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Kariithi HM, Volkening JD, Chiwanga GH, Goraichuk IV, Msoffe PLM, Suarez DL. Molecular Characterization of Complete Genome Sequence of an Avian Coronavirus Identified in a Backyard Chicken from Tanzania. Genes (Basel) 2023; 14:1852. [PMID: 37895200 PMCID: PMC10606662 DOI: 10.3390/genes14101852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/16/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
A complete genome sequence of an avian coronavirus (AvCoV; 27,663 bp excluding 3' poly(A) tail) was determined using nontargeted next-generation sequencing (NGS) of an oropharyngeal swab from a backyard chicken in a live bird market in Arusha, Tanzania. The open reading frames (ORFs) of the Tanzanian strain TZ/CA127/19 are organized as typical of gammaCoVs (Coronaviridae family): 5'UTR-[ORFs 1a/1b encoding replicase complex (Rep1ab) non-structural peptides nsp2-16]-[spike (S) protein]-[ORFs 3a/3b]-[small envelop (E) protein]-[membrane (M) protein]-[ORFs 4a/4c]-[ORFs 5a/5b]-[nucleocapsid (N) protein]-[ORF6b]-3'UTR. The structural (S, E, M and N) and Rep1ab proteins of TZ/CA127/19 contain features typically conserved in AvCoVs, including the cleavage sites and functional motifs in Rep1ab and S. Its genome backbone (non-spike region) is closest to Asian GI-7 and GI-19 infectious bronchitis viruses (IBVs) with 87.2-89.7% nucleotide (nt) identities, but it has a S gene closest (98.9% nt identity) to the recombinant strain ck/CN/ahysx-1/16. Its 3a, 3b E and 4c sequences are closest to the duck CoV strain DK/GD/27/14 at 99.43%, 100%, 99.65% and 99.38% nt identities, respectively. Whereas its S gene phylogenetically cluster with North American TCoVs and French guineafowl COVs, all other viral genes group monophyletically with Eurasian GI-7/GI-19 IBVs and Chinese recombinant AvCoVs. Detection of a 4445 nt-long recombinant fragment with breakpoints at positions 19,961 and 24,405 (C- and N-terminus of nsp16 and E, respectively) strongly suggested that TZ/CA127/19 acquired its genome backbone from an LX4-type (GI-19) field strain via recombination with an unknown AvCoV. This is the first report of AvCoV in Tanzania and leaves unanswered the questions of its emergence and the biological significance.
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Affiliation(s)
- Henry M. Kariithi
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, USDA, Athens, GA 30605, USA
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, P.O. Box 57811, Nairobi 00200, Kenya
| | | | - Gaspar H. Chiwanga
- Tanzania Veterinary Laboratory Agency, South Zone, Mtwara P.O. Box 186, Tanzania
| | - Iryna V. Goraichuk
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, USDA, Athens, GA 30605, USA
- National Scientific Center Institute of Experimental and Clinical Veterinary Medicine, 61023 Kharkiv, Ukraine
| | - Peter L. M. Msoffe
- Department of Veterinary Medicine and Public Health, Sokoine University of Agriculture, Chuo Kikuu, Morogoro P.O. Box 3021, Tanzania
- National Ranching Company Ltd., Dodoma P.O. Box 1819, Tanzania
| | - David L. Suarez
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, USDA, Athens, GA 30605, USA
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Kariithi HM, Volkening JD, Goraichuk IV, Ateya LO, Williams-Coplin D, Olivier TL, Binepal YS, Afonso CL, Suarez DL. Unique Variants of Avian Coronaviruses from Indigenous Chickens in Kenya. Viruses 2023; 15:264. [PMID: 36851482 PMCID: PMC9961390 DOI: 10.3390/v15020264] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 01/19/2023] Open
Abstract
The avian gamma-coronavirus infectious bronchitis virus (AvCoV, IBV; Coronaviridae family) causes upper respiratory disease associated with severe economic losses in the poultry industry worldwide. Here, we report for the first time in Kenya and the Eastern African region two novel AvCoVs, designated IBV/ck/KE/1920/A374/2017 (A374/17) and AvCoV/ck/KE/1922/A376/2017 (A376/17), inadvertently discovered using random nontargeted next-generation sequencing (NGS) of cloacal swabs collected from indigenous chickens. Despite having genome organization (5'UTR-[Rep1a/1ab-S-3a-3b-E-M-4b-4c-5a-5b-N-6b]-3'UTR), canonical conservation of essential genes and size (~27.6 kb) typical of IBVs, the Kenyan isolates do not phylogenetically cluster with any genotypes of the 37 IBV lineages and 26 unique variants (UVs). Excluding the spike gene, genome sequences of A374/17 and