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A little over two weeks ago, in Brazil: Paraná Health Reports Novel H1N2 Flu Case, we looked at a report from Paraná's Secretary of Health on the 2nd detection of a novel H1N2 flu virus in a human in that southern Brazilian state in 2020 (see last July's WHO: Influenza A(H1N2) variant virus – Brazil).
Last summer's case was identified as a swine-origin variant virus, while phylogenetic characterization of this latest virus was still pending.
While most swine variant infections don't appear to transmit well in humans, the CDC's IRAT (Influenza Risk Assessment Tool) lists 3 North American swine viruses as having at least some pandemic potential (2 added in 2019).
H1N2 variant [A/California/62/2018] Jul 2019 5.8 5.7 ModerateH3N2 variant [A/Ohio/13/2017] Jul 2019 6.6 5.8 ModerateH3N2 variant [A/Indiana/08/2011] Dec 2012 6.0 4.5 Moderate
Surveillance and reporting on novel swine variant viruses is notoriously sparse around the world, but there are a number of other swine-origin influenza viruses of concern. Last summer China's EA H1N1 `G4' virus received a lot of attention (see The CDC's Responds to the PNAS EA H1N1 `G4' Swine Flu Study), as have other swine viruses around the globe.
A little over 5 years ago, in EID Journal: Influenza A Viruses of Human Origin in Swine, Brazil, we looked at the rising threat of swine variant viruses in South America. A year later, in EID Journal: Characterization of a Novel Human Influenza A(H1N2) Virus Variant, Brazil, we looked at a report of a swine-variant H1N2v virus virus isolated - once again from Paraná state - in a teenage pig farmer late in 2015.
Overnight the WHO published an overview and risk analysis of this most recent (and 3rd) novel human infection from Paraná state, Brazil.
Some excerpts from this lengthy report, then I'll return with a postscript.
Influenza A(H1N2) variant virus – Brazil
Disease Outbreak News
4 January 2021
On 15 December 2020, the Brazil Ministry of Health reported the second confirmed human infection with influenza A(H1N2) variant virus [A(H1N2)v] in Brazil in 2020. The case was a 4 year-old female who lives on a farm which also functions as a swine slaughter in Irati municipality, Paraná state. On 16 November 2020, the case had illness onset with a fever, cough, coryza, headache and dyspnea, and was provided ambulatory care on the same day at Darcy Vargas Hospital. He was treated with medication for fever and headache and has recovered. No symptomatic contacts were found among the case’s family.
On 18 and 19 November, respiratory samples were collected for testing. The Parana State Laboratory detected an unsubtypeable influenza A virus and the samples were sent to the Oswaldo Cruz Institute (Fiocruz), the National Influenza Centre (NIC) in Rio de Janeiro for complete viral genome sequencing, where influenza A(H1N2)v virus was confirmed on 14 December.
The A(H1N2)v virus is genetically different from other variant viruses previously detected in humans in Brazil in 2015 and in April 2020, based on preliminary genetic analysis conducted by Fiocruz NIC. The preliminary analysis shows that all genes are most similar to those from currently circulating influenza A(H1N1)pdm09 viruses, except for neuraminidase which is most similar to those from influenza A(H3N2) viruses. Further characterization of the virus is underway. All influenza type A viruses detected by sentinel surveillance and viruses submitted from non-sentinel sites (hospital and peripheral laboratories) in Brazil are subtyped by properties of hemagglutinin (H) and neuraminidase (N) surface proteins. To date, no other human infections with variant viruses have been reported in Brazil.
This case is the third human infection of influenza A(H1N2)v virus reported in Parana state and in Brazil. The first case was detected in 2015 and the second in April 2020. These two confirmed cases lived in rural areas with pig farming and one case worked in a pig slaughterhouse.
Public health response
Local authorities carried out epidemiological and veterinary investigations to obtain more information about possible exposure, potential suspected cases, clinical features and evolution of the case among other epidemiological, virological and clinical information. While investigations are ongoing, local authorities enhanced laboratory surveillance and subtyping of influenza samples in Irati municipality where the case was reported.
WHO risk assessment
There has been some limited, non-sustained human-to-human transmission of variant influenza viruses, although ongoing community transmission has not been identified. Current evidence suggests that these viruses have not acquired the ability of sustained transmission among humans. The risk assessment will be reviewed if needed should further epidemiological or virological information become available.
Swine influenza viruses circulate in swine populations in many regions of the world. Depending on the geographic location, genetic characteristics of these viruses vary. When an influenza virus that normally circulates in swine (but not people) is detected in a person, it is called a “variant influenza virus”. Most human cases are the result of exposure to swine influenza viruses through contact with infected swine or in some cases, contaminated environments. Further human cases can be expected because these viruses continue to be detected in swine populations around the world.
Influenza viruses which infect swine may be different from human influenza viruses. Thus, influenza vaccines against human influenza viruses are generally not expected to protect people from influenza viruses that normally circulate in pigs. In addition, pigs are susceptible to avian, human and swine influenza viruses; they potentially may be infected with influenza viruses from different species at the same time. If this happens, it is possible for the genes of these viruses to mix and create a new virus.
This type of major change in the influenza A viruses is known as antigenic shift. If this new virus causes illness in people and can be transmitted easily from person-to-person, an influenza pandemic can occur.
Due to the constantly evolving nature of influenza viruses, WHO continues to stress the importance of global surveillance to detect virological, epidemiological and clinical changes associated with circulating influenza viruses that may affect human or animal health and timely virus sharing for risk assessment.
All human infections caused by a novel influenza subtype are notifiable under the International Health Regulations [IHR (2005)] and State Parties to the IHR (2005) are required to immediately notify WHO of any laboratory-confirmed case of a recent human infection caused by an influenza A virus with the potential to cause a pandemic. Evidence of illness is not required for this report.
Just over two months ago, Alberta Canada Reported a Rare Case of H1N2v `Swine' Flu, as did the Netherlands in September (see WHO Novel Flu Summary & Risk Assessment - December 2020). Over the summer, the United States reported a different swine variant (see CDC FluView: Novel A/H3N2v Case Reported In Hawaii).
Despite these recent reports, the number of novel swine-variant viruses reported in 2020 is down overall, although that could be due to a lack of influenza surveillance and reporting during the COVID-19 pandemic and the closure of public venues that bring pigs and humans together (i.e. Stare Fairs, Agricultural exhibits, etc).
In September we looked at an FAO/OIE/WHO Tripartite Statement on the Pandemic Risk of Swine Influenza, where all parties advised:
It is important that new and updated swine influenza surveillance data collected by countries are rapidly analysed and risk-assessed on a global scale to enable tracking how endemic and novel viruses are spreading.
Sadly, that doesn't happen nearly as often as it should.
H1, H2, and H3 swine-origin flu viruses are not considered `reportable animal diseases' to the OIE - much like many avian flu viruses (H9N2, H6N1, H3N1, H10N8) - and even though they may pose some risk of human infection, are poorly tracked.All of which means the next swine-origin or avian influenza pandemic could be brewing unnoticed just about anywhere in the world - and like we saw in 2009 - our only clue will come when large numbers of sick people start showing up at hospitals.
