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Kamal MM, Sadekuzzaman M, Parvin K, Haque ME, Hayat S, Islam MA, Khatun MM, Siddique MP, Nahar SS, Khasruzzaman AKM, Hossain MT, Islam MA. Characterization of infectious laryngotracheitis virus isolated from commercial layer chickens in Bangladesh during the year 2021-2022. J Adv Vet Anim Res 2024; 11:398-407. [PMID: 39101088 PMCID: PMC11296171 DOI: 10.5455/javar.2024.k789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/01/2024] [Accepted: 05/08/2024] [Indexed: 08/06/2024] Open
Abstract
Objective Infectious laryngotracheitis virus (ILTV) is responsible for causing infectious laryngotracheitis (ILT), which is a rapidly spreading and extremely transmissible disease in chickens. The current research aims to isolate and characterize ILTV from layer chickens in Bangladesh. Materials and Methods A total of 345 samples (trachea, larynx, and lungs) were collected from ILT-suspected dead and sick layer chickens of 32 ILT-suspected farms in three different outbreak districts (Gazipur, Tangail, and Mymensingh) of Bangladesh during the outbreak year 2021-2022. Rapid detection kits examined the samples for avian influenza virus (AIV) and Newcastle disease virus (NDV). ILTV-specific primers were used to screen 72 NDV- and AIV-negative samples by polymerase chain reaction (PCR). Using chorioallantoic membrane (CAM), the study isolated the ILT virus from 9 to 10-day-old seronegative embryonated chicken eggs (ECEs) using selected PCR-positive samples. The virus was confirmed using nucleotide sequencing, agar gel immunodiffusion test (AGIDT), viral neutralization test (VNT), and pathogenicity evaluations using mortality index for chicken embryos (MICEs) and intra-tracheal pathogenicity index (ITPI). Results The results indicated that among the PCR-positive 10 samples, only two (Alim_ILT_1001 and Alim_ILT_1,000) were found positive using ECEs. There were two field isolates of ILTVs, as shown by the amplicon size of the ICP4 gene-based PCR. A phylogenetic study of the ICP4 gene revealed that the recent isolates have a close similarity with the ILTV isolates of Turkey, Bangladesh, and Australia. AGIDT revealed strong precipitation lines due to ILTV-specific antibodies reacting with field viruses, while VNT neutralized both isolates with conventional ILTV antibodies. The pathogenicity testing indicated that Alim_ILT_1001 had MICE and ITPI values of 0.77 and 0.63, whereas Alim_ILT_1,000 had 0.71 and 0.57. Conclusion Both the ILTV isolates have similarities with the isolates of Turkey, Bangladesh, and Australia, and they are highly virulent for chickens.
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Affiliation(s)
- Md Mostofa Kamal
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Mohammad Sadekuzzaman
- Central Disease Investigation Laboratory, Department of Livestock Services, Dhaka, Bangladesh
| | - Kohinoor Parvin
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md Enamul Haque
- Department of Microbiology, Sheikh Hasina University of Science and Technology, Bhairab, Bangladesh
| | - Sajedul Hayat
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md Ariful Islam
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Mst Minara Khatun
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Mahbubul Pratik Siddique
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | | | - A K M Khasruzzaman
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | | | - Md Alimul Islam
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
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Li J, Gao Z, Chen J, Cheng R, Niu J, Zhang J, Yang Y, Yuan X, Xia J, Mao G, Liu H, Dong Y, Wu C. Development of a panel of three multiplex allele-specific qRT-PCR assays for quick differentiation of recombinant variants and Omicron subvariants of SARS-CoV-2. Front Cell Infect Microbiol 2022; 12:953027. [PMID: 36061868 PMCID: PMC9433905 DOI: 10.3389/fcimb.2022.953027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Quick differentiation of the circulating variants and the emerging recombinant variants of SARS-CoV-2 is essential to monitor their transmission. However, the widely used gene sequencing method is time-consuming and costly when facing the viral recombinant variants, because partial or whole genome sequencing is required. Allele-specific real time RT-PCR (qRT-PCR) represents a quick and cost-effective method in SNP genotyping and has been successfully applied for SARS-CoV-2 variant screening. In the present study, we developed a panel of 3 multiplex allele-specific qRT-PCR assays targeting 12 key differential mutations for quick differentiation of SARS-CoV-2 recombinant variants (XD and XE) and Omicron subvariants (BA.1 and BA.2). Two parallel multiplex qRT-PCR reactions were designed to separately target the protype allele and the mutated allele of the four mutations in each allele-specific qRT-PCR assay. The variation of Cp values (ΔCp) between the two multiplex qRT-PCR reactions was applied for mutation determination. The developed multiplex allele-specific qRT-PCR assays exhibited outstanding analytical sensitivities (with limits of detection [LoDs] of 2.97-27.43 copies per reaction), wide linear detection ranges (107-100 copies per reaction), good amplification efficiencies (82% to 95%), good reproducibility (Coefficient of Variations (CVs) < 5% in both intra-assay and inter-assay tests) and clinical performances (99.5%-100% consistency with Sanger sequencing). The developed multiplex allele-specific qRT-PCR assays in this study provide an alternative tool for quick differentiation of SARS-CoV-2 recombinant variants (XD and XE) and Omicron subvariants (BA.1 and BA.2).