A376/17 are only 93.1% similar to each other and 86.7-91.4% identical to genomes of other AvCoVs. All five non-spike genes of the two isolates phylogenetically cluster together and distinctly from other IBVs and turkey coronaviruses (TCoVs), including the indigenous African GI-26 viruses, suggesting a common origin of the genome backbone of the Kenyan isolates. However, isolate A376/17 contains a TCoV-like spike (S) protein coding sequence and is most similar to Asian TCoVs (84.5-85.1%) compared to other TCoVs (75.6-78.5%), whereas isolate A374/17 contains an S1 gene sequence most similar to the globally distributed lineage GI-16 (78.4-79.5%) and the Middle Eastern lineage GI-23 (79.8-80.2%) viruses. Unanswered questions include the actual origin of the Kenyan AvCoVs, the potential pathobiological significance of their genetic variations, whether they have indeed established themselves as independent variants and subsequently spread within Kenya and to the neighboring east/central African countries that have porous live poultry trade borders, and whether the live-attenuated Mass-type (lineage GI-1)-based vaccines currently used in Kenya and most of the African countries provide protection against these genetically divergent field variants.
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Affiliation(s)
- Henry M Kariithi
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, USDA-ARS, 934 College Station Rd, Athens, GA 30605, USA
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kaptagat Rd, Loresho, Nairobi P.O. Box 57811-00200, Kenya
| | | | - Iryna V Goraichuk
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, USDA-ARS, 934 College Station Rd, Athens, GA 30605, USA
- National Scientific Center Institute of Experimental and Clinical Veterinary Medicine, 83 Pushkinska St., 61023 Kharkiv, Ukraine
| | - Leonard O Ateya
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kaptagat Rd, Loresho, Nairobi P.O. Box 57811-00200, Kenya
| | - Dawn Williams-Coplin
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, USDA-ARS, 934 College Station Rd, Athens, GA 30605, USA
| | - Tim L Olivier
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, USDA-ARS, 934 College Station Rd, Athens, GA 30605, USA
| | - Yatinder S Binepal
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kaptagat Rd, Loresho, Nairobi P.O. Box 57811-00200, Kenya
| | | | - David L Suarez
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, USDA-ARS, 934 College Station Rd, Athens, GA 30605, USA
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Abdel-Sabour MA, Rohaim MA, Salman OJA, Abodalal SE, Mohammad FF, Madkour MS, Abdel-Wanis NA, Munir M. Immunogenicity and efficacy of a bivalent vaccine against infectious bronchitis virus. Comp Immunol Microbiol Infect Dis 2021; 77:101670. [PMID: 33992864 DOI: 10.1016/j.cimid.2021.101670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 05/02/2021] [Accepted: 05/06/2021] [Indexed: 11/19/2022]
Abstract
Infectious bronchitis (IB) is a highly contagious viral disease and is responsible for considerable economic losses in the poultry industry, worldwide. To mitigate the IB-associated losses, multiple vaccines are being applied in the sector with variable successes and thus necessitating the development of a potent vaccine to protect against the IB in the poultry. In the present study, we investigated a bivalent live attenuated vaccine consisting of IB virus (IBV) strain H120 (GI-1 lineage) and D274 (GI-12 lineage) to evaluate its protection against heterologous variant of IBV (GI-23 lineage) in chicken. Protection efficacy was evaluated based on the serology, clinical signs, survival rates, tracheal and kidney histopathology and the viral shedding. Results demonstrated that administering live H120 and D274 (named here Classivar®) vaccine in one day-old and 14 days-old provided 100 % protection. We observed a significant increase in the mean antibody titers, reduced virus shedding, and ameliorated histopathology lesions compared to routinely used vaccination regimes. These results revealed that usage of different IBV vaccines combination can successfully ameliorate the clinical outcome and pathology in vaccinated chicks especially after booster vaccination regime using Classivar®. In conclusions, our data indicate that Classivar® vaccine is safe in chicks and may serve as an effective vaccine against the threat posed by commonly circulating IBV strains in the poultry industry.
