Influenza Virus Sequencing

Service type
Molecular Diagnostics/PCR
Species
Avian,
Porcine
Fee
$154.96
Days tested
Wednesdays (samples should arrive at least 24 hours before). In most cases, samples need to be in the lab by noon the day before the scheduled test for processing and preparation.
Turnaround time
2-4 weeks
Specimen Requirements

1) Nasal swabs 2) Viral isolate (at least 0.5 ml) 3) lung (2-3 cm3 or biopsy) 4) Oral Fluids/saliva (at least 2 ml)

Shipping container
1) Synthetic swab 2) Leakproof 1.5 ml microfuge tube 3,4) WHIRL-PAK or plastic bag
Coolant
1,3,4) Frozen gel packs 2) Dry ice
Location Term
St. Paul (VDL)
Submission Form(s)
Swine health test chart
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Best Practice
Nasal/Laryngeal/Bronchial swabs
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Oral fluid
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Tissue/Necropsy
Description

Note:A detection PCR will be performed first and charged to the client on all external samples submitted.

Nasal swabs must come with a copy of a USDA shipping permit.
Lung should be sent next day delivery.
Oral Fluids/Saliva: Do not pool group/pen samples.
When sequencing is requested and a particular sample or number of samples to sequence isn't specified, the lab will default to sequencing the one sample with the lowest ct value (the lowest ct value represents the sample with the most virus or bacteria).
Following the guidelines listed under the Submitted Specimen Requirements will provide an adequate sample volume to conduct this test. If multiple tests are to be requested on a specimen, there may not be adequate sample volume to perform each test. Please submit an adequate sample volume to meet the requirements of each test.
H1 clades are determined using the Swine H1 Clade Classification available from the NIAID Influenza Research Database (IRD) [Zhang Y, et al. (2017)] through the web site at https://www.fludb.org/brc/home.spg?decorator=influenza. For more information on H1 clade information and methodology, please refer to "A Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses." Tavis K. Anderson, Catherine A. Macken, et.al, mSphere Dec 2016, 1 (6) e00275-16; DOI: 10.1128/mSphere.00275-16.
H3 clades are determined using a public data set of Swine H3 Clade Classification reference strains and the BLASTN 2.2.22 tool available from the NIAID Influenza Research Database (IRD) [Zhang Y, et al. (2017)] through the website at https://www.fludb.org/brc/home.spg?decorator=influenza. For more information regarding Swine H3 clade classifications, please refer to "Sequences used in swine H3 clade classification reference tree." Tavis K. Anderson, Catherine A. Macken, et. al. Virus Pathogen Database and Analysis Resource (ViPR) -. N.p., 03 Nov. 2016. Web. 21 Feb. 2017.
For a review of influenza in pigs in the USA, read this lay publication on this website:

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