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Affiliation(s)
- Jianguo Li
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
- *Correspondence: Jianguo Li, ; Changxin Wu,
| | - Zefeng Gao
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Jing Chen
- Shanxi Provincial Key Laboratory for Major Infectious Disease Response, Shanxi Provincial Center for Disease Control and Prevention, Taiyuan, China
| | - Ruiling Cheng
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Jiahui Niu
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Jialei Zhang
- College of Life Sciences, Shanxi University, Taiyuan, China
| | - You Yang
- College of Life Sciences, Shanxi University, Taiyuan, China
| | - Ximei Yuan
- College of Life Sciences, Shanxi University, Taiyuan, China
| | - Juan Xia
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Guoli Mao
- Laboratory, Shanxi Guoxin Caregeno Biotechnology Co., Ltd, Taiyuan, China
| | - Hulong Liu
- Laboratory, Shanxi Guoxin Caregeno Biotechnology Co., Ltd, Taiyuan, China
| | - Yongkang Dong
- Administrative Office, the Fourth People's Hospital of Taiyuan, Taiyuan, China
| | - Changxin Wu
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
- *Correspondence: Jianguo Li, ; Changxin Wu,
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Gowthaman V, Kumar S, Koul M, Dave U, Murthy TRGK, Munuswamy P, Tiwari R, Karthik K, Dhama K, Michalak I, Joshi SK. Infectious laryngotracheitis: Etiology, epidemiology, pathobiology, and advances in diagnosis and control - a comprehensive review. Vet Q 2021; 40:140-161. [PMID: 32315579 PMCID: PMC7241549 DOI: 10.1080/01652176.2020.1759845] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Infectious laryngotracheitis (ILT) is a highly contagious upper respiratory tract disease of chicken caused by a Gallid herpesvirus 1 (GaHV-1) belonging to the genus Iltovirus, and subfamily Alphaherpesvirinae within Herpesviridae family. The disease is characterized by conjunctivitis, sinusitis, oculo-nasal discharge, respiratory distress, bloody mucus, swollen orbital sinuses, high morbidity, considerable mortality and decreased egg production. It is well established in highly dense poultry producing areas of the world due to characteristic latency and carrier status of the virus. Co-infections with other respiratory pathogens and environmental factors adversely affect the respiratory system and prolong the course of the disease. Latently infected chickens are the primary source of ILT virus (ILTV) outbreaks irrespective of vaccination. Apart from conventional diagnostic methods including isolation and identification of ILTV, serological detection, advanced biotechnological tools such as PCR, quantitative real-time PCR, next generation sequencing, and others are being used in accurate diagnosis and epidemiological studies of ILTV. Vaccination is followed with the use of conventional vaccines including modified live attenuated ILTV vaccines, and advanced recombinant vector vaccines expressing different ILTV glycoproteins, but still these candidates frequently fail to reduce challenge virus shedding. Some herbal components have proved to be beneficial in reducing the severity of the clinical disease. The present review discusses ILT with respect to its current status, virus characteristics, epidemiology, transmission, pathobiology, and advances in diagnosis, vaccination and control strategies to counter this important disease of poultry.
