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Spatz S, Afonso CL. Non-Targeted RNA Sequencing: Towards the Development of Universal Clinical Diagnosis Methods for Human and Veterinary Infectious Diseases. Vet Sci 2024; 11:239. [PMID: 38921986 PMCID: PMC11209166 DOI: 10.3390/vetsci11060239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/27/2024] Open
Abstract
Metagenomics offers the potential to replace and simplify classical methods used in the clinical diagnosis of human and veterinary infectious diseases. Metagenomics boasts a high pathogen discovery rate and high specificity, advantages absent in most classical approaches. However, its widespread adoption in clinical settings is still pending, with a slow transition from research to routine use. While longer turnaround times and higher costs were once concerns, these issues are currently being addressed by automation, better chemistries, improved sequencing platforms, better databases, and automated bioinformatics analysis. However, many technical options and steps, each producing highly variable outcomes, have reduced the technology's operational value, discouraging its implementation in diagnostic labs. We present a case for utilizing non-targeted RNA sequencing (NT-RNA-seq) as an ideal metagenomics method for the detection of infectious disease-causing agents in humans and animals. Additionally, to create operational value, we propose to identify best practices for the "core" of steps that are invariably shared among many human and veterinary protocols. Reference materials, sequencing procedures, and bioinformatics standards should accelerate the validation processes necessary for the widespread adoption of this technology. Best practices could be determined through "implementation research" by a consortium of interested institutions working on common samples.
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Affiliation(s)
- Stephen Spatz
- Southeast Poultry Research Laboratory, Agricultural Research Service, United States Department of Agriculture, 934 College Station Road, Athens, GA 30605, USA;
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2
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Van Borm S, Roupie V, Linden A, Vangeluwe D, De Waele V, Lambrecht B, Steensels M. RNA sequencing of avian paramyxovirus (Paramyxoviridae, Avulavirinae) isolates from wild mallards in Belgium, 2021: complete genomes and coinfections. Virus Genes 2023; 59:723-731. [PMID: 37392346 DOI: 10.1007/s11262-023-02015-w] [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: 03/31/2023] [Accepted: 06/10/2023] [Indexed: 07/03/2023]
Abstract
We used untargeted RNA sequencing to characterize three Avulavirinae isolates from pooled samples obtained from wild mallards in Belgium in 2021. The complete genome sequences of two avian Orthoavulavirus-1 (AOAV-1) strains and one avian Paraavulavirus-4 (APMV-4) strain were determined confirming hemagglutination inhibition testing of the virus isolates. In addition, the applied sequencing strategy identified an avian influenza virus (AIV) coinfection in all three virus isolates, confirming weak-positive AIV realtime RT-PCR results from the original sample material. In one AOAV-1 isolate, partial sequences covering all genome segments of an AIV of subtype H11N9 could be de novo assembled from the sequencing data. Besides an AIV coinfection, RNA metagenomic data from the APMV-4 isolate also showed evidence of Alpharetrovirus and Megrivirus coinfection. In total, two AOAV-1 of Class II, genotype I.2 and one APMV-4 complete genome sequences were assembled and compared to publicly available sequences, highlighting the importance of surveillance for poultry pathogens in wild birds. Beyond the insights from full genome characterization of virus isolates, untargeted RNA sequencing strategies provide additional insights in the RNA virome of clinical samples as well as their derived virus isolates that are particularly useful when targeting wild avifauna reservoirs of poultry pathogens.
