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Three days ago the New York Times carried a report indicating that the CDC's recent analysis of the Chilean H5 virus from their first (and to date, only) human case had shown signs of limited mammalian adaptation.
While interesting, it didn't tell us which mammalian adaptations had been found, only where (the PB2 gene). Yesterday the CDC published their findings (see text below), which provide us with considerably more detail.
In this report, we learn first about the condition of the patient (still on a ventilator after 30 days), followed by the good news about what they didn't find:
- HA gene is closely related to avian A(H5) viruses in HA clade 2.3.4.4b and displayed no mammalian adaptations
- The HA gene was very closely related (99% identity) to the A/Astrakhan/3212/2020-like pre-pandemic candidate vaccine viruses
- The NA gene showed no signs of reduced susceptibility to influenza antivirals like oseltamivir
- NA has a full-length stalk which is consistent with avian adapted viruses
- Analysis of the other gene segments (PB2, PB1, PA, NP, M, NS) found no signs of reduced susceptibility to antiviral compounds that target the PA (i.e., baloxavir marboxil) or M2 (i.e., amantadine, rimantadine)
Between being a close match to an existing vaccine candidate virus, and showing no signs of antiviral resistance (even to amantadine), this is encouraging news. The only two `mammalian adaptations' of note were both found in the PB2 gene; and they are two we've seen before:
- The PB2-D701N mutation has been linked to increased severity of infection (see here and here), and has been previously seen in both human H5N1 and H5N6 infections.
- The PB2-Q591K mutation enhances polymerase activity and virus replication of avian viruses in mammals (see PB2-Q591K Mutation Determines the Pathogenicity of Avian H9N2 Influenza Viruses for Mammalian Species).
- This tag-team of D701N and Q591K have been seen previously in zoonotic H7N9 viruses (see Genomic Signatures for Avian H7N9 Viruses Adapting to Humans), and together may compensate for the lack of an E627K mutation which increases viral replication at lower temperatures found in mammals.
Since neither of these adaptations has been found in local poultry or wild birds, it is assumed these are most likely host adaptations that occurred after the patient was infected.
As negative-sense single-stranded segmented RNA viruses, influenza A viruses are prolific, but sloppy replicators. They make millions of copies of themselves while they infect a host, but in the process, often make small transcription errors.
Often, these changes are of little or no effect, or may even be detrimental to the survival of the virus. Those that favor replication in the host, however, tend to carry on to produce more progeny, and if `fit enough', can drown out the earlier `wild type’ virus in the host.
This process is called host adaptation, and while it can (and does) happen in the wild, it can be easily simulated in the laboratory as well via a classic serial passage study (see graphic below).
The source of this patient's infection is still under investigation, and while the CDC's findings could have been far worse, there is enough here to warrant our continued vigilance.
The full text of the CDC's report follows:
Human Infection with highly pathogenic avian influenza A(H5N1) virus in Chile
Updated April 17, 2023
This addendum to Technical Report: Highly Pathogenic Avian Influenza A(H5N1) Viruses, originally published on March 17, 2023, provides a summary of the case and the genomic analysis of the virus from the first H5N1 infection reported in a human in Chile. The overall risk to human health associated with the ongoing A(H5N1) outbreaks in wild birds and poultry has not changed and remains low at this time.
On March 29, 2023, Chile reported its first human infection with HPAI A(H5N1) virus. This is the second human case of A(H5N1) ever reported in South America, which includes a January 2023 case reported by Ecuador (1).
The Chilean patient was a 53-year-old man with symptom onset on March 13. He was hospitalized with severe illness and remains in respiratory isolation under multidisciplinary management, with mechanical ventilation due to pneumonia.
After hospital admission on March 22, the patient received antiviral treatment with oseltamivir and antibiotic treatment. HPAI A(H5) was detected in wild birds and sea lions in the Antofagasta region of coastal northern Chile where the patient lived (2). Potential contact of the patient with wild birds, marine mammals and/or environmental exposures remains under investigation. Close contacts of the patient have been asymptomatic and have tested negative for influenza viruses, indicating that no known human-to-human transmission occurred (2).