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Affiliation(s)
- Vasudevan Gowthaman
- Poultry Disease Diagnosis and Surveillance Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Namakkal, Tamil Nadu, India
| | - Sachin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Monika Koul
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Urmil Dave
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - T R Gopala Krishna Murthy
- Poultry Disease Diagnosis and Surveillance Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Namakkal, Tamil Nadu, India
| | - Palanivelu Munuswamy
- Division of Pathology, ICAR - Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, UP Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura, Uttar Pradesh, India
| | - Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, India
| | - Kuldeep Dhama
- Division of Pathology, ICAR - Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
| | - Izabela Michalak
- Faculty of Chemistry, Department of Advanced Material Technologies, Wrocław University of Science and Technology, Wrocław, Poland
| | - Sunil K Joshi
- Department of Microbiology & Immunology, Department of Pediatrics, Division of Hematology, Oncology and Bone Marrow Transplantation, University of Miami School of Medicine, Miami, Florida, USA
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Turner AJ, Aggarwal P, Boone EC, Haidar CE, Relling MV, Derezinski AD, Broeckel U, Gaedigk A. Identification of CYP2D6 Haplotypes that Interfere with Commonly Used Assays for Copy Number Variation Characterization. J Mol Diagn 2021; 23:577-588. [PMID: 33631352 DOI: 10.1016/j.jmoldx.2021.01.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/16/2020] [Accepted: 01/22/2021] [Indexed: 01/08/2023] Open
Abstract
Cytochrome P450 2D6 (CYP2D6) copy number (CN) variation affects the metabolism of numerous prescribed drugs. Sequence variation within primer or probe target regions of hydrolysis probe CN assays can generate false-positive calls for CN loss. Furthermore, CYP2D6-CYP2D7 hybrids and gene conversions can cause difficult to interpret discordant CN calls. The identification of haplotypes with CN variations and structural arrangements is important to predict phenotype accurately. During clinical testing with hydrolysis probe assays targeting three CYP2D6 regions (intron 2, intron 6, and exon 9), samples with haplotypes causing inconsistent CN calls were identified. To resolve these cases, next-generation sequencing and allele-specific Sanger sequencing was performed. Sequence analysis of 16 samples, all but one from subjects of African descent, identified six novel suballeles containing single-nucleotide polymorphisms, which cause false-positive calls for CN loss in introns 2 and 6. Five samples with an exon 9 CN loss contained CYP2D6/CYP2D7 hybrids (∗13 or ∗36) and one sample was found to have a novel haplotype, CYP2D6∗141. Interestingly, CYP2D6∗141 contains a CYP2D7-derived exon 9 conversion and core single-nucleotide polymorphisms that are otherwise found in CYP2D6∗17 and ∗27. Although these variants are rare, they can cause inconsistent CN calls that typically are reported as no calls or indeterminant, and thus may deprive patients, particularly those of African descent, from taking full benefit of pharmacogenetic testing.
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Affiliation(s)
- Amy J Turner
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin; Right Patient Right Drug Diagnostics, Wauwatosa, Wisconsin
| | - Praful Aggarwal
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin; Right Patient Right Drug Diagnostics, Wauwatosa, Wisconsin
| | - Erin C Boone
- Clinical Pharmacology, Toxicology, and Therapeutic Innovation, Children's Mercy Kansas City, University of Missouri-Kansas City, Kansas City, Missouri
| | - Cyrine-Eliana Haidar
- Pharmaceutical Science Department, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Mary V Relling
- Pharmaceutical Science Department, St. Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Ulrich Broeckel
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin; Right Patient Right Drug Diagnostics, Wauwatosa, Wisconsin
| | - Andrea Gaedigk
- Clinical Pharmacology, Toxicology, and Therapeutic Innovation, Children's Mercy Kansas City, University of Missouri-Kansas City, Kansas City, Missouri.
