Tuesday, August 21, 2018

Transbound Emerg Dis: H5N2, H1N2 & Other Reassortants In Mexican Swine


While we know that swine-origin influenza viruses (particularly H1, H2, and H3 subtypes) are endemic in pigs around the world - outside of the United States, Canada, and sometimes China and Europe - we only rarely see surveillance for, and the characterization of, circulating subtypes.
In 2009, a swine-origin reassorted H1N1 virus - one that had been circulating almost unnoticed in North American pigs for a decade or more - jumped to humans (possibly first in Mexico) and sparked the first pandemic in over 40 years. 
Pigs are susceptible to - and are able to support reassortment of - a wide range of influenza viruses (swine-origin, human & avian), and so the potential for seeing this happen again is not inconsequential.
Since the most common swine flu viruses (H1, H2 & H3) are similar to those that have caused all of the human pandemics going back 130 years (see Are Influenza Pandemic Viruses Members Of An Exclusive Club?), we pay close attention whenever a swine flu virus manages to jump to humans (see last Friday's  CDC FluView: An Additional Four Cases Of H1N2v Reported Across 3 States (CA, MI, OH)).
But increasingly we're seeing reports of other subtypes - primarily of avian origin - circulating in pigs.  Some recent blogs include:

Sci. Repts.: Characterization Of Avian Influenza Virus Attachment Patterns To Human & Pig Tissues
Virology: Detection & Characterization Of Avian H4N6 In Midwestern Swine (2015)
Emerg. Infect. & Microbes: Novel Triple-Reassortant influenza Viruses In Pigs, Guangxi, China
During the 2014-2015 clade HPAI H5 epizootic in North America, concerns were raised over the possibility that H5N2 or H5N8 could enter the swine population (see H5N2: The Other Biosecurity Concern).

While some officials were quick to dismiss these concerns, the University of Minnesota’s Swine Disease Eradication Center offered a slightly less sanguine assessment, writing:
To date, there is no evidence that the new strains of HPAI (H5N2 or H5N8 subtypes) have infected pigs in the US. However, producers should be diligent about their biosecurity practices. Avian influenza viruses are highly contagious, extremely variable and wide-spread in birds. Preventing introduction of birds into swine facilities, avoiding contact with wild birds and bird droppings in general, and avoiding non-chlorinated surface water should be emphasized.
Since then, we've seen scattered reports of H5 viruses showing up in pigs around the globe including:
Arch. Virology: Isolation & Characterization Of H5N1 In Swine - China 2015

Sci. Rpts.: Evidence Of H5N1 Exposure In Domestic Pigs - Nigeria

Indonesian Media: An Unusual Report Of H5N1 in Pigs

And during the height of the 2016-2017 HPAI H5N8 epizootic in Europe, we saw the UK's DEFRA Caution Pig Farmers Over Avian Flu.

While the most obvious concern is that an avian H5 virus co-circulating in pigs alongside more `humanized' viruses might pick up - via reassortment - the ability to spread more easily as a pandemic virus, the opposite is also possible; that a swine-origin H1N1, H1N2, or H3N2 virus might pick up increased virulence by  acquiring internal genes from an avian flu virus. 
The only thing that is certain is that the more influenza subtypes co-circulating in pigs, the more reassortment combinations that are possible.  How many would be viable, or a human health threat, is unknown.
All of which leads up to a brief report - which is currently in press, meaning we only have the abstract available - which identifies and characterizes a number of novel flu viruses circulating in Mexican swine; including at least two H5N2 viruses.
Although some of the findings above involved HPAI H5 viruses, Mexico has a long history of LPAI (low pathogenic) H5N2 outbreaks going back more than 20 years (1994). The abstract provided below doesn't tell us anything about the clade, lineage or pathogenicity of the H5N2 virus these researchers isolated. 
Presumably, when the full paper is published, we'll learn more.

Identification and genomic characterization of influenza viruses with different origin in Mexican pigs

Manuel Saavedra‐Montañez, Luis Vacam, Humberto Ramírez‐Mendoza, Carmen Gaitán‐Peredo, Rebeca Bautista‐Martínez, Rene Segura‐Velázquez …  

First published: 20 August 2018

This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1111/tbed.12998


Swine influenza is a worldwide disease, which causes damage to the respiratory system of pigs. The H1N1 and H3N2 subtypes circulate mainly in the swine population of Mexico. There is evidence that new subtypes of influenza virus have evolved genetically and have been rearranged with human viruses and from other species; therefore, the aim of our study was to identify and characterize the genetic changes that have been generated in the different subtypes of the swine influenza virus in Mexican pigs.
By sequencing and analyzing phylogenetically the eight segments that form the virus genome, the following subtypes were identified: H1N1, H3N2, H1N2 and H5N2; of which, a H1N1 subtype had a high genetic relationship with the human influenza virus.
In addition, a H1N2 subtype related to the porcine H1N2 virus reported in the United States was identified, as well as, two other viruses of avian origin from the H5N2 subtype.
Particularly for the H5N2 subtype, this is the first time that its presence has been reported in Mexican pigs. The analysis of these sequences demonstrates that in the swine population of Mexico, circulate viruses that have suffered punctual‐specific mutations and rearrangements of their proteins with different subtypes, which have successfully adapted to the Mexican swine population.