bronchitis and turkey enteritis.