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Fakhri O, Devlin JM, Browning GF, Coppo MJC, Quinteros JA, Diaz-Méndez A, Lee SW, Hartley CA. Superinfection and recombination of infectious laryngotracheitis virus vaccines in the natural host. Vaccine 2020; 38:7508-7516. [PMID: 33012604 DOI: 10.1016/j.vaccine.2020.09.064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/17/2020] [Accepted: 09/22/2020] [Indexed: 10/23/2022]
Abstract
Infectious laryngotracheitis virus (ILTV, Gallid alphaherpesvirus 1) causes severe respiratory disease in chickens and has a major impact on the poultry industry worldwide. Live attenuated vaccines are widely available and are administered early in the life of commercial birds, often followed by one or more rounds of revaccination, generating conditions that can favour recombination between vaccines. Better understanding of the factors that contribute to the generation of recombinant ILTVs will inform the safer use of live attenuated herpesvirus vaccines. This study aimed to examine the parameters of infection that allow superinfection and may enable the generation of recombinant progeny in the natural host. In this study, 120 specific-pathogen free (SPF) chickens in 8 groups were inoculated with two genetically distinct live-attenuated ILTV vaccine strains with 1-4 days interval between the first and second vaccinations. After inoculation, viral genomes were detected in tracheal swabs in all groups, with lowest copies detected in swabs collected from the groups where the interval between inoculations was 4 days. Superinfection of the host was defined as the detection of the virus that was inoculated last, and this was detected in tracheal swabs from all groups. Virus could be isolated from swabs at a limited number of timepoints, and these further illustrated superinfection of the birds as recombinant viruses were detected among the progeny. This study has demonstrated superinfection at host level and shows recombination events occur under a very broad range of infection conditions. The occurrence of superinfection after unsynchronised infection with multiple viruses, and subsequent genomic recombination, highlight the importance of using only one type of vaccine per flock as the most effective way to limit recombination.
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Affiliation(s)
- Omid Fakhri
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Joanne M Devlin
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Glenn F Browning
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Mauricio J C Coppo
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - José A Quinteros
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Andrés Diaz-Méndez
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Sang-Won Lee
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia; College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea.
| | - Carol A Hartley
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Genomic recombination between infectious laryngotracheitis vaccine strains occurs under a broad range of infection conditions in vitro and in ovo. PLoS One 2020; 15:e0229082. [PMID: 32119681 PMCID: PMC7051062 DOI: 10.1371/journal.pone.0229082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 01/29/2020] [Indexed: 02/06/2023] Open
Abstract
Gallid alphaherpesvirus 1 causes infectious laryngotracheitis (ILT) in farmed poultry worldwide. Intertypic recombination between vaccine strains of this virus has generated novel and virulent isolates in field conditions. In this study, in vitro and in ovo systems were co-infected and superinfected under different conditions with two genomically distinct and commonly used ILTV vaccines. The progeny virus populations were examined for the frequency and pattern of recombination events using multi-locus high-resolution melting curve analysis of polymerase chain reaction products. A varied level of recombination (0 to 58.9%) was detected, depending on the infection system (in ovo or in vitro), viral load, the composition of the inoculum mixture, and the timing and order of infection. Full genome analysis of selected recombinants with different in vitro phenotypes identified alterations in coding and non-coding regions. The ability of ILTV vaccines to maintain their capacity to recombine under such varied conditions highlights the significance of recombination in the evolution of this virus and demonstrates the capacity of ILTV vaccines to play a role in the emergence of recombinant viruses.
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Thilakarathne DS, Hartley CA, Diaz-Méndez A, Coppo MJC, Devlin JM. Development and application of a combined molecular and tissue culture-based approach to detect latent infectious laryngotracheitis virus (ILTV) in chickens. J Virol Methods 2019; 277:113797. [PMID: 31821819 DOI: 10.1016/j.jviromet.2019.113797] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 12/03/2019] [Accepted: 12/07/2019] [Indexed: 01/09/2023]
Abstract
Infectious laryngotracheitis virus (ILTV) causes severe respiratory disease in chickens. ILTV can establish latency and reactivate later in life, but there have been few investigations of ILTV latency. This study aimed to contribute to the methodologies available to detect latent ILTV. A nested PCR was developed which was more sensitive than three other molecular methods investigated in this study. This nested PCR was then used in conjunction with in vitro reactivation culture methods that were optimized and applied to trigeminal ganglia (TG) and tracheal samples from ILTV-vaccinated commercial layer birds (n = 30). ILTV DNA was detected by nested PCR in the upper respiratory tract (URT) or eye of 22 birds. Of the remaining 8 birds, ILTV could be detected by co-culture in TG of 5 birds, with reactivated virus mostly detected 6 days post-explant (dpe). ILTV was also detected in tracheal cultures by 6 dpe. In the ILTV-positive URT samples, the virus could be characterised as vaccine strains SA2 (n = 9) or A20 (n = 5). This study provides evidence for reactivation and shedding of vaccine ILTV in commercial layer birds. Moreover, this study produced a molecular and in-vitro culture method to detect latent viral infection.
