Sunday, December 04, 2016

EID Journal: Characterization of a Novel Human Influenza A(H1N2) Virus Variant, Brazil


Although it is rarely remembered footnote today, between 2000 and 2003 we saw a brief introduction of a human H1N2 virus - a reassortment between seasonal H1N1 and H3N2 - that was widely reported across much of the Northern Hemisphere. 
While only sporadically reported in most regions, H1N2 was the predominant Influenza A(H1) virus reported during the UK's 2001–02 influenza season (cite).

From a 2014 EID Journal article -  A Historical Perspective of Influenza A(H1N2) Virus - we learn that the virus vanished in early 2003, as suddenly as it arrived:
By early 2003, A(H1N2) viruses were no longer being isolated from human samples. In 2006, an A(H1N2) virus that was a triple reassortant-like virus and, with the exception of the matrix gene, genetically similar to A(H1N2)pdm09 viruses, was isolated from swine in China (41).
In late 2009, a novel A(H1N2) virus was isolated from a human in India (5). This H1N2 virus was a reassortant of A(H1N1)pdm09 and A(H3N2) viruses co-circulating in the population. Although this virus had a similar genetic makeup to previously observed A(H1N2) viruses, the source of the HA component differed and was derived from the A(H1N1)pdm09 virus (5).

These were predominantly human-origin H1N2 viruses, not to be confused with the swine-origin variant H1N2 viruses that have circulated in pigs for decades and that we've seen occasionally jump to humans.

Over the past 10 years we've seen nearly 400 human infections with swine variant viruses in the United States, with the H3N2v strain the most common, making up 94% of all reported cases (n=372) and  H1N1v coming in 2nd, with 20 cases (4%).
Least common, with just 9 reported cases, has been H1N2v, with the most recent reported just over a week ago (see CDC FluView Week 46: 1 Novel H1N2v Infection In Iowa).

Increasingly we are seeing a mixture of classical swine influenza A viruses with human influenza A viruses, such as in last October's MMWR: Investigation Into H3N2v Outbreak In Ohio & Michigan - Summer 2016, which found 16 of the 18 cases H3N2v cases reported last August to belong to a new genotype not previously detected in humans. They wrote:
Whereas these viruses contained seven gene segments similar to segments detected in previously reported variant virus outbreaks, one gene segment coding for an influenza A(H3) hemagglutinin (HA) gene was determined to be similar to HA genes found in human seasonal influenza A(H3N2) viruses from 2010 and 2011.
This HA gene was likely introduced from humans into swine in 2010 or 2011, and has since circulated and evolved in swine to be genetically and antigenically different from both previous and currently circulating human seasonal influenza A(H3N2) viruses (3).

Only a few months before, in Front. Microbiol.: A Novel H1N2 Reassorted Influenza Virus In Chinese Pigs, we saw another swine-human flu reassortment  `containing genes from classical swine (PB2, PB1, HA, NP, and NS genes), triple-reassortant swine (PA and M genes) and recent human (NA gene) lineages'.

And just a day prior to that, we looked at EID Journal: Influenza A Viruses of Human Origin in Swine, Brazil, which found multiple strains of human H1N2 and H3N2 viruses had been circulating in Brazilian swine for a decade or longer.

All of which serves as prelude to a letter - published in the EID Journal - which describes a novel variant H1N2v virus isolated from a Brazilian teenage pig farmer late in 2015.

One that turns out to be a triple reassortant with genetic contributions from H1N2 (hemagglutinin), H3N2 (neuraminidase), and pandemic H1N1 (remaining genes).

I've only included the abstract, and some excerpts from the discussion, so you'll want to follow the link to read it in its entirety.

Paola Cristina Resende
 , Priscila Silva Born, Aline Rocha Matos, Fernando Couto Motta, Braulia Costa Caetano, Maria do Carmo Debur, Irina Nastassja Riediger, David Brown, and Marilda M. Siqueira

Volume 23, Number 1—January 2017



We report the characterization of a novel reassortant influenza A(H1N2) virus not previously reported in humans. Recovered from a a pig farm worker in southeast Brazil who had influenza-like illness, this virus is a triple reassortant containing gene segments from subtypes H1N2 (hemagglutinin), H3N2 (neuraminidase), and pandemic H1N1 (remaining genes).


This virus was identified from a nasopharyngeal aspirate collected on November 26, 2015, from a 16-year-old girl from a rural area in Castro City, ParanĂ¡, in the southern region of Brazil. Castro has ≈67,000 inhabitants and is a major livestock hub for dairy cattle, poultry, and pigs. The patient did not present any risk factors for influenza but showed development of an influenza-like illness with an onset of symptoms (fever, cough, sore throat, chest pain, and myalgia) on November 23, 2015. The follow-up local investigation reported that she had been working at a swine farm and confirmed direct patient contact with pigs. She had not received a prior influenza vaccine or antiviral treatment, and her clinical recovery was uneventful.  


To date, no further H1N2 subtype human cases have been detected in Brazil; however, influenza virus strains from this region and period are under investigation to confirm whether more H1N2v subtype cases may have occurred. This report highlights the need for influenza surveillance in humans and animals, as well as in their interface, especially during influenza season when transmission is high. To ensure early detection, surveillance should focus on geographic areas when influenza A viruses subtypes co-circulate and where human–animal contact is frequent.

Dr. Resende is a postdoctoral researcher at the Laboratory of Respiratory Viruses at Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil, National Influenza Center for the World Health Organization. Her research interests are reconstructing the phylogenetic profile of influenza viruses and on identifying genomic viral polymorphisms associated with an increase in virulence and antiviral drug resistance.
Unlike with avian flu - which prompts high profile containment and culling efforts whenever it is found in livestock - swine influenza is a relatively mild (and highly endemic) virus in pigs.
One that goes largely ignored around the world.

But, as the 2009 H1N1 Swine-origin pandemic proved, we ignore these viruses and their continual evolution at our peril.