Targeted detection and molecular epidemiology of turkey coronavirus spike gene variants in turkeys and chickens

Turkey coronavirus (TCoV) is a member of the Avian coronavirus species with infectious bronchitis virus (IBV), which is considered to be the source of TCoV. These 2 viruses are highly similar in all regions of their genomes, except for the spike gene, which is necessary for virus attachment. Although TCoV causes severe enteric disease in turkey poults, it does not cause clinical disease in chickens. However, considering that TCoV can infect chickens, it is important to distinguish TCoV from IBV in chickens. This is particularly true for chickens that are housed near turkeys and thus might be infected with TCoV and serve as a silent source of TCoV for turkeys. We developed and validated a real-time PCR assay to detect the spike gene of TCoV and sequenced a portion of this gene to evaluate the molecular epidemiology of TCoV infections associated with a commercial turkey premises in the United States in 2020-2021. We identified natural infections of TCoV in chickens, and based on the molecular epidemiology of the viruses detected, these chickens may have served as a source of infection for the commercial turkey premises located nearby.

Molecular Epidemiology of Turkey Coronaviruses in Poland

The only knowledge of the molecular structure of European turkey coronaviruses (TCoVs) comes from France. These viruses have a quite distinct S gene from North American isolates. The aim of the study was to estimate the prevalence of TCoV strains in a Polish turkey farm during a twelve-year period, between 2008 and 2019, and to characterize their full-length S gene. Out of the 648 flocks tested, 65 (10.0%, 95% CI: 7.9–12.6) were positive for TCoV and 16 of them were molecularly characterized. Phylogenetic analysis showed that these strains belonged to two clusters, one formed by the early isolates identified at the beginning of the TCoV monitoring (from 2009 to 2010), and the other, which was formed by more recent strains from 2014 to 2019. Our analysis of the changes observed in the deduced amino acids of the S1 protein suggests the existence of three variable regions. Moreover, although the selection pressure analysis showed that the TCoV strains were evolving under negative selection, some sites of the S1 subunit were positively selected, and most of them were located within the proposed variable regions. Our sequence analysis also showed one TCoV strain had recombined with another one in the S1 gene. The presented investigation on the molecular feature of the S gene of TCoVs circulating in the turkey population in Poland contributes interesting data to the current state of knowledge.

Comparison of 3'-end encoding regions of turkey coronavirus isolates from Indiana, North Carolina, and Minnesota with chicken infectious bronchitis coronavirus strains

Objective

To analyze the 3′-end structural protein-encoding region of turkey coronavirus (TCoV) isolates associated with outbreaks of acute enteritis in Indiana, North Carolina, or Minnesota.

Methods

Four isolates of TCoV were sequenced over the entire 3′-end structural protein-encoding region and compared phylogenetically along with the corresponding sequences of infectious bronchitis virus (IBV) strains.

Results

The sequence similarity between TCoV and IBV was lower than that among TCoV isolates or that among IBV strains. The variation of sequences between TCoV and IBV was mainly contributed by the S protein gene. The sequence similarity of S gene between TCoV and IBV was lower than that among TCoV isolates or that among IBV strains. The phylogenetic tree based on the S protein region was similar to that based on the entire 3′-end structural protein-encoding region with TCoV isolates and IBV strains grouped in two separate clusters. The phylogenetic tree based on other genes had a very different topology with TCoV isolates randomly forming groups with different IBV strains.

Conclusions

These results suggested that TCoV probably shared the same origin with that of IBV and acquired sequences of S gene for turkey intestine tropism during the process of evolution in a separate environment.