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Affiliation(s)
- Mohammad A Abdel-Sabour
- Department of Poultry Viral Vaccines, Veterinary Serum and Vaccine Research Institute (VSVRI), Agriculture Research Centre (ARC), Cairo, 11381, Egypt
| | - Mohammed A Rohaim
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Owais J A Salman
- Department of Poultry Viral Vaccines, Veterinary Serum and Vaccine Research Institute (VSVRI), Agriculture Research Centre (ARC), Cairo, 11381, Egypt
| | - Samah E Abodalal
- Department of Poultry Viral Vaccines, Veterinary Serum and Vaccine Research Institute (VSVRI), Agriculture Research Centre (ARC), Cairo, 11381, Egypt
| | - Faten F Mohammad
- Department of Pathology, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Mohammad S Madkour
- Department of Poultry Viral Vaccines, Veterinary Serum and Vaccine Research Institute (VSVRI), Agriculture Research Centre (ARC), Cairo, 11381, Egypt
| | - Nabil A Abdel-Wanis
- Department of Poultry Viral Vaccines, Veterinary Serum and Vaccine Research Institute (VSVRI), Agriculture Research Centre (ARC), Cairo, 11381, Egypt
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK.
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Sultan HA, Ali A, El Feil WK, Bazid AHI, Zain El-Abideen MA, Kilany WH. Protective Efficacy of Different Live Attenuated Infectious Bronchitis Virus Vaccination Regimes Against Challenge With IBV Variant-2 Circulating in the Middle East. Front Vet Sci 2019; 6:341. [PMID: 31649942 PMCID: PMC6794438 DOI: 10.3389/fvets.2019.00341] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/20/2019] [Indexed: 01/16/2023] Open
Abstract
Six vaccination regimes using classical (Mass-type) and variant (IB-VAR2 and IB-793B) live vaccines were evaluated against Middle Eastern variant-2 infectious bronchitis virus challenge. Six groups of SPF chicks (30 birds/group) were vaccinated using prime-boost regimes at day-1 and day-14 using; IB-M41:IB-VAR2, IB-VAR2:IB-VAR2, IB-VAR2:IB-M41, IB-Ma5:IB-793B, IB-793B:IB-793B, and IB-793B:IB-Ma5, respectively. Ciliostasis and lesion scores were evaluated at day-5 after each vaccination. Birds were challenged intranasally at 14-day post 2nd vaccination using 105EID50/0.1 ml/bird of wild-type IBV (Eg/1212B/2012). At 3, 5, and 7-day post challenge (DPC) virus shedding was monitored by real-time RT-PCR. Five chicks/group were euthanized at 7DPC for ciliostasis and lesion scoring and histopathology was conducted on 3 chicks/group. Seroconversion was evaluated at 14 DPC. All groups primed with the 793B vaccine showed relatively higher ciliostasis scores compared to other groups. The IB-VAR2 vaccinated groups showed the highest protection rates (80–100%) and high protection score (67.6–73.2%) compared to the 793B vaccine groups (50–60%). The virus shedding was significantly reduced at 3 and 5DPC in groups received the IBV-VAR2 (prime or booster) compared to those received the 793B vaccine. In conclusion, the homologous IBV-VAR2 vaccine showed superior results compared to 793B or Mass-type vaccines confirming the importance of IBV vaccine seed homology to the circulating IBV strains.