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Affiliation(s)
- Dulari S Thilakarathne
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia.
| | - Carol A Hartley
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia
| | - Andrés Diaz-Méndez
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia
| | - Mauricio J C Coppo
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia
| | - Joanne M Devlin
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia
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Spatz SJ, Garcia M, Riblet S, Ross TA, Volkening JD, Taylor TL, Kim T, Afonso CL. MinION sequencing to genotype US strains of infectious laryngotracheitis virus. Avian Pathol 2019; 48:255-269. [PMID: 30722676 DOI: 10.1080/03079457.2019.1579298] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Over the last decade the US broiler industry has fought long-lasting outbreaks of infectious laryngotracheitis (ILTV). Previously, nine genotypes (I-IX) of ILTVs have been recognized using the polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP) method with three viral alleles (gB, gM and UL47/gG). In this study, the genotyping system was simplified to six genotypes by amplicon sequencing and examining discriminating single nucleotide polymorphisms (SNPs) within these open reading frames. Using phylogenomic analysis of 27 full genomes of ILTV, a single allele (ORF A/ORF B) was identified containing SNPs that could differentiate ILTVs into genotypes congruent with the phylogenetic partitioning. The allelic variations allowed for the cataloging of the 27 strains into 5 genotypes: vaccinal TCO, vaccinal CEO, virulent CEO-like, virulent US and virulent US backyard flocks from 1980 to 1990, correlating with the PCR-RFLP genotypes I/ II/ III (TCO), IV (CEO), V (virulent CEO-like), VI (virulent US) and VII/VIII/IX (virulent US backyard flock isolates). With the unique capabilities of third generation sequencing, we investigated the application of Oxford Nanopore MinION technology for rapid sequencing of the amplicons generated in the single-allele assay. This technology was an improvement over Sanger-based sequencing of the single allele amplicons due to a booster amplification step in the MinION sequencing protocol. Overall, there was a 90% correlation between the genotyping results of the single-allele assay and the multi-allele assay. Surveillance of emerging ILTV strains could greatly benefit from real-time amplicon sequencing using the single-allele assay and MinION sequencing. RESEARCH HIGHLIGHTS A multi-allelic assay identified nine ILTV genotypes circulating in the US Single-allele genotyping is congruent with whole genome phylogenetic partitioning US ILTV strains can be grouped into five genotypes using the single-allele assay The single-allele assay can be done using MinION sequencing of barcoded amplicons.
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Affiliation(s)
- Stephen J Spatz
- a United States Department of Agriculture , Agricultural Research Service, US National Poultry Research Center , USDA ARS USNPRC, Athens , GA , USA
| | - Maricarmen Garcia
- b Department of Population Health , College of Veterinary Medicine, Poultry Diagnostic and Research Center, University of Georgia , Athens , GA , USA
| | - Sylva Riblet
- b Department of Population Health , College of Veterinary Medicine, Poultry Diagnostic and Research Center, University of Georgia , Athens , GA , USA
| | - Teresa A Ross
- a United States Department of Agriculture , Agricultural Research Service, US National Poultry Research Center , USDA ARS USNPRC, Athens , GA , USA
| | | | - Tonya L Taylor
- a United States Department of Agriculture , Agricultural Research Service, US National Poultry Research Center , USDA ARS USNPRC, Athens , GA , USA
| | - Taejoong Kim
- a United States Department of Agriculture , Agricultural Research Service, US National Poultry Research Center , USDA ARS USNPRC, Athens , GA , USA
| | - Claudio L Afonso
- a United States Department of Agriculture , Agricultural Research Service, US National Poultry Research Center , USDA ARS USNPRC, Athens , GA , USA
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Wang M, Xu F, Chen K, Li X, Li K, Zhou Y, Xiao J. A multiplex SNP genotyping by allele-specificspecific PCR based on stem-loop and universal fluorescent primers of Chr1 daxin mice. Electrophoresis 2019; 40:1600-1605. [PMID: 30801725 DOI: 10.1002/elps.201900052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 02/23/2019] [Accepted: 02/18/2019] [Indexed: 01/16/2023]
Abstract
Single nucleotide polymorphisms (SNPs) are one of the most common markers in mammals. Rapid, accurate, and multiplex typing of SNPs is critical for subsequent biological and genetic research. In this study, we have developed a novel method for multiplex genotyping SNPs in mice. The method involves allele-specific PCR amplification of genomic DNA with two stem-loop primers accompanied by two different universal fluorescent primers. Blue and green fluorescent signals were conveniently detected on a DNA sequencer. We verified four SNPs of 65 mice based on the novel method, and it is well suited for multiplex genotyping as it requires only one reaction per sample in a single tube with multiplex PCR. The use of universal fluorescent primers greatly reduces the cost of designing different fluorescent probes for each SNP. Therefore, this method can be applied to many biological and genetic studies, such as multiple candidate gene testing, genome-wide association study, pharmacogenetics, and medical diagnostics.