Differential detection of turkey coronavirus, infectious bronchitis virus, and bovine coronavirus by a multiplex polymerase chain reaction

The objective of the present study was to develop a multiplex polymerase chain reaction (PCR) method for differential detection of turkey coronavirus (TCoV), infectious bronchitis coronavirus (IBV), and bovine coronavirus (BCoV). Primers were designed from conserved or variable regions of nucleocapsid (N) or spike (S) protein gene among TCoV, IBV, and BCoV and used in the same PCR reaction. Reverse transcription followed by the PCR reaction was used to amplify a portion of N or S gene of the corresponding coronaviruses. The PCR products were detected on agarose gel stained with ethidium bromide. Two PCR products, a 356-bp band corresponding to N gene and a 727-bp band corresponding to S gene, were obtained for TCoV isolates. In contrast, one PCR product of 356 bp corresponding to a fragment of N gene was obtained for IBV strains and one PCR product of 568 bp corresponding to a fragment of S gene was obtained for BCoV. There were no PCR products with the same primers for Newcastle disease virus, Marek's disease virus, turkey pox virus, pigeon pox virus, fowl pox virus, reovirus, infectious bursal disease virus, enterovirus, astrovirus, Salmonella enterica, Escherichia coli, and Mycoplasma gallisepticum. Performance of the assay with serially diluted RNA demonstrated that the multiplex PCR could detect 4.8 × 10⁻³ μg of TCoV RNA, 4.6 × 10⁻⁴ μg of IBV RNA, and 8.0 × 10⁻² μg of BCoV RNA. These results indicated that the multiplex PCR as established in the present study is a rapid, sensitive, and specific method for differential detection of TCoV, IBV, and BCoV in a single PCR reaction.

Multiplex real-time reverse transcription-polymerase chain reaction for the detection of three viruses associated with poult enteritis complex: turkey astrovirus, turkey coronavirus, and turkey reovirus

Poult enteritis complex (PEC) is an economically important disease of young turkeys characterized by diarrhea, poor weight gain, and, in some cases, high mortality. Although PEC is considered to be a polymicrobial disease, numerous viruses, including turkey coronavirus (TCV), turkey astrovirus type 2 (TAstV-2), and avian reoviruses (ARVs), have been associated with PEC-like disease. Real-time reverse transcription-polymerase chain reaction (RRT-PCR), a highly sensitive and specific detection method for viral RNA, was developed in a multiplex format for the simultaneous detection of TAstV-2 and TCV and for the detection of two genetic types of ARV. Assay sensitivity was determined using in vitro transcribed RNA and varied by target between 150 gene copies for TAstV-2 alone and 2200 gene copies for TCV when multiplexed. Virus detection was evaluated with samples collected from poults inoculated at 1 day of age with each of the viruses. Cloacal swabs and intestinal samples were obtained at 1, 2, 3, 4, 6, 9, 14, 17, and 21 days after inoculation, processed, and tested for virus detection by RRT-PCR Cloacal swabs from TAstV-2- and TCV-infected poults were shown to have sensitivity for virus detection similar to that of intestinal samples when compared directly. ARV detection by RRT-PCR was compared with virus isolation and had similar sensitivity.

Complete sequences of 3' end coding region for structural protein genes of turkey coronavirus

Overlapping fragments of genomic RNA spanning 6963 nucleotides from 5′ end of spike (S) protein gene to 3′ end of nucleocapsid (N) protein gene of turkey coronavirus (TCoV) were amplified by reverse-transcription-polymerase chain reaction (RT-PCR). The primers were derived from the corresponding sequences of infectious bronchitis virus (IBV). The PCR products were cloned and sequenced and their nucleic acid structure and similarity to published sequences of other coronaviruses were analyzed. Sequencing and subsequent analysis revealed 9 open reading frames (ORFs) representing the entire S protein gene, tricistronic gene 3, membrane (M) protein gene, bicistronic gene 5, and N protein gene in the order of 5′–3′. The overall nucleic acid structures of these encoding regions of TCoV were very similar to the homologous regions of IBV. The consensus transcription-regulating sequence (TRS) of IBV, CT(T/G)AACAA, was highly conserved in TCoV genome at the levels of nucleotide sequence and location in regarding to the initiation codon of individual genes. Pair-wise comparison of gene 3, M gene, gene 5, or N gene sequences with their counterparts of IBV revealed high levels (82.1–92.0%) of similarity. Phylogenetic analysis based on the deduced amino acid sequences of S, M, or N protein demonstrated that TCoV was clustered within the same genomic lineage as the IBV strains while all the other mammalian coronaviruses were grouped into separate clusters corresponding to antigenic groups I or II. There were substantial differences of S protein sequence between TCoV and IBV with only 33.8–33.9% of similarity.