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Affiliation(s)
- Steven Van Borm
- Avian Virology and Immunology, Sciensano, Brussels, Belgium.
| | - V Roupie
- Avian Virology and Immunology, Sciensano, Brussels, Belgium
| | - A Linden
- Fundamental and Applied Research for Animals and Health (FARAH), Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - D Vangeluwe
- Belgian Ringing Scheme (BeBirds), Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - V De Waele
- Department of Natural and Agricultural Environment Studies, Public Service of Wallonia, Gembloux, Belgium
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3
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Rtishchev A, Treshchalina A, Shustova E, Boravleva E, Gambaryan A. An Outbreak of Newcastle Disease Virus in the Moscow Region in the Summer of 2022. Vet Sci 2023; 10:404. [PMID: 37368790 DOI: 10.3390/vetsci10060404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
In August 2022 on a backyard farm in the Moscow region of Russia, mortality was observed among chickens, and all 45 birds of a particular farm died or were slaughtered after the onset of symptoms within a few days. Paramyxovirus was isolated from the diseased birds. Based on the nucleotide sequences of the F and NP gene fragments, it was determined that the virus belonged to subgenotype VII.1 AAvV-1 class II. The cleavage site of the F gene 109SGGRRQKRFIG119 and T in 546 and 555 position of the NP gene were typical for the velogenic type. The genetically closest NDV isolates were found in Iran. The mean time of death of 10-day-old chicken embryos upon infection with the minimal infectious dose was 52 h, which is typical for the velogenic pathotype. The virus caused 100% death of six-week-old chickens during oral infection as well as 100% mortality of all contact chickens, including those located in remote cages, which proves the ability of the virus to spread not only by the fecal-oral route but also by the aerosol route. That demonstrates a high level of pathogenicity and contagiousness of the isolated strain for chicken. However, mice intranasally infected with high doses of the virus did not die.
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Affiliation(s)
- Artyom Rtishchev
- Federal State Budgetary Scientific Institution «I. Mechnikov Research Institute of Vaccines and Sera», 105064 Moscow, Russia
| | - Anastasia Treshchalina
- Chumakov Federal Scientific Center for the Research and Development of Immune-and-Biological Products, Village of Institute of Poliomyelitis, Settlement "Moskovskiy", 108819 Moscow, Russia
| | - Elena Shustova
- Chumakov Federal Scientific Center for the Research and Development of Immune-and-Biological Products, Village of Institute of Poliomyelitis, Settlement "Moskovskiy", 108819 Moscow, Russia
| | - Elizaveta Boravleva
- Chumakov Federal Scientific Center for the Research and Development of Immune-and-Biological Products, Village of Institute of Poliomyelitis, Settlement "Moskovskiy", 108819 Moscow, Russia
| | - Alexandra Gambaryan
- Chumakov Federal Scientific Center for the Research and Development of Immune-and-Biological Products, Village of Institute of Poliomyelitis, Settlement "Moskovskiy", 108819 Moscow, Russia
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Goraichuk IV, Gerilovych A, Bolotin V, Solodiankin O, Dimitrov KM, Rula O, Muzyka N, Mezinov O, Stegniy B, Kolesnyk O, Pantin-Jackwood MJ, Miller PJ, Afonso CL, Muzyka D. Genetic diversity of Newcastle disease viruses circulating in wild and synanthropic birds in Ukraine between 2006 and 2015. Front Vet Sci 2023; 10:1026296. [PMID: 36742982 PMCID: PMC9893288 DOI: 10.3389/fvets.2023.1026296] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 01/02/2023] [Indexed: 01/20/2023] Open
Abstract
Newcastle disease virus (NDV) infects a wide range of bird species worldwide and is of importance to the poultry industry. Although certain virus genotypes are clearly associated with wild bird species, the role of those species in the movement of viruses and the migratory routes they follow is still unclear. In this study, we performed a phylogenetic analysis of nineteen NDV sequences that were identified among 21,924 samples collected from wild and synanthropic birds from different regions of Ukraine from 2006 to 2015 and compared them with isolates from other continents. In synanthropic birds, NDV strains of genotype II, VI, VII, and XXI of class II were detected. The fusion gene sequences of these strains were similar to strains detected in birds from different geographical regions of Europe and Asia. However, it is noteworthy to mention the isolation of vaccine viruses from synanthropic birds, suggesting the possibility of their role in viral transmission from vaccinated poultry to wild birds, which may lead to the further spreading of vaccine viruses into other regions during wild bird migration. Moreover, here we present the first publicly available complete NDV F gene from a crow (genus Corvus). Additionally, our phylogenetic results indicated a possible connection of Ukrainian NDV isolates with genotype XXI strains circulating in Kazakhstan. Among strains from wild birds, NDVs of genotype 1 of class I and genotype I of class II were detected. The phylogenetic analysis highlighted the possible exchange of these NDV strains between wild waterfowl from the Azov-Black Sea region of Ukraine and waterfowl from different continents, including Europe, Asia, and Africa.
