Variant Viruses detected between 2020-2023
#18,520
While avian influenza currently has most of our attention, over the past 15 years we've seen more than 500 novel swine flu infections reported in the United States, and scores of others around the globe.
We know the 2009 H1N1 pandemic virus emerged from swine in Mexico following a quadruple reassortment of genes from human, avian, and swine influenza viruses.
Of the CDC's IRAT (Influenza Risk Assessment Tool) list of 25 zoonotic influenza A viruses with pandemic potential, 4 are swine variant viruses and the virus with the highest emergence & impact score is a Swine Variant H1N1 from China.
Preprint: Rapid Surge of Reassortant A(H1N1) Influenza Viruses in Danish Swine and their Zoonotic Potential
Review Article - Influenza A Viruses in the Swine Population: Ecology and Geographical Distribution
CDC FluView Week #37: 2 Additional Novel Flu Infections (H3N2v) in Minnesota
WHO: Influenza A(H1N1) Variant Virus - Viet Nam
Nature Comms: Potential Pandemic Risk of Circulating Swine H1N2 Influenza Viruses
One of the hotspots for swine variant influenza has been Brazil, which is the 4th largest producer of pork in the world.
Last February, in WHO Update & Risk Assessment: H1N1v Case In Brazil, we looked at the 9th known case of a human infection with a swine variant virus reported in the state of Paraná, Brazil, since 2015.
Influenza A (H1N1) variant virus - Brazil
7 February 2024
Situation at a Glance
On 16 January 2024, Brazil notified the World Health Organization (WHO) of a laboratory-confirmed human infection with swine-origin influenza A(H1N1) variant (v) virus, in the municipality of Toledo, State of Paraná. The patient, who had underlying medical conditions, developed symptoms and was hospitalized on 16 December 2023. He had no history of exposure to pigs and has fully recovered. From the epidemiological investigation, no close contacts were identified. This is the first human infection caused by an influenza A(H1N1)v virus reported in Brazil in 2024, and the ninth case of a human infection with a swine variant virus reported in the state of Paraná, Brazil, since 2015.
While most swine variant infections are generally mild or moderate, and are seen in people with occupational contact with pigs, that isn't always the case.
Over the summer of 2023 we looked at a fatal infection in a 42-year-old woman (see WHO Risk Assessment) - also from Paraná, Brazil - with underlying medical conditions who lived near a swine farm, but who did not have any direct contact with pigs.
Other reports from that same region include (WHO: Overview & Risk Assessment On Novel H1N2v Virus Detected In Paraná, Brazil (Dec. 2020) and EID Journal: Influenza A Viruses of Human Origin in Swine, Brazil).
All of which brings us to a new article which looks at the diverse array of swine variant viruses reported from Paraná, Brazil between 2020 and 2023. This is a highly detailed review, so I've only posted some of the highlights below.
Follow the link to read it in its entirety. I'll have a brief postscript after the break.
Zoonotic transmission of novel Influenza A variant viruses detected in Brazil during 2020 to 2023
Paola Cristina Resende, Dennis M. Junqueira, Caroline Tochetto, Maria Ogrzewalska, Fernando C. Motta, Jonathan Lopes, Luciana Appolinario, Larissa Macedo, Braulia Caetano, Aline Matos, Thauane Silva, Elisa Cavalcante Pereira, Leticia Ferreira Lima, Irina Riediger, Maria do Carmo Debur, Guilherme Nardi Becker, Aline Andrade, Acácia Maria Lourenço Francisco Nasr, Rosana Aparecida Piler, Ana Carolina Dalla Vecchia, Walquíria Almeida, David Brown, Rejane Schaefer & Marilda M. Siqueira
Nature Communications volume 15, Article number: 10748 (2024) Cite this article
Abstract
Zoonotic infections (swine-human) caused by influenza A viruses (IAVs) have been reported and linked to close contact between these species. Here, we describe eight human IAV variant infections (6 mild and 2 severe cases, including 1 death) detected in Paraná, Brazil, during 2020–2023.
Genomes recovered were closely related to Brazilian swIAVs of three major lineages (1 A.3.3.2/pdm09, 1B/human-like, and H3.1990.5), including three H1N1v, two H1N2v, two H3N2v and one H1v. Five H1v were closely related to pdm09 lineage, one H1v (H1N2v) grouped within 1B.2.3 clade, and the two H3v grouped within a clade composed exclusively of Brazilian H3 swIAV (clade H3.1990.5.1). Internal gene segments were closely related to H1N1pdm09 isolated from pigs.
IAV variant rarely result in sustained transmission between people, however the potential to develop such ability is of concern and must not be underestimated. This study brings into focus the need for continuous influenza surveillance and timely risk assessment.
(SNIP)
Influenza A viruses can be regularly transmitted from humans to swine15. The viruses can adapt to the swine host, evolve over time, and might then be reintroduced to humans as novel reassortant viruses.
The eight influenza variant viruses described here were first detected by LACEN and sent for sequencing at the NIC, that is responsible for characterizing strains for which regional laboratories detect either influenza A or B viruses but are not able to identify the viruses to the subtype or lineage level.
With few exceptions, the gene segments of all variant viruses grouped within swine clades, exhibiting a full-genome of swine-origin. In a few cases, some gene segments were closely related to human viruses (for instance, the HA of case 3); however, the intensive surveillance of human influenza along with the long branch observed in the phylogenetic tree suggest the absence of swine sequences rather than unsampled human viruses.
(SNIP)
The comparison of the current seasonal influenza vaccine strains, H1N1 and H3N2 components, recommended for the Southern Hemisphere31 with the variants reported in this study revealed a significant genetic distance from the current vaccine, consistent with the phylogenetic analysis. The genetic data observed may indicate antigenic mismatch and a potential lack of immune protection against the IAV variants.
Increased surveillance of swine and human viruses in this region of Paraná could potentially contribute to the solution of this issue and even help control the spread of these virus strains. Besides, vaccination of pigs in Brazil may be perhaps the easiest way to control and block new infections in humans, since cartography data indicates that no vaccine recommended for controlling the influenza virus in humans would offer protection against the H1 and H3 viruses currently circulating in swine47. The worker’s swine industry should be included in the preferential group for influenza vaccination of the Brazilian MoH, once the transmission of human seasonal influenza viruses to swine has heavily influenced the extensive genetic diversity observed in swIAVs (15).
Continuous influenza surveillance and monitoring are decisive to timely assess the associated risks of seasonal, zoonotic, and pandemic outbreaks. The strengthening of One Health approaches would allow the monitoring of cross-species transmission events and the identification of potential pandemic situations48. These new Brazilian IAV variant cases were considered as sporadic cases and had good clinical outcomes that did not spread throughout the local human population. However, a worst-case scenario could have occurred. Maintaining sensitive, articulated, and actionable surveillance systems remains the key to early detection of the threat posed by new influenza variants.
One of the reasons why we don't concentrate solely on avian H5 influenza is that there are too many other ways the next pandemic could emerge. Nature's lab is truly open 24/7, and is perfectly capable of delivering a nasty surprise out of left field.
