#18,512
When an avian influenza virus manages to infect a mammalian host, it begins to produce millions of copies of itself, but as a single-stranded RNA virus it lacks the `error-checking' skills of DNA viruses, and is prone to making errors.
When a transcription error makes the virus better suited to a mammalian host, it is more likely to thrive, allowing it to make many more copies with this `host adaptation'.
As a result of these `spontaneous mutations', at some point during an infection you may have multiple `variants' of the virus all circulating within a single host, each battling for dominance. Most mutations offer no benefits - or are even detrimental to the virus - but a number are known to convey a significant advantage.
An avian virus that acquires the PB2-E627K substitution, for instance, is able to replicate efficiently at the lower temperatures (roughly 33C) found in the upper respiratory tract of mammals, while the HA-Q226L mutation switches binding preferentially to human receptor cells.
Mutations that occur in an infected host, but are not transmitted onward, are of less concern than those found in the `wild'. A prime example, the H275Y mutation which occurs in roughly 1% of patients receiving oseltamivir was thought incapable of spreading efficiently as late as 2007.
That is, until several `permissive' mutations in the NA changed the rules (see Permissive Secondary Mutations Enable the Evolution of Influenza Oseltamivir Resistance) unexpectantly sending a resistant H1N1 virus on a world tour in 2008.
Last night the CDC published a report on the genetic sequences from the first severe H5N1 infection in the United States, which was linked to backyard bird exposure in Louisiana.
While `red flag' mutations (e.g. PB2-E627K, HA-Q226L, etc.) were absent, they did find some mutations in the HA that suggest potential mammalian adaptation. Mutations that were not found in the birds they tested, suggesting they were `in-host' spontaneous mutations.
Both the Canadian and the U.S. severe cases were caused by the new D1.1 genotype, which is spreading rapidly in birds. They also share an E186D mutation, which has previously been linked to increased virulence and improved binding to a2,6 human receptor cells.
I've reproduced extended excerpts from the CDC's report below. Follow the link to read it in its entirety. I'll have a postscript when you return.
Genetic Sequences of Highly Pathogenic Avian Influenza A(H5N1) Viruses Identified in a Person in Louisiana
CDC Update
December 26, 2024 – CDC has sequenced the HPAI A(H5N1) avian influenza viruses in two respiratory specimens collected from the patient in Louisiana who was severely ill from an A(H5N1) virus infection. CDC received two specimens collected at the same time from the patient while they were hospitalized for severe respiratory illness: a nasopharyngeal (NP) and combined NP/oropharyngeal (OP) swab specimens. Initial attempts to sequence the virus from the patient's clinical respiratory specimens using standard RNA extraction and multisegment-RTPCR (M-RTPCR)1 techniques yielded only partial genomic data and virus isolation was not successful. Nucleic acid enrichment was needed to sequence complete genomes with sufficient coverage depth to meet quality thresholds. CDC compared the influenza gene segments from each specimen with A(H5N1) virus sequences from dairy cows, wild birds, poultry and other human cases in the U.S. and Canada. The genomes of the virus (A/Louisiana/12/2024) from each clinical specimen are publicly posted in GISAID (EPI_ISL_19634827 and EPI_ISL_19634828) and GenBank (PQ809549-PQ809564).
Summary of amino acid mixtures identified in the hemagglutinin (HA) of clinical specimens from the patient.
Overall, the hemagglutinin (HA) sequences from the two clinical specimens were closely related to HA sequences detected in other D1.1 genotype viruses, including viruses sequenced from samples collected in November and December 2024 in wild birds and poultry in Louisiana. The HA genes of these viruses also were closely related to the A/Ezo red fox/Hokkaido/1/2022 candidate vaccine virus (CVV) with 2 or 3 amino acid changes detected.
These viruses have, on average, 3 or 4 amino acid changes in the HA when compared directly to the A/Astrakhan/3212/2020 CVV sequence. These data indicate the viruses detected in respiratory specimens from this patient are closely related to existing HPAI A(H5N1) CVVs that are already available to manufacturers, and which could be used to make vaccines if needed.