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Affiliation(s)
- Iryna V. Goraichuk
- National Scientific Centre, Institute of Experimental and Clinical Veterinary Medicine, Kharkiv, Ukraine,Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, Athens, GA, United States
| | - Anton Gerilovych
- National Scientific Centre, Institute of Experimental and Clinical Veterinary Medicine, Kharkiv, Ukraine
| | - Vitaliy Bolotin
- National Scientific Centre, Institute of Experimental and Clinical Veterinary Medicine, Kharkiv, Ukraine
| | - Olexii Solodiankin
- National Scientific Centre, Institute of Experimental and Clinical Veterinary Medicine, Kharkiv, Ukraine
| | - Kiril M. Dimitrov
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, Athens, GA, United States
| | - Oleksandr Rula
- National Scientific Centre, Institute of Experimental and Clinical Veterinary Medicine, Kharkiv, Ukraine
| | - Nataliia Muzyka
- National Scientific Centre, Institute of Experimental and Clinical Veterinary Medicine, Kharkiv, Ukraine
| | - Oleksandr Mezinov
- The F.E. Falz-Fein Biosphere Reserve “Askania Nova”, National Academy of Agrarian Sciences of Ukraine, Askania-Nova, Kherson Oblast, Ukraine
| | - Borys Stegniy
- National Scientific Centre, Institute of Experimental and Clinical Veterinary Medicine, Kharkiv, Ukraine
| | - Olena Kolesnyk
- National Scientific Centre, Institute of Experimental and Clinical Veterinary Medicine, Kharkiv, Ukraine
| | - Mary J. Pantin-Jackwood
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, Athens, GA, United States
| | - Patti J. Miller
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, Athens, GA, United States
| | - Claudio L. Afonso
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, Athens, GA, United States
| | - Denys Muzyka
- National Scientific Centre, Institute of Experimental and Clinical Veterinary Medicine, Kharkiv, Ukraine,Department of Zoology, H.S. Skovoroda Kharkiv National Pedagogical University, Kharkiv, Ukraine,*Correspondence: Denys Muzyka ✉
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5
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Pigeon Circovirus over Three Decades of Research: Bibliometrics, Scoping Review, and Perspectives. Viruses 2022; 14:v14071498. [PMID: 35891478 PMCID: PMC9317399 DOI: 10.3390/v14071498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/03/2022] [Accepted: 07/04/2022] [Indexed: 11/22/2022] Open
Abstract
The pigeon circovirus (PiCV), first described in the literature in the early 1990s, is considered one of the most important infectious agents affecting pigeon health. Thirty years after its discovery, the current review has employed bibliometric strategies to map the entire accessible PiCV-related research corpus with the aim of understanding its present research landscape, particularly in consideration of its historical context. Subsequently, developments, current knowledge, and important updates were provided. Additionally, this review also provides a textual analysis examining the relationship between PiCV and the young pigeon disease syndrome (YPDS), as described and propagated in the literature. Our examination revealed that usages of the term ‘YPDS’ in the literature are characterizations that are diverse in range, and neither standard nor equivalent. Guided by our understanding of the PiCV research corpus, a conceptualization of PiCV diseases was also presented in this review. Proposed definitions and diagnostic criteria for PiCV subclinical infection (PiCV-SI) and PiCV systemic disease (PiCV-SD) were also provided. Lastly, knowledge gaps and open research questions relevant to future PiCV-related studies were identified and discussed.
