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Iowa scientist sees ‘a lot of genetic diversity’ in swine influenza viruses

How diverse are influenza A viruses circulating in US swine herds?

“There are at least 16 different surface genes and these may be combined with an additional 30 different internal gene constellations/combinations, so there is a lot of genetic diversity,” said Tavis Anderson, PhD, an Oak Ridge Institute for Science and Education research scientist posted at the National Animal Disease Center, Ames, Iowa.

“Each of these different combinations may affect virus transmission and clinical disease.”

If a novel virus spills into the swine population from humans, these influenza viruses can acquire swine-adapted internal genes because of co-infection and re-assortment Anderson said.

“Once that happens, they can rapidly spread through swine herds in the US,” he added.

Anderson works closely with the USDA National Animal Health Monitoring System, and his focus is on the sequence data collected from diagnostic testing.

“A lot of the on-farm work feeds into the National Animal Health Laboratory Network [NAHLN]. If the sample is IAV-positive, the surface proteins (hemagglutinin, HA; neuraminidase, NA) are sequenced, publicly released, and the virus isolate is deposited at the National Veterinary Services Laboratory at USDA,” Anderson said.

“Since the system was initiated in 2009, we’ve collected a large amount of genetic sequence data primarily on the surface proteins of flu — the hemagglutinin (HA) and neuraminidase (NA).”

The lab accumulates about 1,000 HA gene sequences every year through a passive surveillance system.

“We can’t make statements about prevalence, but we can analyze the sequence data and determine what’s going on in terms of genetic diversity and regional circulation,” Anderson added.

Significant diversity

There is a lot of flu circulating, and there is also a great deal of diversity within the influenza virus, Anderson said. Three subtypes are familiar ⸺ H1N1, H1N2 and H3N2 ⸺ but a subtype is not enough to differentiate a strain anymore.

“If you start digging into the H1 genetic data, there are three major divisions within the H1 subtype,” Anderson explained. “Within each of these linages, an additional seven clades are co-circulating,” Anderson said.

“These clades are important because a vaccine constructed to provide protection within one HA genetic clade is unlikely to provide protection against a different HA genetic clade. Tracking that information and how it’s changing over time and also through space in different production systems is important,” he noted.

It’s a similar scenario with the H3 strains, which are broken down by each decade of introduction from humans into swine.

“We have two major H3 clades in the US, with introduction first occurring in the late 1990s,” Anderson said. “A triple reassortant or TRIG is an H3 virus that has human, swine and avian components across its entire genome. More recently, there’s been an introduction between 2010 and 2012, and again in 2016 from humans into swine.”

These introductions have created even more influenza genetic diversity circulating among US pigs.

What’s driving all the diversity?

Anderson and his counterparts are trying to determine what’s driving the co-circulation and diversity of the different clades. They are focused on five key factors:

  1. Human-to-swine transmission: “All of the influenza viruses in our pigs in the US are evolutionarily derived from human-to-swine transmission events over the last 100 years,” Anderson said. “For example, at some point around 2012, a human infected with seasonal H3 flu went onto a farm and [accidentally infected] a pig. That established the strain on that farm, and because of production practices and pig movement, the virus was able to establish, re-assort and pick up internal swine genes. It was then disseminated widely across the US, establishing a new lineage.”
  2. Pig movement: Because of the way production systems are structured, pigs may move across the country and virus transmission can happen rapidly, Anderson said. Pigs may be shedding virus for multiple days, so they can be infected as they’re being loaded onto a truck in one state and then bring the virus with them to another state over that 1- to 2-day period. “Obviously, when you pack one asymptomatic but infected pig onto a truck, there is the potential to unload many more infected pigs,” Anderson said. “Genetic clades can be very minor in surveillance at 1% to 2% of detections but over time, regional movement of pigs and virus can result in minor clades increasing in importance with detections of 10% or more in our surveillance system, primarily driven by the rapid movement of pigs across the landscape.”
  3. Strong regional patterns: Despite rapid movement and homogenization of influenza, there are strong regional patterns. “What you have in your production system may just be restricted to you, but you have to consider everything that’s around you,” he said. “There is distinct genetic diversity within and between regions, so thinking regionally is important.”
  4. Antigenic drift: Antigenic drift is possible within a clade because a virus is not a static entity. It is constantly evolving, accruing mutations over time, which reduces vaccine efficacy. Every time a virus replicates, a couple more mutations may occur. “Tracking genetic diversity using surveillance data helps us see how mutations are accruing and whether or not the mutations are changing the structure of the proteins and the efficacy of a vaccine,” Anderson said.
  5. Re-assortment: Flu viruses reassort because they have segmented genomes. “When you have multiple genetic clades of viruses, and relatively high densities of pigs, you can get co-infection,” Anderson said. “With co-infection is the opportunity for re-assortment. There are at least 30 different possibilities of HA and NA genetic-clade combinations, and reassortment can drive rapid evolution and emergence of even more genetic clades, and you can’t put all of those in one vaccine.”