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Affiliation(s)
- Hesham A Sultan
- Birds and Rabbit Diseases Department, Faculty of Veterinary Medicine, Sadat City University, Sadat City, Egypt
| | - Ahmed Ali
- Poultry Diseases Department, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef, Egypt
| | - Wael K El Feil
- Poultry Diseases Department, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Abdel Hamid I Bazid
- Virology Department, Faculty of Veterinary Medicine, Sadat City University, Sadat City, Egypt
| | - Mohamed A Zain El-Abideen
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Giza, Egypt
| | - Walid H Kilany
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Giza, Egypt
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Chen YN, Wu CC, Lin TL. Real-Time Reverse Transcription-Polymerase Chain Reaction for Detection and Quantitation of Turkey Coronavirus RNA in Feces and Intestine Tissues. SPRINGER PROTOCOLS HANDBOOKS 2016. [PMCID: PMC7120390 DOI: 10.1007/978-1-4939-3414-0_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Turkey coronavirus (TCoV) infection causes acute atrophic enteritis in turkey poults, leading to significant economic loss in the turkey industry. Rapid detection, differentiation, and quantitation of TCoV are critical to the diagnosis and control of the disease. A specific one-step real-time reverse transcription-polymerase chain reaction (RT-PCR) assay using TCoV-specific primers and dual-labeled fluorescent probe for detection and quantitation of TCoV in feces and intestine tissues is described in this chapter. The fluorogenic probe labeled with a reporter dye (FAM, 6-carboxytetramethylrhodamine) and a quencher dye (Absolute Quencher™) was designed to bind to a 186 base-pair fragment flanked by the two PCR primers targeting the 3′ end of spike gene (S2) of TCoV. The assay is highly specific and sensitive and can quantitate between 102 and 1010 copies/mL of viral genome. It is useful in monitoring the progression of TCoV-induced atrophic enteritis in the turkey flocks.
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Abstract
Turkey coronavirus (TCoV) infection induces the production of protective antibodies against the sequent exposure of TCoV. Serological tests to determine TCoV-specific antibodies are critical to evaluate previous exposure to TCoV in the turkey flocks and differentiate serotypes from different isolates or strains. A specific virus neutralization assay using embryonated turkey eggs and immunofluorescent antibody assay for determining TCoV-specific neutralizing antibodies is described in this chapter. Virus neutralization titer of turkey serum from turkeys infected with TCoV is the dilution of serum that can inhibit TCoV infection in 50 % of embryonated turkey eggs. Virus neutralization assay for TCoV is useful to monitor the immune status of turkey flocks infected with TCoV for the control of the disease.
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Affiliation(s)
- Leyi Wang
- Animal Disease Diagnostic Lab, Ohio Department of Agriculture, Reynoldsburg, Ohio USA
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Genotyping of turkey coronavirus field isolates from various geographic locations in the Unites States based on the spike gene. Arch Virol 2015; 160:2719-26. [PMID: 26254026 PMCID: PMC7086652 DOI: 10.1007/s00705-015-2556-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/27/2015] [Indexed: 11/22/2022]
Abstract
Turkey flocks have experienced turkey coronaviral enteritis sporadically in the United States since the 1990s. Twenty-four field isolates of turkey coronavirus (TCoV) from multiple states in the United States were recovered from 1994 to 2010 to determine the genetic relationships among them. The entire spike (S) gene of each TCoV isolate was amplified and sequenced. Pairwise comparisons were performed using the Clustal W program, revealing 90.0 % to 98.4 % sequence identity in the full-length S protein, 77.6 % to 96.6 % in the amino terminus of the S1 subunit (containing one hypervariable region in S1a), and 92.1 % to 99.3 % in the S2 subunit at the deduced amino acid sequence level. The conserved motifs, including two cleavage recognition sequences of the S protein, two heptad repeats, the transmembrane domain, and the Golgi retention signal were identified in all TCoV isolates. Phylogenetic analysis based on the full-length S gene was used to distinguish North American TCoV isolates from French TCoV isolates. Among the North American TCoV isolates, three distinct genetic groups with 100 % bootstrap support were observed. North Carolina isolates formed group I, Texas isolates formed group II, and Minnesota isolates formed Group III. The S genes of 24 TCoV isolates from the United States remained conserved because they contained predominantly synonymous substitutions. The findings of the present study suggest endemic circulation of distinct TCoV genotypes in different geographic locations.