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Tal S, Ben Izhak M, Wachtel C, Wiseman A, Braun T, Yechezkel E, Golan E, Hadas R, Turjeman A, Banet-Noach C, Bronstein M, Lublin A, Berman E, Raviv Z, Pirak M, Klement E, Louzoun Y. Evaluating methods for Avian avulavirus-1 whole genome sequencing. Gene 2019; 721S:100004. [PMID: 32550541 PMCID: PMC7285907 DOI: 10.1016/j.gene.2019.100004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 01/03/2019] [Indexed: 11/18/2022]
Abstract
Background Avian avulavirus-1 (AAvV-1, previously Newcastle Disease Virus) is responsible for poultry and wild birds' disease outbreaks. Numerous whole genome sequencing methods were reported for this virus. These methods included cloning, specific primers amplification, shotgun PCR approaches, Sequence Independent Single Primer Amplification and next generation sequencing platform kits. Methods Three methods were used to sequence 173 Israeli Avian avulavirus-1 field isolates and one vaccine strain (VH). The sequencing was performed on Proton and Ion Torrent Personal Genome Machine and to a lesser extent, Illumina MiSeq and NextSeq sequencers. Target specific primers (SP) and Sequence Independent Single Primer Amplification (SISPA) products sequenced via the Ion torrent sequencer had a high error rate and truncated genomes. All the next generation sequencing platform sequencing kits generated high sequence accuracy and near-complete genomic size. Results A high level of mutations was observed in the intergenic regions between the avian avulavirus-1 genes. Within genes, multiple regions are more mutated than the Fusion region currently used for typing. Conclusions Our findings suggest that the whole genome sequencing by the Ion torrent sequencing kit is sufficient. However, when higher fidelity is desired, the Illumina NextSeq and Proton torrent sequencing kits were found to be preferable.
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Affiliation(s)
- Saar Tal
- The Poultry Health Laboratories, The Egg and Poultry Board, Israel
| | - Meirav Ben Izhak
- Life Science faculty and Gonda Brain Research Center, Bar Ilan University, Israel
| | | | - Anat Wiseman
- The Poultry Health Laboratories, The Egg and Poultry Board, Israel
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Israel
| | - Tzipi Braun
- Life Science faculty and Gonda Brain Research Center, Bar Ilan University, Israel
| | - Elinor Yechezkel
- The Poultry Health Laboratories, The Egg and Poultry Board, Israel
| | - Einav Golan
- The Poultry Health Laboratories, The Egg and Poultry Board, Israel
| | - Ruth Hadas
- Kimron Veterinary Institute, Division of Avian Diseases, Israel
| | - Adi Turjeman
- The Center for Genomic Technologies, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | | | - Michal Bronstein
- The Center for Genomic Technologies, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Avishai Lublin
- Kimron Veterinary Institute, Division of Avian Diseases, Israel
| | - Elyakum Berman
- The Poultry Health Laboratories, The Egg and Poultry Board, Israel
| | - Ziv Raviv
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Israel
| | - Michael Pirak
- The Poultry Health Laboratories, The Egg and Poultry Board, Israel
| | - Eyal Klement
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Israel
| | - Yoram Louzoun
- Department of Mathematics and Gonda Brain Research Center, Bar Ilan University, Israel
- Corresponding author at: Math Department and Gonda Brain Research Center, Bar Ilan University, Ramat Gan 52900, Israel.