Tools to track IAV-S

Anderson said the industry needs tools that describe genetic diversity and quantify reassortment so IAV-S can be tracked spatially and temporally to determine how it changes over time.

“Fundamentally, this relies on phylogenetics,” he said. Phylogenetics is the area of research concerned with finding the evolutionary history and relationships between species.1 The term phylogeny refers to a hypothesis of these relationships, and is usually presented as a phylogenetic tree.2

The phylogenetic tree shows the relationship between different gene sequences and their hypothetical common ancestors.

“We can group things together that are more related to each other than they are to a different out-group,” Anderson said. “An example out-group might be the vaccine sequence that you have previously used in your herd as your reference point.”

The smallest group or clade is just two viruses together, then it is expanded.

“If you start seeing unexpected similarities or groupings of different genes, you may have a previously unseen link between two farms. This is displayed in the phylogenetic tree as virus genes that are more similar to each other than they are to other viruses that are out there,” Anderson explained. “Similar virus genes form monophyletic clades that share a hypothetical common ancestor. You’re classifying virus genes and potential virus transmission based on groupings in your phylogeny.

“For example, you may think the viruses are all the same in your production system, but if you sequence the viruses, they may be from two separate genetic clades,” he continued. “Because the HA clades are unlikely to provide cross-protection, you would need to create a solution for one group and then a solution for the second group as well. A single vaccine solution to cover all the genetic diversity from multiple HA genetic clades is much less likely to work.”
Anderson said researchers also look at vaccine-driven or immune-driven selection with phylogenies.

“This appears as a ladder-like structure in the phylogenetic tree and may be because of immune escape. The core idea is that one successful virus escaped from your vaccine, seeded the next population, and there is directional selection driving the observed viruses further from where your vaccine is,” he said. “The challenge is knowing how many steps down the ladder you need to be before you update your vaccine.

“We’re working to make the tools easier to use, but it still requires someone to look at the phylogenies and the diagnostic lab report to provide context and interpret the information,” he continued. “That on-farm knowledge is invaluable because it can help identify areas where producers and veterinarians can intervene…to reduce the risk of human-to-swine transmission, and improve the health of pigs.”

Surveillance is critical

The USDA-APHIS Influenza A Virus in Swine surveillance system has been “a success for everyone involved, the producers, veterinarians, and researchers” Anderson summarized. Surveillance systems provide critical data on genetic diversity of circulating IAV-S and have allowed researchers to:

  • Track the origins of the 2009 H1N1 pandemic.
  • Document the importance of human-to-swine transmission and how critical movement is in disseminating virus across the USA.
  • Identify regional patterns and provide epidemiological context by knowing what regions are linked together.
  • Understand the role of modern agricultural practices in IAV-S. “There is a lot of re-assortment, and we’re building tools that will quantify and determine when you have a new virus in your system,” Anderson said.
  • Genetic diversity does impact vaccine efficacy. “We don’t have hard and fast thresholds, but the virus is constantly evolving, and genetic sequence data can help inform when and where you need to use vaccine” he said.


1 http://www.cs.tau.ac.il/~rshamir/algmb/00/scribe00/html/lec08/node2.html Accessed 9.15.20.
2 Ibid.

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How diverse are influenza A viruses circulating in US swine herds? There are at least 16 different surface genes and these may be combined with an additional 30 different internal gene constellations/combinations, so there is a lot of genetic diversity.

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Posted on November 24, 2020

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