Development of a Multiplex Reverse Transcription–Polymerase Chain Reaction Diagnostic Test Specific for Turkey Astrovirus and Coronavirus

A multiplex reverse transcription-polymerase chain reaction (RT-PCR) assay was developed for the simultaneous detection of two enteric viruses of poultry: turkey enteric coronavirus (TCV) and turkey astrovirus (TAstV). PCR primers were designed to conserved regions within the nucleocapsid gene of TCV and to the polymerase gene of TAstV-2. The primer pairs were successfully used in a multiplex RT-PCR to detect nucleic acid of TAstV-2 and TCV. The test was optimized for use with intestines/feces from naturally infected turkeys. The primers were specific and did not amplify other common RNA or DNA avian viruses. The detection limit was determined to be 10 ng of RNA used as starting template. The use of this specific test allows the rapid and early diagnosis of two financially costly viruses affecting the commercial turkey industry.

A reverse transcriptase-polymerase chain reaction assay for the diagnosis of turkey coronavirus infection

This study reports on the development of a reverse transcriptase-polymerase chain reaction (RT-PCR) for the specific detection of turkey coronavirus (TCoV). Of the several sets of primers tested, 1 set of primers derived from the P gene and 2 sets derived from the N gene of TCoV could amplify the TCoV genome in the infected samples. The RT-PCR was sensitive and specific for TCoV and did not amplify other avian RNA and DNA viruses tested except the infectious bronchitis virus (IBV). To overcome the problem of IBV amplification, a set of separate primers was designed from the spike protein gene of IBV. The RT-PCR under the same conditions as above could effectively differentiate between TCoV and IBV. The closely related bovine coronavirus and transmissible gastroenteritis virus of pigs were differentiated from TCoV using the same RT-PCR with slight modifications. The results of RT-PCR correlated well with the results of the immunofluorescent test for the same samples tested at the Purdue University Animal Disease Laboratory, West Lafayette, Indiana. The nucleotide sequence and projected amino acid sequence comparison of the P gene of different isolates of TCoV from 5 different states in the United States revealed a close association among the different isolates of TCoV.

Existence of gene 5 indicates close genomic relationship of Turkey coronavirus to infectious bronchitis virus

A segment of genomic RNA extending from the 3'-end of the membrane (M) protein gene to the 5'-end of the nucleocapsid (N) protein gene of Turkey coronavirus (TCV) was amplified by reverse transcription-polymerase chain reaction (RT-PCR). The primers were derived from the corresponding sequences of Infectious bronchitis virus (IBV). The PCR products were cloned and sequenced and their nucleic acid structure and similarity to the published sequences of IBV were analyzed. Gene 5 containing two overlapping open reading frames (ORFs), 5a and 5b, was localized between M and N genes of TCV. The overall nucleotide sequences of the amplified regions from TCV isolates shared 88.4% to 91.8% similarity to the corresponding region of IBV strains. The consensus transcription-associated sequence of IBV, CTTAACAA, was highly conserved in the TCV genome with regard to nucleotide sequence and location in terms of the initiation codons of the genes 5 and N. The similarities between the predicted amino acid sequences of ORFs 5a and 5b of TCV isolates and the homologous genes of IBV strains were 85.4% to 94.0%. The results indicate the existence of gene 5 in the genome of TCV and a close relatedness of the TCV gene 5 to the IBV gene 5 in location and nucleotide sequence.