There were some differences detected between the NP/OP and the NP specimens. Despite the very close similarity of the D1.1 sequences from the Louisiana human case to bird viruses, deep sequence analysis of the HA gene segment from the combined NP/OP sample detected low frequency mixed nucleotides corresponding to notable amino acid residues (using mature HA sequence numbering):A134A/V [Alanine 88%, Valine 12%];N182N/K [Asparagine 65%, Lysine 35%]; and
E186E/D [Glutamic acid 92%, Aspartic Acid 8%].
The NP specimen, notably, did not have these low frequency changes indicating they may have been detected from swabbing the oropharyngeal cavity of the patient. While these low frequency changes are rare in humans, they have been reported in previous cases of A(H5N1) in other countries and most often during severe disease2345. The E186E/D mixture, for example, was also identified in a specimen collected from the severe human case detected in British Columbia, Canada67.
This summary analysis focuses on mixed nucleotide detections at residues A134V, N182K, E186D as these changes may result in increased virus binding to α2-6 cell receptors found in the upper respiratory tract of humans. It is important to note that these changes represent a small proportion of the total virus population identified in the sample analyzed (i.e., the virus still maintains a majority of 'avian' amino acids at the residues associated with receptor binding). The changes observed were likely generated by replication of this virus in the patient with advanced disease rather than primarily transmitted at the time of infection. Comparison of influenza A(H5) sequence data from viruses identified in wild birds and poultry in Louisiana, including poultry identified on the property of the patient, and other regions of the United States did not identify these changes. Of note, virus sequences from poultry sampled on the patient's property were nearly identical to the virus sequences from the patient but did not have the mixed nucleotides identified in the patient's clinical sample, strongly suggesting that the changes emerged during infection as virus replicated in the patient.
Although concerning, and a reminder that A(H5N1) viruses can develop changes during the clinical course of a human infection, these changes would be more concerning if found in animal hosts or in early stages of infection (e.g., within a few days of symptom onset) when these changes might be more likely to facilitate spread to close contacts. Notably, in this case, no transmission from the patient in Louisiana to other persons has been identified. The Louisiana Department of Public Health and CDC are collaborating to generate additional sequence data from sequential patient specimens to facilitate further genetic and virologic analysis.
Additional genomic analysis
The genetic sequences of the A(H5N1) viruses from the patient in Louisiana did not have the PB2 E627K change or other changes in polymerase genes associated with adaptation to mammals and no evidence of low frequency changes at critical positions. And, like other D1.1 genotype viruses found in birds, the sequences lack PB2 M631L, which is associated with viral adaptation to mammalian hosts, and which has been detected in >99% of dairy cow sequences but is only sporadically found in birds. Analysis of the N1 neuraminidase (NA), matrix (M) and polymerase acid (PA) genes from the specimens showed no changes associated with known or suspected markers of reduced susceptibility to antiviral drugs. The remainder of the genetic sequences of A/Louisiana/12/2024 were closely related to sequences detected in wild bird and poultry D1.1 genotype viruses, including poultry identified on the property of the patient, providing further evidence that the human case was most likely infected following exposure to birds infected with D1.1 genotype virus.
Follow Up Actions
Overall, CDC considers the risk to the general public associated with the ongoing U.S. HPAI A(H5N1) outbreak has not changed and remains low. The detection of a severe human case with genetic changes in a clinical specimen underscores the importance of ongoing genomic surveillance in people and animals, containment of avian influenza A(H5) outbreaks in dairy cattle and poultry, and prevention measures among people with exposure to infected animals or environments.
While many seem reassured by the relatively mild presentation (so far) of the `bovine' B3.13 genotype in humans, this D1.1 genotype has already produced 2 severe illnesses, and is very aggressive in both poultry and wild birds.
The superpower of influenza A is its ability to continually reinvent itself, either through random mutations (antigenic drift), or via reassortment (antigenic shift).
Genotype D1.1 may currently lack the ability to spread efficiently between humans, but it is truly a work in progress. Each new spillover, particularly into a mammalian host, provides the virus with another opportunity to evolve and adapt.
And the D1.1 genotype isn't alone.
More than 100 genotypes have been documented in North America since H5N1 arrived in 2001 2021, and more are expected. Globally, the number is much higher. Most fail to thrive, but each represents another free spin for the virus on the genetic wheel of fortune.
It is obviously not easy for nature to create a pandemic virus. If it were, we'd be knee deep in pandemics all the time.
But nature is nothing, if not persistent. And we underestimate its ability to serve up curve balls at our considerable peril.
