The veterinary high throughput sequencing laboratory (VHTSL) offers you a very flexible and varied service that will meet your objectives.

From complete genome sequencing of bacteria and viruses to complex research projects, including bioinformatics analyzes if necessary, our turnkey service will meet your needs.

The VHTSL has two high throughput sequencers with advanced technologies, MiSeq from Illumina and S5 Prime from Ion Torrent. In addition, we have just acquired a MinION from Nanopore, for which we will offer you a service shortly.

For questions, or to discuss your specific project needs and the options available, contact Dr. Chantale Provost. Email:

Assistance such as a turnkey service can be provided on request.


Sequencing service

The VHTSL offers many analyzes such as:

    • MiSeq (Illumina)
    • S5 Prime (Ion Torrent)
    • Bioanalyzer
      • Device to check the quality and quantity of libraries, DNA and RNA
    • QIAxcel
      • Device to check the quality and quantity of libraries, as well as DNA and RNA gel analysis
    • Microbiome 16S
      • Most used kit: QIAseq 16S / ITS Screening Panel, which allows 6 amplicons to be separated into 3 pools which, together, can cover the entire 16S ribosomal gene. In addition, the QIAseq 16S / ITS screening panel contains primers for ITS to amplify fungal DNA.
    • MicroRNA
      • Sequencing of the small fragments of cellular RNA, which prevent the production of a particular protein by binding to and destroying the messenger RNA
    • AmpliSeq
      • Sequencing of a pre-amplification of a certain number of targeted genes or predefined gene region
    • RNA-Seq
      • Random sequencing of the transcriptome
    • Metagenomics (virome)
      • Sequencing of the total genetic content of a sample, then comparison of the sequences obtained with microorganism databases
    • De novo
      • Assembly of genomic sequences without reference
    • Re-sequencing
      • Assembly of genomic sequences with a reference

Bioinformatics analyzes

The VHTSL can provide a complete bioinformatic analysis service. This service mainly uses two analysis programs, CLC Genomic Workbench and Geneious Prime. Several analysis options are available such as:

    • Genome assembly
      • De novo
          • Assembly of genetic sequences without reference
      • Re-sequencing
          • Assembly of genetic sequences with reference
      • Annotations
          • Identification of gene locations and all coding regions of a genome
      • Plasmids
    • MLST
      • Multi-focus sequence typing (MLST): typing of several loci allowing the characterization of isolates of microbial species using the DNA sequences of internal fragments of several household genes
    • PFGE
      • Pulsed field gel electrophoresis: Type of DNA fingerprint for a bacterial isolate
    • Antimicrobial resistance genes
      • Portion of DNA encoding the survival of an organism when exposed to antibiotics
    • Genes coding for virulence factors
      • Portion of coding DNA of an infectious agent, which contributes to its pathogenic nature when infecting host
    • Phylogenetic trees
      • Schematic tree showing the relationships between the organisms compared
    • Genetic alignments
      • Comparison of the genetic sequences of several viral strains or different organisms
    • Metagenomic analyzes
      • 4 different databases:
          • Kraken Metagenomics by BaseSpace Labs
          • Microbial Genome Database by CLC Genomic Workbench
          • NCBI reference by Taxonomic Profiling Index – CLC Genomic Workbench
          • Nucleotide (GenBank) by NCBI


The VHTSL Publications


Ana Perez Contreras, Frank van der Meer, Sylvia Checkley, Tomy Joseph, Robin King, Madhu Ravi, Delores Peters, Kevin Fonseca, Carl A. Gagnon, Chantale Provost, Davor Ojkic and Mohamed Faizal Abdul-Careem. Analysis of Whole-Genome Sequences of Infectious laryngotracheitis Virus Isolates from Poultry Flocks in Canada: Evidence of Recombination. Viruses 2020, 12, 1302; doi:10.3390/v12111302.