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Affiliation(s)
- Maochun Wang
- Institute of Biological Science and Biotechnology, Donghua University, Shanghai, P. R. China
| | - Fuyi Xu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, USA
| | - Ke Chen
- College of Environmental Science and Engineering, Donghua University, Shanghai, P. R. China
| | - Xiaoning Li
- Institute of Biological Science and Biotechnology, Donghua University, Shanghai, P. R. China
| | - Kai Li
- Institute of Biological Science and Biotechnology, Donghua University, Shanghai, P. R. China
| | - Yuxun Zhou
- Institute of Biological Science and Biotechnology, Donghua University, Shanghai, P. R. China
| | - Junhua Xiao
- Institute of Biological Science and Biotechnology, Donghua University, Shanghai, P. R. China
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Single Nucleotide Polymorphism Genotyping Analysis Shows That Vaccination Can Limit the Number and Diversity of Recombinant Progeny of Infectious Laryngotracheitis Viruses from the United States. Appl Environ Microbiol 2018; 84:AEM.01822-18. [PMID: 30242009 DOI: 10.1128/aem.01822-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/12/2018] [Indexed: 11/20/2022] Open
Abstract
Infectious laryngotracheitis (ILTV; Gallid alphaherpesvirus 1) causes mild to severe respiratory disease in poultry worldwide. Recombination in this virus under natural (field) conditions was first described in 2012 and more recently has been studied under laboratory conditions. Previous studies have revealed that natural recombination is widespread in ILTV and have also demonstrated that recombination between two attenuated ILTV vaccine strains generated highly virulent viruses that produced widespread disease within poultry flocks in Australia. In the United States, natural ILTV recombination has also been detected, but not as frequently as in Australia. To better understand recombination in ILTV strains originating from the United States, we developed a TaqMan single nucleotide polymorphism (SNP) genotyping assay to detect recombination between two virulent U.S. field strains of ILTV (63140 and 1874c5) under experimental in vivo conditions. We also tested the capacity of the Innovax-ILT vaccine (a recombinant vaccine using herpesvirus of turkeys as a vector) and the Trachivax vaccine (a conventionally attenuated chicken embryo origin vaccine) to reduce recombination. The Trachivax vaccine prevented ILTV replication, and therefore recombination, in the trachea after challenge. The Innovax-ILT vaccine allowed the challenge viruses to replicate and to recombine, but at a significantly lower rate than in an unvaccinated group of birds. Our results demonstrate that the TaqMan SNP genotyping assay is a useful tool to study recombination between these ILTV strains and also show that vaccination can limit the number and diversity of recombinant progeny viruses.IMPORTANCE Recombination allows alphaherpesviruses to evolve over time and become more virulent. Historically, characterization of viral vaccines in poultry have mainly focused on limiting clinical disease, rather than limiting virus replication, but such approaches can allow field viruses to persist and evolve in vaccinated populations. In this study, we vaccinated chickens with Gallid alphaherpesvirus 1 vaccines that are commercially available in the United States and then performed coinoculations with two field strains of virus to measure the ability of the vaccines to prevent field strains from replicating and recombining. We found that vaccination reduced viral replication, recombination, and diversity compared to those in unvaccinated chickens, although the extent to which this occurred differed between vaccines. We suggest that characterization of vaccines could include studies to examine the ability of vaccines to reduce viral recombination in order to limit the rise of new virulent field strains due to recombination, especially for those vaccines that are known not to prevent viral replication following challenge.