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Qiu X, Meng C, Zhan Y, Yu S, Li S, Ren T, Yuan W, Xu S, Sun Y, Tan L, Song C, Liao Y, Ding Z, Liu X, Ding C. Phylogenetic, antigenic and biological characterization of pigeon paramyxovirus type 1 circulating in China. Virol J 2017; 14:186. [PMID: 28962631 PMCID: PMC5622419 DOI: 10.1186/s12985-017-0857-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 09/22/2017] [Indexed: 11/11/2022] Open
Abstract
Background For many years, ND has been one of the most important infectious pigeon diseases in China. In recent years, a high mortality has been observed in ND-infected pigeons in China. Mortality is from 40% to 80% or 100% in some cases. Methods The full-length genomes of four pigeon paramyxovirus type 1 (PPMV-1) strains, which were isolated from infected pigeons in China in 2012 and 2013, were sequenced and analyzed to determine the phylogenetic characteristics of PPMV-1 circulating in pigeons of China in recent years. Furthermore, cross hemagglutination inhibition and cross virus neutralization assays, as well as animal experiments were conducted to determine the antigenicity and pathogenicity of those viruses. Proteolytic cleavage sites (residues 112–117) of the F proteins were identified as the typical virulence motif, 112RRQKR↓F117 for all four PPMV-1 strains investigated. Results Phylogenetic analysis based on sequences of complete genomes and F gene revealed that the four PPMV-1 isolates and most of recent isolates in China were highly homologous to European isolates from 1998 to 2011. All those isolates were clustered in one clade of genotype VI NDV, termed as subgroup 4bii f. The R value was calculated based on cross hemagglutination inhibition and cross virus neutralization results, and confirmed antigenic difference of the PPMV-1 strains isolated in 2013 from the LaSota vaccine strain. Several mutations were identified in the surface glycoproteins F and HN, which probably gave rise to those antigenic differences. Conclusion Our result suggested that the PPMV-1 strain prevailing in China in the last decade diverged from a common ancestor and was presumably transmitted from Europe. PPMV-1 isolates displayed obvious antigenic differences from vaccine strain LaSota. Even though PPMV-1 did not cause high mortality in experimental pigeons, the infected pigeons were exhibiting viral shedding for 3 weeks after infection, suggesting PPMV-1 is a potential threat to NDV control worldwide. Electronic supplementary material The online version of this article (10.1186/s12985-017-0857-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xusheng Qiu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China
| | - Chunchun Meng
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China
| | - Yuan Zhan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China
| | - Shengqing Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China
| | - Shichao Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China
| | - Tingting Ren
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China
| | - Weifeng Yuan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China
| | - Shuqin Xu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China
| | - Yingjie Sun
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China
| | - Lei Tan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China
| | - Cuiping Song
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China
| | - Ying Liao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China
| | - Zhuang Ding
- Laboratory of Infectious Diseases, College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
| | - Xiufan Liu
- Key Laboratory of Animal Infectious Diseases, Yangzhou University, Yangzhou, Jiangsu, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
| | - Chan Ding
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China. .,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China.
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8
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Dodovski A, Cvetkovikj I, Krstevski K, Naletoski I, Savić V. Characterization and Epidemiology of Pigeon Paramyxovirus Type-1 Viruses (PPMV-1) Isolated in Macedonia. Avian Dis 2017; 61:146-152. [PMID: 28665727 DOI: 10.1637/11517-101816-reg.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We have characterized in this study 10 PPMV-1 isolated from domestic pigeons and one PPMV-1 isolated from a feral pigeon in the period 2007-2012, using both classical methods (HI test and ICPI test) and molecular methods (RT-qPCR, RT-PCR, and nucleotide sequencing). Using phylogenetic analysis of partial fusion gene sequences, these viruses clustered with recent European PPMV-1 isolates (EU/re) within the genotype VIb/1. All isolates possessed virulent cleavage site motifs with variable morbidity and mortality in pigeons. The intracerebral pathogenecity indices of the five isolates ranged from 0.59 to 1.53. The repetitive isolation of PPMV-1 viruses for several consecutive years led toward establishing enzootic presence of the disease in pigeons. A high nucleotide sequence homology between the Macedonian isolates and EU/re isolates was shown. Co-circulation of different isolates in the same holdings was detected. This is the first study to extensively describe the molecular epidemiology of PPMV-1 isolated in Macedonia.