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Day JM, Gonder E, Jennings S, Rives D, Robbins K, Tilley B, Wooming B. Investigating turkey enteric coronavirus circulating in the Southeastern United States and Arkansas during 2012 and 2013. Avian Dis 2014; 58:313-7. [PMID: 25055640 DOI: 10.1637/10674-092313-resnote.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Periodic monitoring of poultry flocks in the United States via molecular diagnostic methods has revealed a number of potential enteric viral pathogens in continuous circulation in turkeys and chickens. Recently turkey integrators in the Southeastern United States and Arkansas experienced an outbreak of moderate to severe enteritis associated with turkey enteric coronavirus (TCoV), and numerous enteric samples collected from turkey flocks in these areas tested positive for TCoV via real-time reverse-transcriptase PCR (RRT-PCR). This report details the subsequent sequence and phylogenetic analysis of the TCoV spike glycoprotein and the comparison of outbreak-associated isolates to sequences in the public database. TCoVs investigated during the present outbreak grouped geographically based upon state of origin, and the RRT-PCR assay was a good indicator of subsequent seroconversion by TCoV-positive turkey flocks.
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Chen YN, Wu CC, Yeo Y, Xu P, Lin TL. A DNA prime-protein boost vaccination strategy targeting turkey coronavirus spike protein fragment containing neutralizing epitope against infectious challenge. Vet Immunol Immunopathol 2013; 152:359-69. [PMID: 23428360 PMCID: PMC7112546 DOI: 10.1016/j.vetimm.2013.01.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 01/10/2013] [Accepted: 01/12/2013] [Indexed: 11/15/2022]
Abstract
The present study was undertaken to determine immune response and protection efficacy of a spike (S) protein fragment containing neutralizing epitopes (4F/4R) of turkey coronavirus (TCoV) by priming with DNA vaccine and boosting with the recombinant protein from the corresponding DNA vaccine gene segment. Turkeys were vaccinated by priming with either one dose (G1-750DP) or two doses (G3-750DDP) of 750 μg DNA vaccine expressing 4F/4R S fragment and boosting with one dose of 200 μg 4F/4R S fragment. One dose of 100 μg DNA vaccine mixed with polyethyleneimine (PEI) and sodium hyaluronate (HA) followed by one dose of 750 μg DNA vaccine and one dose of 200 μg 4F/4R S fragment were given to the turkeys in group G2-100DPH. After infectious challenge by TCoV, clinical signs and TCoV detected by immunofluorescence antibody (IFA) assay were observed in less number of turkeys in vaccination groups than that in challenge control groups. TCoV viral RNA loads measured by quantitative real-time reverse transcription-PCR were lower in vaccinated turkeys than those in challenge control turkeys. The turkeys in G3-750DDP produced the highest level of TCoV S protein-specific antibody and virus neutralization (VN) titer. Comparing to the turkeys in G1-750DP, significantly less TCoV were detected by IFA in the turkeys in G2-100DPH receiving an extra dose of 100 μg DNA mixed with PEI and HA. The results indicated that DNA-prime protein-boost DNA vaccination regimen targeting TCoV S fragment encompassing neutralizing epitopes induced humoral immune response and partially protected turkeys against infectious challenge by TCoV.
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Affiliation(s)
- Yi-Ning Chen
- Department of Comparative Pathobiology, Purdue University 406 South University Street, West Lafayette, IN 47907, USA
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