Avian Influenza basics
Over the lunch the other day, a veterinarian friend pointed out that some of my readers might find a bird flu terminology primer useful. It also woldn’t hurt for me to get things clear in my own mind. So here are some basic terms and definitions—with the caveat that this is how I use them.1 Another caveat: different viruses have different qualities; sometimes they are also described with different terminology. Here I am talking specifically about Avian Influenza. Once more, though, I will remind you that I’m merely an interested amateur—it’s very possible I’m using these terms wrongly (if so, please drop a comments—I’m happy to make corrections); for official info, refer to the CDC, CIDRAP, and other sources I’ve referenced previously. And finally I’m writing this in haste so it’s less than systematic. If I’ve left anything obvious out, again, drop a comment and I’ll fix it as and when I can.
Terms and definitions
Avian influenza is caused by influenza Type A virus (influenza A). See Influenza A taxonomic tree above. All the definitions below come after all that stuff.
Avian-origin influenza viruses are broadly categorised based on a combination of two groups of proteins on the surface of the influenza A virus: hemagglutinin or “H” proteins, of which there are 16 (H1–H16), and neuraminidase or “N” proteins, of which there are 9 (N1–N9). Many different combinations of “H” and “N” proteins are possible. Each combination is considered a different subtype, and related viruses within a subtype may be referred to as a lineage. Avian influenza viruses are classified as either low pathogenic or highly pathogenic based on their genetic features and the severity of the disease they cause in poultry. (Note: Poultry only—nothing to do with how they affect cats or people or other mammals or even other birds.) Most subtypes are of low pathogenicity, meaning they cause no signs or only minor clinical signs of infection in poultry.
What I talk about here on this blog is Highly Pathogenic Avian Influenza (HPAI), H5N1.
A virus isolate is the name for a virus isolated from an infected host and propagated in culture. An isolate comes from a single host. Very few hosts get their particular virus isolated and genotyped. (I tend to mention isolates in context of very sick human hosts.)
A virus variant is an isolate whose genome sequence differs from that of a reference virus—so, for example, when a person gets very sick with H5N1 from a wild bird, and as that original, reference virus replicates in vivo (in the patient’s body) it mutates, then the isolate from the patient is different from the reference virus in the bird, and that isolate is then a variant.
A clade is a group of viruses composed of an ancestor and its descendants. So, for example, clade 2.3.4.4b is a clade that contains various H5N1 genotypes.
The term genotype describes the genetic makeup of a virus. Here I’ve been talking about two different H5N1 genotypes: B3.13, circulating in bovine species (e.g. dairy herds) and some commercial poultry flocks, and D1.1, circulating in wild birds—particularly waterfowl—and some backyard flocks.2
Right now, specifically within the last year, while both genotypes seem very dangerous to cats—large and small—only D1.1 has caused severe infections in humans in North America.3 So far there have been only two of those severe cases: an otherwise-healthy teenage girl in British Columbia, who very nearly died, and an over-65-year-old man in Louisiana, who did die. So until nomenclature changes, or some other genotype evolves nastily, when I talk about bird flu here I’ll mostly be focused on HPAI H5N1 clade 2.3.4.4b, genotype D1.1—which I might sometimes refer to as the wildfowl strain (think D for Duck, just as I might call the B3.13 genotype the bovine strain—B for Bovine) but I admit I’m not sure how this would fly (cough) in virology circles.
If you have questions/suggestions/corrections, please leave a comment.
But—huge caveat—I’ve seen different medical/epidemiology/researchers use different terms—no one seems to agree with everyone. So I just try to be consistent with myself.
︎I’ve seen a lot—a lot—of confusion between clade and genotype when it comes to HPAI H5N1. I’ve been confused myself (but writing this post had made it all a bit clearer, so hopefully avoid major mistakes). Even more confusingly, at some point I’d guess—emphasis on guess (not an expert, remember?)—it’s even vaguely possible that either or both B3.13 and D1.1 will form clades—but then they’ll be called something else. Clear? If not, I don’t blame you. ︎I’m being very specific, not to say parochial, here simply because I don’t have time today to go look at human illness severity/mortality rates in the rest of the world, or at historical data. ︎