Antigenic relationship of turkey coronavirus isolates from different geographic locations in the United States

The purpose of the present study was to examine the antigenicity of turkey coronavirus (TCV) isolates from various geographic areas with antibodies to different viruses. Seventeen isolates of TCV were recovered from intestinal samples submitted to Animal Disease Diagnostic Laboratory, Purdue University, from turkey farms located in different geographic areas. The prototype TCV Minnesota isolate (TCV-ATCC) was obtained from the American Type Culture Collection. Intestinal sections were prepared from turkey embryos infected with different TCV isolates and reacted with polyclonal or monoclonal antibodies to TCV, infectious bronchitis virus (IBV), bovine coronavirus (BCV), transmissible gastroenteritis virus (TGEV), reovirus, rotavirus, adenovirus, or enterovirus in immunofluorescent antibody staining. All 18 TCV isolates have the same antigenic reactivity pattern with the same panel of antibodies. Positive reactivity was seen with polyclonal antibodies to the TCV Indiana isolate, the TCV Virginia isolate, TCV-ATCC, and the IBV Massachusetts strain as well as monoclonal antibodies to the TCV North Carolina isolate or the membrane protein of IBV. Antibodies to BCV or TGEV were not reactive with any of the TCV isolates. Reactivity of antibodies to unrelated virus, rotavirus, reovirus, adenovirus, or enterovirus with different TCV isolates was all negative, except positive response was seen between enterovirus antibody and a TCV western North Carolina isolate, suggesting coinfection of turkeys with TCV and enterovirus in that particular case. The results indicated that the TCV isolates from these geographic locations in the U.S. shared close antigenicity and were antigenically related to IBV.

Characterization of turkey coronavirus from turkey poults with acute enteritis

The present study was to characterize turkey coronavirus associated with turkey poult enteritis and mortality. Intestinal contents or intestines from affected turkey poults and inoculated turkey embryos contained coronaviruses as revealed by electron microscopy or were positive for turkey coronavirus by immunofluorescent antibody assay. Sucrose density gradient ultracentrifugation of the virus-containing intestinal homogenate yielded two opalescent bands corresponding to the buoyant densities of 1.14-1.15 and 1.18-1.20 g/ml, respectively. Coronaviral particles from intestinal contents or the sucrose density gradient preparation were mainly spherical in shape and had envelope and central depression. They were surrounded by a fringe of regularly spaced petal-shaped projections attached to the particles by a short stalk. Purified viruses hemagglutinated rabbit erythrocytes with a titer of 16. Major protein bands of purified viruses analyzed by SDS-PAGE were located at 200, 100-110, 50-60, and 30-35 kDa. The patterns of protein bands were consistent with those of Minnesota or Quebec turkey coronavirus isolates. A 568 bp nucleotide fragment of turkey coronavirus spike protein gene was amplified from RNA of inoculated turkey embryo intestine or purified virus. Sequence analysis of the 568 bp PCR product revealed high degree of identity with the corresponding spike protein gene sequence of human and bovine coronaviruses. The results indicated that turkey coronavirus was associated with turkey poults with acute enteritis.

Antigenic and genomic relatedness of turkey-origin coronaviruses, bovine coronaviruses, and infectious bronchitis virus of chickens

In earlier studies in our laboratory, we found that bovine coronavirus (BCV) was pathogenic for 1-day-old turkey poults. This finding prompted us to study the antigenic and genomic relatedness of turkey origin coronaviruses (TOCVs) to BCV. A one-step reverse transcription (RT)-polymerase chain reaction (PCR) targeting a 730-base pair fragment of the nucleocapsid (N) gene of BCV and a nested PCR targeting a 407-base pair fragment of the N gene were used in an attempt to detect TOCV from North Carolina, Indiana, and a prototype turkey coronavirus (TCV) obtained from the American Type Culture Collection. Both the one-step RT-PCR and the nested PCR amplified cell culture-passaged isolates of calf diarrhea strains of BCV but none of the 15 tested TOCVs or transmissible gastroenteritis coronavirus of swine. TOCVs also did not cross-react in a BCV antigen-capture (AC) enzyme-linked immunosorbent assay (ELISA) system with monoclonal antibodies (MAbs) against N, spike glycoprotein, and hemagglutinin esterase glycoprotein proteins of BCV as coating antibodies. The same TOCVs could be detected with primers designed from the genome of infectious bronchitis virus (IBV) of chickens. These primers amplified a 1082-base pair region spanning portions of the membrane glycoprotein (M) and N protein genes of IBV and TCV. The TOCVs also cross-reacted in an AC-ELISA with MAbs against the M and subunit 2 of spike glycoprotein of IBV.