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Affiliation(s)
- A Dodovski
- A Ss. Cyril and Methodius University in Skopje, Faculty of Veterinary Medicine in Skopje, Veterinary Institute, Lazar Pop Trajkov 5-7, MK-1000, Skopje, Macedonia
| | - I Cvetkovikj
- A Ss. Cyril and Methodius University in Skopje, Faculty of Veterinary Medicine in Skopje, Veterinary Institute, Lazar Pop Trajkov 5-7, MK-1000, Skopje, Macedonia
| | - K Krstevski
- A Ss. Cyril and Methodius University in Skopje, Faculty of Veterinary Medicine in Skopje, Veterinary Institute, Lazar Pop Trajkov 5-7, MK-1000, Skopje, Macedonia
| | - I Naletoski
- B Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Vienna International Centre, A-1400 Vienna, Austria
| | - Vladimir Savić
- C Poultry Center, Croatian Veterinary Institute, Heinzelova 55, HR-10000 Zagreb, Croatia
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Dimitrov KM, Sharma P, Volkening JD, Goraichuk IV, Wajid A, Rehmani SF, Basharat A, Shittu I, Joannis TM, Miller PJ, Afonso CL. A robust and cost-effective approach to sequence and analyze complete genomes of small RNA viruses. Virol J 2017; 14:72. [PMID: 28388925 PMCID: PMC5384157 DOI: 10.1186/s12985-017-0741-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 03/29/2017] [Indexed: 01/26/2023] Open
Abstract
Background Next-generation sequencing (NGS) allows ultra-deep sequencing of nucleic acids. The use of sequence-independent amplification of viral nucleic acids without utilization of target-specific primers provides advantages over traditional sequencing methods and allows detection of unsuspected variants and co-infecting agents. However, NGS is not widely used for small RNA viruses because of incorrectly perceived cost estimates and inefficient utilization of freely available bioinformatics tools. Methods In this study, we have utilized NGS-based random sequencing of total RNA combined with barcode multiplexing of libraries to quickly, effectively and simultaneously characterize the genomic sequences of multiple avian paramyxoviruses. Thirty libraries were prepared from diagnostic samples amplified in allantoic fluids and their total RNAs were sequenced in a single flow cell on an Illumina MiSeq instrument. After digital normalization, data were assembled using the MIRA assembler within a customized workflow on the Galaxy platform. Results Twenty-eight avian paramyxovirus 1 (APMV-1), one APMV-13, four avian influenza and two infectious bronchitis virus complete or nearly complete genome sequences were obtained from the single run. The 29 avian paramyxovirus genomes displayed 99.6% mean coverage based on bases with Phred quality scores of 30 or more. The lower and upper quartiles of sample median depth per position for those 29 samples were 2984 and 6894, respectively, indicating coverage across samples sufficient for deep variant analysis. Sample processing and library preparation took approximately 25–30 h, the sequencing run took 39 h, and processing through the Galaxy workflow took approximately 2–3 h. The cost of all steps, excluding labor, was estimated to be 106 USD per sample. Conclusions This work describes an efficient multiplexing NGS approach, a detailed analysis workflow, and customized tools for the characterization of the genomes of RNA viruses. The combination of multiplexing NGS technology with the Galaxy workflow platform resulted in a fast, user-friendly, and cost-efficient protocol for the simultaneous characterization of multiple full-length viral genomes. Twenty-nine full-length or near-full-length APMV genomes with a high median depth were successfully sequenced out of 30 samples. The applied de novo assembly approach also allowed identification of mixed viral populations in some of the samples. Electronic supplementary material The online version of this article (doi:10.1186/s12985-017-0741-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kiril M Dimitrov
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, USA
| | - Poonam Sharma
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, USA
| | | | - Iryna V Goraichuk
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, USA.,National Scientific Center Institute of Experimental and Clinical Veterinary Medicine, 83 Pushkinskaya Street, Kharkiv, 61023, Ukraine
| | - Abdul Wajid
- Quality Operations Laboratory (QOL), University of Veterinary and Animal Sciences, Syed Abdul Qadir Jilani Road, Lahore, 54000, Pakistan.,Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Syed Abdul Qadir Jilani Road, Lahore, 54000, Pakistan
| | - Shafqat Fatima Rehmani
