Tuesday, June 23, 2015

EID Journal: Influenza A Viruses of Human Origin in Swine, Brazil


The swine-human-swine flu cycle


# 10,252


Just over 6 years ago (June 11th, 2009) the World Health Organization declared the start of the first influenza pandemic in 40 years – due to an H1N1 virus that spread stealthily among North American swine herds for at least a decade before jumping to humans.


While the potential for swine to serve as influenza `mixing vessels’  had long been noted, 2009 was an unexpected live demonstration

Despite their known carriage of a variety of flu strains, routine surveillance of swine influenza strains remains rare around the world. Limited testing is done in the United States, in Hong Kong, and in Europe . . . but for the most part, we don’t have a very good idea of the state of swine influenza around the world.


While the most obvious concern is that a swine virus could jump to humans – viruses travel a two-way street.  Human viruses very often jump to pigs - and once introduced into the swine population - these viruses have an opportunity to meet up with, and reassort with, other flu strains.

Reassortant pig[6]


Here in North America we’ve been watching the evolution of several swine variant viruses (H1N1v, H1N2v, H3N2v) over the past few years, all of which have reassorted with - and picked up the M gene segment from – the 2009 H1N1 virus (see FluView Week 17: Fatal Swine Variant (H1N1v) Case In Ohio). 


We’ve also seen similar reassortant viruses emerge in other parts of the world (see J. Virol: Continued Reassortment Of Swine Flu Viruses With Genes From pH1N1 In China).


While most reassortant viruses are evolutionary failures, the concern is that over time another swine variant virus might emerge – as did the 2009 H1N1 virus – and start another human epidemic or pandemic.


As global pig production grows – particularly in places where biosecurity and surveillance may be lax – it creates increasing opportunities for a new, biologically `fit’  swine variant virus to emerge.  As you can see by the chart below, swine production is growing fastest in developing countries, where biosecurity is likely to be the least stringent.


Source: FAO

Brazil is one of the largest swine producers in the world, but until 2009, influenza was not believed endemic in their swine population.  Primarily because the strains circulating there produced few clinical symptoms.  That  all changed when the 2009 H1N1 virus jumped from humans to pigs and reassorted with existing swine strains in Brazil.

This from the EID Journal:.


Volume 21, Number 8—August 2015

Influenza A Viruses of Human Origin in Swine, Brazil

Martha I. Nelson1Comments to Author , Rejane Schaefer1, Danielle Gava, Maurício Egídio Cantão, and Janice Reis Ciacci-Zanella


The evolutionary origins of the influenza A(H1N1)pdm09 virus that caused the first outbreak of the 2009 pandemic in Mexico remain unclear, highlighting the lack of swine surveillance in Latin American countries. Although Brazil has one of the largest swine populations in the world, influenza was not thought to be endemic in Brazil’s swine until the major outbreaks of influenza A(H1N1)pdm09 in 2009.

Through phylogenetic analysis of whole-genome sequences of influenza viruses of the H1N1, H1N2, and H3N2 subtypes collected in swine in Brazil during 2009–2012, we identified multiple previously uncharacterized influenza viruses of human seasonal H1N2 and H3N2 virus origin that have circulated undetected in swine for more than a decade. Viral diversity has further increased in Brazil through reassortment between co-circulating viruses, including A(H1N1)pdm09. The circulation of multiple divergent hemagglutinin lineages challenges the design of effective cross-protective vaccines and highlights the need for additional surveillance.



Our recently initiated influenza virus surveillance in Brazil uncovered multiple new lineages of swIAVs that are related to seasonal influenza viruses that circulated in humans more than a decade ago. These swIAVs have not been detected in any other country, including the well-sampled swine populations of the United States, although surveillance for swIAVs is infrequent or lacking altogether in neighboring Latin America countries. Therefore, the possibility that these swIAVs have circulated, or even originated, in other Latin America countries that do not routinely conduct surveillance in swine cannot be excluded.

At this time, however, the most parsimonious explanation based on the data available is that human seasonal viruses were introduced at least 3 times into swine in Brazil: H3N2 viruses were introduced twice into swine during the late 1990s, and a human seasonal H1N2 virus was introduced during the early 2000s. Viral segments from all 3 introductions have persisted in swine at least until 2011, the most recent date of sample collection. However, the internal gene segments were replaced in the intervening years by reassortment with pH1N1 viruses transmitted from humans to swine in Brazil multiple times since 2009.

These findings highlight the importance of human-to-swine transmission in the evolution of swIAV diversity in Brazil. The detection of multiple influenza viruses of human seasonal and pandemic origin circulating within Brazil’s large swine herds is entirely consistent with the frequency of human-to-swine transmission that recently has been highlighted on a global scale for seasonal (35) and for pandemic (40) influenza viruses. The swIAVs of human seasonal and pandemic origin also have been identified in Argentina in recent years (17,22). Our findings also match the globally observed pattern that new HA and NA segments of human seasonal virus origin persist at higher rates than the internal genes, which frequently are replaced through reassortment by circulating swine viruses, particularly pH1N1 (35).

(Continue . . . )


The entire report is well worth reading, as it illustrates major gaps in our understanding and surveillance of influenza viruses around the world.  The intermixing of human and swine flu strains in Brazil is also likely happening out of our view in places like China, the Russian Federation, Vietnam and much of the rest of the world


Although avian flu rightfully has the bulk of our attention right now  - much as it did between 2004-2009, until a swine-origin pandemic virus emerged unannounced out of left field -  this is a reminder that birds are not the only  host species from which a novel flu could emerge.  


While pigs are the second most likely source for a new flu to emerge,  for more on some of the other influenza hosts we keep an eye on, you might wish to revisit:


Eurosurveillance: Avian H10N7 Influenza In Harbor Seals
Canine H3N2 Reassortant With pH1N1 Matrix Gene
Study: Dogs As Potential `Mixing Vessels’ For Influenza
EID Journal: Equine H3N8 In Mongolian Bactrian Camel