Nucleocapsid protein gene sequence analysis reveals close genomic relationship between turkey coronavirus and avian infectious bronchitis virus

Antibodies to infectious bronchitis virus (IBV) cross-react with turkey coronavirus (TCV) in immunofluorescence assay (IFA) indicating that IBV and TCV may share an amino acid sequence similarity. To determine its extent, the gene encoding the nucleocapsid (N) protein of TCV was amplified by reverse transcription-PCR (RT-PCR) from RNA purified from intestines of embryos of turkeys infected with various TCV isolates and from allantoic fluid of chicken embryos infected with IBV M41 strain, the obtained N genes were cloned, sequenced and compared with known sequences of N genes of five IBV strains. The primers for amplification were designed from the genome of IBV PCR products were obtained only from two of eight TCV isolates tested. It was found that the two TCV isolates were identical with five IBV strains by 90.1-94.1% at the N gene level. It was also observed that the N gene of eight TCV isolates originating from various regions of the USA could not be amplified by the primers designed from the N gene of bovine coronavirus (BCV).

Sequence analysis of the turkey coronavirus nucleocapsid protein gene and 3' untranslated region identifies the virus as a close relative of infectious bronchitis virus

The 3' end of the turkey coronavirus (TCV) genome (1740 bases) including the nucleocapsid (N) gene and 3' untranslated region (UTR) were sequenced and compared with published sequences of other avian and mammalian coronaviruses. The deduced sequence of the TCV N protein was determined to be 409 amino acids with a molecular mass of approximately 45 kDa. The TCV N protein was identical in size and had greater than 90% amino acid identity with published N protein sequences of infectious bronchitis virus (IBV); less than 21% identity was observed with N proteins of bovine coronavirus and transmissible gastroenteritis virus. The 3' UTR showed some variation among the three TCV strains examined, with two TCV strains, Minnesota and Indiana, containing 153 base segments which are not present in the NC95 strain. Nucleotide sequence identity between the 3' UTRs of TCV and IBV was greater than 78%. Similarities in both size and sequence of TCV and IBV N proteins and 3' UTRs provide additional evidence that these avian coronaviruses are closely related.

PCR for specific detection of haemorrhagic enteritis virus of turkeys, an avian adenovirus

A hexon gene based PCR was developed for specific amplification of DNA sequences from the haemorrhagic enteritis virus (HEV) of turkeys. The hexon genes of different avian adenoviruses were compared for primer construction. Two regions with low sequence homology between HEV and fowl adenovirus (FAV) hexon genes were selected for primer localisation. In correlation with the known sequence data a fragment of 1647 bp was amplified from a live vaccine and spleens of turkeys suffering from haemorrhagic enteritis (HE). All other avian adenoviruses which are able to infect turkeys, i.e. FAV and turkey adenoviruses (TAV), were negative. This is the first PCR for specific detection of HEV DNA which should be useful for rapid diagnosis and epidemiological investigations of HEV infections in turkeys.

Sequence analysis of the matrix/nucleocapsid gene region of turkey coronavirus

A reverse transcriptase, polymerase chain reaction (RT-PCR) procedure was used to amplify a segment of the genome of turkey coronavirus (TCV) spanning portions of the matrix and nucleocapsid (MN) protein genes (approximately 1.1 kb). The MN gene region of three epidemiologically distinct TCV strains (Minnesota, NC95, Indiana) was amplified, cloned into pUC19, and sequenced. TCV MN gene sequences were compared with published sequences of other avian and mammalian coronaviruses. A high degree of similarity (>90%) was observed between the nucleotide, matrix protein, and nucleocapsid protein sequences of TCV strains and published sequences of infectious bronchitis virus (IBV). The matrix and nucleocapsid protein sequences of TCV had limited homology (<30%) with MN sequences of mammalian coronaviruses. These results demonstrate a close genetic relationship between the avian coronaviruses, IBV and TCV.