Palomino-Tapia V, Mitevski D, Inglis T, van der Meer F, Martin E, Brash M, Provost C, Gagnon CA, Abdul-Careem MF. Chicken Astrovirus (CAstV) Molecular Studies Reveal Evidence of Multiple Past Recombination Events in Sequences Originated from Clinical Samples of White Chick Syndrome (WCS) in Western Canada. Viruses. 2020 Sep 28;12(10):E1096. doi: 10.3390/v12101096. PMID: 32998356


Gagnon CA, Lalonde C, Provost C. Porcine reproductive and respiratory syndrome virus whole-genome sequencing efficacy with field clinical samples using a poly(A)-tail viral genome purification method. J Vet Diagn Invest. 2020 Aug 28:1040638720952411. doi: 10.1177/1040638720952411. Online ahead of print. PMID: 32856560.


Lalonde C, Provost C, Gagnon CA. Whole genome sequencing of porcine reproductive and respiratory syndrome virus (PRRSV) from field clinical samples improves the genomic surveillance of the virus. J Clin Microbiol. 2020 Aug 12:JCM.00097-20. doi: 10.1128/JCM.00097-20. Online ahead of print. PMID: 32817228


Le Net R, Provost C, Lalonde C, Régimbald L, Vézina F, Gagnon CA, Lair S. Whole Genome Sequincing of an Avipoxvirus Associated with Infections in a Group of Aviary-Housed Snow Buntings (Plectrophenax Nivalis). J Zoo Wildl Med. 2020 Jan 9;50(4):803-812. doi: 10.1638/2018-0102. PMID: 31926510


Chénier S, Desroches M, Provost C, Bournival V, St-Sauveur VG, Koszegi M, Gagnon CA. First reported outbreak of Duck atadenovirus A tracheobronchitis in 3-week-old ducklings in Québec including whole genome sequence of the virus. Can Vet J. 2019 Dec;60(12):1285-1288. PMID: 31814632.


Our customers’ publications


Hassan MSH, Ojkic D, Coffin CS, Cork SC, van der Meer F, Abdul-Careem MF. Delmarva (DMV/1639) Infectious Bronchitis Virus (IBV) Variants Isolated in Eastern Canada Show Evidence of Recombination. Viruses. 2019 Nov 13;11(11). PMID: 31766215

Whole genome sequencing by HTS offered at a promotional price of 240$ for a limited time.

Contact us for more details.

Sample type:

The VHTSL has developed expertise in sequencing a wide variety of samples, such as:

  • Identification, sequencing of the entire genome of pathogens from clinical samples (feces, tissues, serum, etc.)
  • Isolated / purified viruses
  • Isolated bacterial strains
  • RNA
  • DNA
  • cDNA
  • AmpliSeq samples
  • Fixed or waxed samples
  • Other

It is important to note that the microbial load and the type of sample will greatly affect the quality of the sequencing. For more information, please contact our laboratory.


Sequencing of complete viral genomes

  • Swine influenza virus
  • Porcine reproductive and respiratory syndrome virus (PRRSV; arterivirus)
  • Avian poxvirus
  • Avian reovirus
  • Avian infectious bronchitis virus (IBV; coronavirus)
  • Avian infectious laryngotracheitis virus (ILTV; herpesvirus)
  • Swine epidemic diarrhea virus (PEDV; coronavirus)
  • Bacteriophages
  • Avian adenovirus
  • Turkey hemorrhagic enteritis virus (HEV; adenovirus)
  • Pig rotavirus
  • Viral strains of vaccine origin
  • Bovine viral diarrhea virus (BVDV; pestivirus)
  • Sapelovirus
  • Astrovirus
  • Porcine Hemagglutinating Encephalomyelitis Virus (PHEV; coronavirus)


Sequencing of whole bacterial genomes

  • Streptococcus suis
  • Streptococcus equis
  • Salmonella enterica
  • Actinobacillus suis
  • Brachyspira hyodysenteriae
  • Bordetella bronchiseptica
  • Escherichia coli
  • Photobacterium
  • Staphylococcus hyicus
  • Staphylococcus aureus
  • Mycoplasma gallisepticum
  • Mycoplasma hemotropic



  • RNASeq of porcine cells coinfected with PRRSV and swine influenza virus
  • Metagenomics of many samples