Tuesday, September 16, 2014

USDA IAV-S Surveillance Program Detects Novel H3N1 In US Swine




# 9081


While Ebola and MERS have had the bulk of our attention recently, high up on our perennial list of concerns are the non-human influenza viruses that circulate in birds, pigs, horses and even dogs that – with a little evolutionary help – could make the jump to mankind.  


The 2009 H1N1 virus was one such virus that had bounced around swine farms for years before it jumped species and sparked a pandemic.


Over the past several years we’ve been watching several swine variant influenza viruses – H3N2v, H1N1v, H1N2v – making tentative jumps into the human population (see Keeping Our Eyes On The Prize Pig) and each summer the CDC issues advice on preventing infection at county and state fairs (see Measures to Minimize Influenza Transmission at Swine Exhibitions, 2014).


Today, thanks to a report in the National Hog Farmer (picked up by ProMed Mail) we’ve learned of new version of an older swine flu virus – H3N1 – that has recently been detected in at least two states. 


While swine H3N1 has been known to circulate in pigs for nearly a decade (see EID Journal 2006 article Novel Swine Influenza Virus Subtype H3N1, United States) this latest variant, which has been reported on several occasions since December 2013, differs in that it has picked up the human seasonal H3 HA protein.


First the email sent out from the USDA to all SIV (swine influenza virus) approved NAHLN (National Animal Health Laboratory Network) labs published by the National Hog Farmer, then I’ll be back with a bit more.


H3N1 Identified in Swine in Two States

Sep 11, 2014 Source: USDA Animal and Plant Health Inspection Service, Veterinary Services

The U.S. Department of Agriculture IAV-S surveillance program has identified several H3N1s in U.S. swine in at least two states since December 2013. Although this is not the first time H3N1s have been detected in swine in the United States, it is a rare occurrence and needs further examination.

More importantly, two of these H3N1s carry a novel human seasonal HA gene from contemporary human viruses and are distinct from our current swine H3 viruses.

A review of Genbank data indicates there may be more human-like H3 genes (in either H3N1 or H3N2) circulating in U.S. swine subtypes than what the USDA surveillance data has captured. Potential spread of H3N1 or H3N2 that carries the human-like H3 could have significant impact in swine herds due to poor herd immunity as well as potential public health ramifications. Preliminary findings by the USDA-ARS from testing of one of these H3N1 isolates with the human-like H3 gene in swine indicate the virus is fully virulent, causing typical influenza disease.

We are sharing this information to alert producers, veterinarians, and National Animal Health Laboratory Network labs of this occurrence. The surveillance program for IAV-S in swine was established to:

  • Monitor the genetic evolution of endemic IAV-S to better understand endemic and emerging influenza virus ecology,
  • Make IAV-S isolates and associated epidemiologic data available for research and analysis, and
  • Select proper isolates for the development of relevant diagnostic reagents, updating diagnostic assays, and vaccine seed stock products in swine.

The identification of this new human-like H3 in swine subtypes is a key example of how IAV-S surveillance can benefit swine health.

It is anticipated that additional information about swine subtypes carrying the human-like H3 will be captured through the surveillance system to assist in determining how wide-spread the virus is and whether additional actions may be needed by veterinarians, producers and vaccine manufacturers.

The USDA’s surveillance program for influenza A in Swine (IAV-S) began in 2009 with the intent of monitoring the 2009 H1N1 pandemic virus in swine. Since that time their surveillance efforts have broadened to include monitoring all types of influenza circulating in pigs, with the primary goal of tracking the evolution of these viruses.

Since participation is voluntary, and many swine farmers remain reluctant to have their herds tested after the financial beating the industry took in 2009, there are some limitations to this type of surveillance.


The following report shows that of the three major swine strains tracked, H1N1, H1N2 & H3N2 incidence has far overshadowed H3N1.


USDA Update on Surveillance for Influenza A Virus in Swine


USDA IAV-Surveillance

The following IAV-S surveillance summary data covers data received as of July 1, 2014 and spans November 2009 to June 2014. Note that there can be a monthly time lag in data submission and sequence deposits into GenBank.

Total samples submitted: 61,060 (99.3% from sick pig submissions to diagnostic laboratories)

Accessions submitted: 14,899
Number of positive accessions 5,517
Accessions subtyped 3,633
Accessions with viral isolates 3,100
Number of samples sequenced 2,455
to GenBank


While humans have a long history of exposure to seasonal H3N2 flu viruses, research has shown only limited community immunity to earlier swine variant strains (see CIDRAP: Children & Middle-Aged Most Susceptible To H3N2v). 


It is far to early to know when, or even if, this novel H3N1 will present a significant human disease threat. But with county and State fair season going into high gear, public health officials will no doubt be keeping a close watch to see if any clusters of influenza are reported associated with fair attendance.


Swine are highly susceptible to a variety of flu viruses (human, swine, avian) - and are viewed as excellent `mixing vessels’, allowing viruses to reassort into new hybrid strains, a topic well covered by Helen Branswell a few years ago in a SciAm article called called Flu Factories.

Reassortant pig[6]


Some of my earlier blogs on swine variant influenza include: H3N2v: When Pigs Flu , You Say You Want An Evolution? & The (Swine) Influenza Reassortment Puzzle while last July we looked at J. Virol: Continued Reassortment Of Swine Flu Viruses With Genes From pH1N1 In China


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