Transmissible enteritis of turkeys: experimental inoculation studies with tissue-culture-adapted turkey and bovine coronaviruses

Four Quebec isolates of turkey enteric coronaviruses (TCVs) and three isolates of bovine enteric coronaviruses (BCVs) were serially propagated in HRT-18 and compared for their pathogenicity in turkey embryos and turkey poults. By immunoelectron microscopy, hemagglutination-inhibition, and Western immunoblotting assays, tissue-culture-adapted Quebec TCV isolates were found to be closely related to the reference Minnesota strain of TCV and the Mebus strain of BCV. Genomic relationships between TCV isolates and the reference BCV strain were confirmed by hybridization assays with BCV-specific radiolabeled recombinant plasmids containing sequences of the N and M genes. Only TCV isolates could be propagated by inoculation in the amniotic cavity of chicken and turkey embryonating eggs, and induced clinical disease in turkey poults. Nevertheless, coronavirus particles or antigens were detected by electron microscopy or indirect enzyme-linked immunosorbent assay in the clarified intestinal contents of BCV-infected poults up to day 14 PI, and genomic viral RNA was detected by slot-blot hybridization using BCV cDNA probes.

Genomic relationship between turkey and bovine enteric coronaviruses identified by hybridization with BCV or TCV specific cDNA probes

Genomic relationships between turkey and bovine coronavirus (TCV and BCV), which are currently placed in distinct antigenic groups, were demonstrated by hybridization using specific cDNA probes. BCV-specific recombinant plasmid probes p 52, p 27, and p 247, holding inserts derived from (probably nonstructural) genes, and plasmids pN 17 and pN 9 holding the N and M gene, respectively, permitted the detection of isolates of both BCV and TCV with similar sensitivities. Similarly, probing supernatants of cell cultures infected with several isolates of TCV, using probes pN 17 and pM 78, respectively holding the N gene of BCV and TCV, resulted in equally intense detection signals. Only a slight detection of MHV-3, which is antigenically related to BCV, was observed, whereas the probes did not allow the detection of IBV, TGEV, and HCV-229E, which are placed in antigenic groups separate from those of BCV and TCV. Detection of TCV was improved by hybridization with BCV-specific single-stranded (ss) probes holding sequences of the N and M genes and synthesized by the polymerase chain reaction. Diagnosis of TCV in 134 clinical samples by hybridization was better with PCR-produced ss BCV-specific probes than with ds PCR-produced probes or a combination of six recombinant plasmid probes holding non-overlapping BCV-specific cDNA sequences. Detection signals were absent when probing clinical samples with 32P-labelled pUC-DNA.

Antigenic and genomic relationships among turkey and bovine enteric coronaviruses

Antigenic and genomic relationships among tissue culture-adapted turkey enteric coronavirus (TCV) isolates, three strains of avian infectious bronchitis virus (IBV), and mammalian coronaviruses were investigated. Immunoblotting and immunoprecipitation experiments using polyclonal antisera showed that the four major structural proteins of TCV cross-reacted with the four homologous proteins of bovine enteric coronavirus (BCV), the N and M proteins of mouse hepatitis virus serotype 3, and the N protein of IBV. Close antigenic relationships between TCV and BCV were also established by seroneutralization and hemagglutination-inhibition. Of 49 monoclonal antibodies produced against either TCV or BCV, 11 differentiated the two viruses. Five of these monoclonal antibodies had neutralizing activities and were directed to either the peplomeric S (gp200-gp100) or hemagglutinin HE (gp140-gp65) glycoproteins. BCV cDNA probes tested on purified viral preparations and coronavirus-positive (by electron microscopy) fecal samples from diarrheic turkey poults confirmed the relatedness of TCV and BCV. The two viruses produced distinct cytopathic changes in HRT-18 cells in the presence of trypsin, whereas only TCV isolates were able to reproduce the clinical symptoms in turkey poults. Their matrix (M) proteins undergo different glycosylation processes.