- Quality Operations Laboratory (QOL), University of Veterinary and Animal Sciences, Syed Abdul Qadir Jilani Road, Lahore, 54000, Pakistan
| | - Asma Basharat
- Quality Operations Laboratory (QOL), University of Veterinary and Animal Sciences, Syed Abdul Qadir Jilani Road, Lahore, 54000, Pakistan
| | - Ismaila Shittu
- Regional Laboratory for Animal Influenza and other Transboundary Animal Diseases, National Veterinary Research Institute, PMB01, Vom, 930010, Plateau State, Nigeria
| | - Tony M Joannis
- Regional Laboratory for Animal Influenza and other Transboundary Animal Diseases, National Veterinary Research Institute, PMB01, Vom, 930010, Plateau State, Nigeria
| | - Patti J Miller
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, USA
| | - Claudio L Afonso
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, US National Poultry Research Center, Agricultural Research Service, USDA, 934 College Station Road, Athens, GA, 30605, USA.
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10
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Genomic Characterizations of Six Pigeon Paramyxovirus Type 1 Viruses Isolated from Live Bird Markets in China during 2011 to 2013. PLoS One 2015; 10:e0124261. [PMID: 25928057 PMCID: PMC4415766 DOI: 10.1371/journal.pone.0124261] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 03/12/2015] [Indexed: 11/19/2022] Open
Abstract
The genomes of six pigeon paramyxovirus type 1 (PPMV-1) isolated from symptomless pigeons in live poultry markets during the national active surveillance from 2011 to 2013 were sequenced and analyzed in this study. The complete genome lengths of all isolates were 15,192 nucleotides with the gene order of 3’-NP-P-M-F-HN-L-5’. All isolates had the same motif of 112RRQKRF117 at the cleavage site of the fusion protein, which was typical of velogenic Newcastle disease virus (NDV). Several mutations were identified in the functional domains of F and HN proteins, including fusion peptide, heptad repeat region, transmembrane domains and neutralizing epitopes. Phylogenetic analysis based on sequences of complete genomes and six genes revealed that all isolates belonged to genotype VI in class II, but at least 2 sub-genotypes were identified. Most isolates were placed into sub-genotype VIb with the exception of pi/GX/1015/13, which was classified in sub-genotype VIa. The obvious antigenic difference between PPMV-1 isolates and La Sota strain was found based on the R-value calculated by cross hemagglutination inhibition (HI) assay. These results provided the evidence that PPMV-1 could be detected from healthy pigeons, and our study may be useful in designing vaccines used in pigeon, and developing molecular diagnostic tools to monitor and prevent future PPMV-1 outbreaks.
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Mahzounieh M, Heidari Khoei H, Ghasemi Shamsabadi M, Dastjerdi A. Detection and phylogenetic characterization of Columbid circoviruses in Chaharmahal va Bakhtiari province, Iran. Avian Pathol 2014; 43:524-8. [DOI: 10.1080/03079457.2014.966648] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Wang Y, Wang H, Xu K, Ni P, Zhang H, Ma J, Yang H, Xu F. A survey of overlooked viral infections in biological experiment systems. PLoS One 2014; 9:e105348. [PMID: 25144530 PMCID: PMC4140767 DOI: 10.1371/journal.pone.0105348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 07/23/2014] [Indexed: 12/04/2022] Open
Abstract
It is commonly accepted that there are many unknown viruses on the planet. For the known viruses, do we know their prevalence, even in our experimental systems? Here we report a virus survey using recently published small (s)RNA sequencing datasets. The sRNA reads were assembled and contigs were screened for virus homologues against the NCBI nucleotide (nt) database using the BLASTn program. To our surprise, approximately 30% (28 out of 94) of publications had highly scored viral sequences in their datasets. Among them, only two publications reported virus infections. Though viral vectors were used in some of the publications, virus sequences without any identifiable source appeared in more than 20 publications. By determining the distributions of viral reads and the antiviral RNA interference (RNAi) pathways using the sRNA profiles, we showed evidence that many of the viruses identified were indeed infecting and generated host RNAi responses. As virus infections affect many aspects of host molecular biology and metabolism, the presence and impact of viruses needs to be actively investigated in experimental systems.