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Fakhri O, Hartley CA, Devlin JM, Browning GF, Noormohammadi AH, Lee SW. Development and application of high-resolution melting analysis for the classification of infectious laryngotracheitis virus strains and detection of recombinant progeny. Arch Virol 2018; 164:427-438. [PMID: 30421085 PMCID: PMC6373279 DOI: 10.1007/s00705-018-4086-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/15/2018] [Indexed: 12/15/2022]
Abstract
Live attenuated vaccines against infectious laryngotracheitis virus (ILTV) are widely used in the poultry industry to control disease and help prevent economic losses. Molecular epidemiological studies of currently circulating strains of ILTV within poultry flocks in Australia have demonstrated the presence of highly virulent viruses generated by genomic recombination events between vaccine strains. In this study, high-resolution melting (HRM) analysis was used to develop a tool to classify ILTV isolates and to investigate ILTV recombination. The assay was applied to plaque-purified progeny viruses generated after co-infection of chicken embryo kidney (CEK) monolayers with the A20 and Serva ILT vaccine strains and also to viruses isolated from field samples. The results showed that the HRM analysis is a suitable tool for the classification of ILTV isolates and can be used to detect recombination between ILTV vaccine strains in vitro. This method can be used to classify a broad range of ILTV strains to facilitate the classification and genotyping of ILTV and help to further understand recombination in these viruses.
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Affiliation(s)
- Omid Fakhri
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.
| | - Carol A Hartley
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Joanne M Devlin
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Glenn F Browning
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Amir H Noormohammadi
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, VIC, Australia
| | - Sang-Won Lee
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.,College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
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Loncoman CA, Hartley CA, Coppo MJC, Browning GF, Quinteros JA, Diaz-Méndez A, Thilakarathne D, Fakhri O, Vaz PK, Devlin JM. Replication-independent reduction in the number and diversity of recombinant progeny viruses in chickens vaccinated with an attenuated infectious laryngotracheitis vaccine. Vaccine 2018; 36:5709-5716. [PMID: 30104116 DOI: 10.1016/j.vaccine.2018.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/28/2018] [Accepted: 08/05/2018] [Indexed: 01/10/2023]
Abstract
Recombination is closely linked with virus replication and is an important mechanism that contributes to genome diversification and evolution in alphaherpesviruses. Infectious laryngotracheitis (ILTV; Gallid alphaherpesvirus 1) is an alphaherpesvirus that causes respiratory disease in poultry. In the past, natural (field) recombination events between different strains of ILTV generated virulent recombinant viruses that have caused severe disease and economic loss in poultry industries. In this study, chickens were vaccinated with attenuated ILTV vaccines to examine the effect of vaccination on viral recombination and diversity following subsequent co-inoculation with two field strains of ILTV. Two of the vaccines (SA2 and A20) prevented ILTV replication in the trachea after challenge, but the level of viral replication after co-infection in birds that received the Serva ILTV vaccine strain did not differ from that of the mock-vaccinated (control) birds. Even though the levels of viral replication were similar in the two groups, the number of recombinant progeny viruses and the level of viral diversity were significantly lower in the Serva-vaccinated birds than in mock-vaccinated birds. In both the mock-vaccinated and Serva-vaccinated groups, a high proportion of recombinant viruses were detected in naïve in-contact chickens that were housed with the co-inoculated birds. Our results indicate that vaccination can limit the number and diversity of recombinant progeny viruses in a manner that is independent of the level of virus replication. It is possible that immune responses induced by vaccination can select for virus genotypes that replicate well under the pressure of the host immune response.