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Affiliation(s)
- Yajing Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
| | - Hui Wang
- NERC/Centre for Ecology and Hydrology, Wallingford, Oxfordshire, United Kingdom
- Beijing Genome Institute (BGI), Yantian District, Shenzhen, China
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Kunhan Xu
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China
| | - Peixiang Ni
- BGI-Tianjin, Airport Economic Area, Tianjin, China
| | - Huan Zhang
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China
| | - Jinmin Ma
- Beijing Genome Institute (BGI), Yantian District, Shenzhen, China
| | - Huanming Yang
- Beijing Genome Institute (BGI), Yantian District, Shenzhen, China
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Prince Aljawhra Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
- James D. Watson Institute of Genome Science, Hangzhou, China
| | - Feng Xu
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China
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Cunha MV, Inácio J, Freimanis G, Fusaro A, Granberg F, Höper D, King DP, Monne I, Orton R, Rosseel T. Next-generation sequencing in veterinary medicine: how can the massive amount of information arising from high-throughput technologies improve diagnosis, control, and management of infectious diseases? Methods Mol Biol 2014; 1247:415-36. [PMID: 25399113 PMCID: PMC7123048 DOI: 10.1007/978-1-4939-2004-4_30] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The development of high-throughput molecular technologies and associated bioinformatics has dramatically changed the capacities of scientists to produce, handle, and analyze large amounts of genomic, transcriptomic, and proteomic data. A clear example of this step-change is represented by the amount of DNA sequence data that can be now produced using next-generation sequencing (NGS) platforms. Similarly, recent improvements in protein and peptide separation efficiencies and highly accurate mass spectrometry have promoted the identification and quantification of proteins in a given sample. These advancements in biotechnology have increasingly been applied to the study of animal infectious diseases and are beginning to revolutionize the way that biological and evolutionary processes can be studied at the molecular level. Studies have demonstrated the value of NGS technologies for molecular characterization, ranging from metagenomic characterization of unknown pathogens or microbial communities to molecular epidemiology and evolution of viral quasispecies. Moreover, high-throughput technologies now allow detailed studies of host-pathogen interactions at the level of their genomes (genomics), transcriptomes (transcriptomics), or proteomes (proteomics). Ultimately, the interaction between pathogen and host biological networks can be questioned by analytically integrating these levels (integrative OMICS and systems biology). The application of high-throughput biotechnology platforms in these fields and their typical low-cost per information content has revolutionized the resolution with which these processes can now be studied. The aim of this chapter is to provide a current and prospective view on the opportunities and challenges associated with the application of massive parallel sequencing technologies to veterinary medicine, with particular focus on applications that have a potential impact on disease control and management.
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Affiliation(s)
- Mónica V. Cunha
- Instituto Nacional de Investigação Agrária e Veterinária, IP and Centro de Biologia Ambiental, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - João Inácio
- Instituto Nacional de Investigação Agrária e Veterinária, IP, Lisboa, Portugal and School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
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Molecular epidemiology of viral diseases in the era of next generation sequencing. J Clin Virol 2013; 57:378-80. [PMID: 23726419 DOI: 10.1016/j.jcv.2013.04.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 04/22/2013] [Accepted: 04/24/2013] [Indexed: 12/17/2022]
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