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Affiliation(s)
- Carlos A Loncoman
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Carol A Hartley
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Mauricio J C Coppo
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Glenn F Browning
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - José A Quinteros
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andrés Diaz-Méndez
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Dulari Thilakarathne
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Omid Fakhri
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Paola K Vaz
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Joanne M Devlin
- Asia-Pacific Centre for Animal Health, Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
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Magouz A, Medhat S, Abou Asa S, Desouky A. Detection of infectious laryngotracheitis virus (Gallid herpesvirus-1) from clinically infected chickens in Egypt by different diagnostic methods. IRANIAN JOURNAL OF VETERINARY RESEARCH 2018; 19:194-201. [PMID: 30349566 PMCID: PMC6184029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 02/01/2018] [Accepted: 05/01/2018] [Indexed: 06/08/2023]
Abstract
Infectious laryngotracheitis (ILT) disease is an acute highly contagious viral disease leading to massive economic losses to the national poultry industry. This study aimed to identify the most accurate and rapid diagnostic methods to rescue layer poultry farms from intense outbreaks in Egypt. Fifty pathological specimens were collected and subjected to virus isolation (VI), histopathology, direct fluorescent antibody technique (FAT) and polymerase chain reaction (PCR). Egg inoculation revealed stunted growth and white pock lesions on chorioallantoic membranes (CAM) in 23 samples. Isolation and propagation of infectious laryngotracheitis virus (ILTV) in cell culture showed syncytia formation 5 days post infection in 20 inoculated samples. PCR resulted in successful amplification of a 647 bp fragment of the thymidine kinase (TK) gene in 25 field samples. Histopathological examination of inoculated CAM showed intranuclear inclusion bodies with infiltration of inflammatory cells. Direct FAT showed intra-cytoplasmic apple green reactions in 18 examined tracheal tissues. PCR has been shown to be more sensitive, accurate and rapid than VI, FAT and histopathological examination.
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Affiliation(s)
- A. Magouz
- Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt
| | - Sh. Medhat
- Department of Virology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt
| | - S. Abou Asa
- Department of Pathology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt
| | - A. Desouky
- Department of Parasitology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt
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Genetic Diversity of Infectious Laryngotracheitis Virus during In Vivo Coinfection Parallels Viral Replication and Arises from Recombination Hot Spots within the Genome. Appl Environ Microbiol 2017; 83:AEM.01532-17. [PMID: 28939604 DOI: 10.1128/aem.01532-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 09/12/2017] [Indexed: 02/07/2023] Open
Abstract
Recombination is a feature of many alphaherpesviruses that infect people and animals. Infectious laryngotracheitis virus (ILTV; Gallid alphaherpesvirus 1) causes respiratory disease in chickens, resulting in significant production losses in poultry industries worldwide. Natural (field) ILTV recombination is widespread, particularly recombination between attenuated ILTV vaccine strains to create virulent viruses. These virulent recombinants have had a major impact on animal health. Recently, the development of a single nucleotide polymorphism (SNP) genotyping assay for ILTV has helped to understand ILTV recombination in laboratory settings. In this study, we applied this SNP genotyping assay to further examine ILTV recombination in the natural host. Following coinoculation of specific-pathogen-free chickens, we examined the resultant progeny for evidence of viral recombination and characterized the diversity of the recombinants over time. The results showed that ILTV replication and recombination are closely related and that the recombinant viral progeny are most diverse 4 days after coinoculation, which is the peak of viral replication. Further, the locations of recombination breakpoints in a selection of the recombinant progeny, and in field isolates of ILTV from different geographical regions, were examined following full-genome sequencing and used to identify recombination hot spots in the ILTV genome.IMPORTANCE Alphaherpesviruses are common causes of disease in people and animals. Recombination enables genome diversification in many different species of alphaherpesviruses, which can lead to the evolution of higher levels of viral virulence. Using the alphaherpesvirus infectious laryngotracheitis virus (ILTV), we performed coinfections in the natural host (chickens) to demonstrate high levels of virus recombination. Higher levels of diversity in the recombinant progeny coincided with the highest levels of virus replication. In the recombinant progeny, and in field isolates, recombination occurred at greater frequency in recombination hot spot regions of the virus genome. Our results suggest that control measures that aim to limit viral replication could offer the potential to limit virus recombination and thus the evolution of virulence. The development and use of vaccines that are focused on limiting virus replication, rather than vaccines that are focused more on limiting clinical disease, may be indicated in order to better control disease.
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