Viral RNA obtained from a bronchoalveolar lavage specimen from the patient has been sequenced and genetically analyzed by the National Influenza Centre in Chile (Instituto de Salud Pública) and by the Influenza Division/CDC. The virus was identified as having a clade 2.3.4.4b HA and was determined to be the same genotype that has been detected in the majority of wild birds in South America, indicating no evidence for genetic reassortment compared to A(H5N1) viruses predominating in birds in South America. The virus was 99% identical to many viruses identified in A(H5N1) virus-infected wild birds in Chile. Overall, the genomic analysis of the virus in this specimen does not change CDC’s risk assessment related to the avian A(H5) clade 2.3.4.4b viruses. The overall risk to human health associated with the ongoing A(H5) outbreaks in wild birds and poultry remains low.
The hemagglutinin (HA) gene codes for one of the two surface glycoproteins and is central to species specificity because it is responsible for virus attachment and fusion with host cells. Analysis of this HA gene shows that it is closely related to avian A(H5) viruses in HA clade 2.3.4.4b and lacked amino acid changes that improve recognition of mammalian receptors or fusion of the viral membrane with the host endosomal membranes. The HA is also the primary target of neutralizing antibodies elicited by infection or vaccination, and the HA of virus from this specimen is very closely related (99% identity) to the A/Astrakhan/3212/2020-like pre-pandemic candidate vaccine viruses (e.g., IDCDC-RG71A (3)) that is available to vaccine manufacturers. There are only three amino acid changes (i.e., L104M, L115Q, V210A) between the HA of the virus from the Chilean case and A/Astrakhan/3212/2020-like candidate vaccine, and they are not in major antigenic epitopes strongly suggesting that antibodies elicited by the A/Astrakhan/3212/2020-like vaccine would be expected to have good cross-reactivity – and therefore protection – against this virus.
The neuraminidase (NA) gene encodes the other surface protein of the virus. The major role of the NA is to release new progeny virions from an infected cell by enzymatically cleaving sialic acid receptors, which aids virus spread to uninfected cells within an infected host. The enzymatic activity of NA is inhibited by one class of antiviral drugs that are FDA-approved for treatment of influenza (i.e., NA inhibitors). Analysis of the N1 NA gene from the Chile specimen showed that it did not have any known or suspected markers of reduced susceptibility to this class of antivirals (i.e., oseltamivir). Furthermore, the NA has a full-length stalk which is consistent with viruses that naturally circulate in wild birds. In previous A(H5N1) outbreaks and zoonosis the NA stalk region often had deletions (e.g., a 20 amino acid deletion at positions 49–68 relative to A/goose/Guangdong/1/1996) that enhances replication and/or pathogenesis in terrestrial poultry and mice (4-6).
Analysis of the other gene segments (PB2, PB1, PA, NP, M, NS) was also conducted. No known or suspected markers of reduced susceptibility to antiviral compounds that target the PA (i.e., baloxavir marboxil) or M2 (i.e., amantadine, rimantadine) were found.
In addition to the HA and NA, the RNA transcription and replication complex (PB2, PB1, PA, NP) also have species-specific determinants that impact efficient replication in humans and other mammals, particularly polymerase basic protein 2 (PB2). The PB1, PA and NP lacked markers of mammalian adaptation. The PB2 of this specimen had two changes compared to PB2 genes typically found in A(H5N1) viruses circulating in wild birds. A PB2-D701N substitution was found and this is understood to be associated with mammalian adaptation because it improves RNA polymerase activity and replication efficiency in mammalian cells; based on experimental studies in mice, guinea pigs and ferrets, it has the potential to impact pathogenesis or transmission in infected mammals (7-11). PB2 D701N substitution has previously been identified in human cases of A(H5N1) with no evidence of onward transmission among humans (12) as well as in human cases of clade 2.3.4.4b A(H5N6) (13).
The other PB2 change was Q591K; this substitution has been less frequently identified and is also associated with enhanced replication efficiency in mammalian cells and increased pathogenesis in experimentally infected mice (14, 15). This change has also been identified in human cases of A(H5N1) in the past. The combination of PB2 substitutions of Q591K and D701N have previously been detected in zoonotic avian A(H7N9) viruses (16). It is important to note that these two substitutions are not typical of closely related PB2 genes in viruses circulating in wild birds or poultry in the surrounding area in Chile, strongly suggesting they were acquired in the patient during the course of illness. Viruses can undergo changes in a host as they replicate after infection, and it is not uncommon or surprising for A(H5N1) viruses to undergo these and other polymerase gene changes in patients who experience prolonged infection and severe illness.
The protein products from the M (M1 and M2) and NS (N1 and N2) genes lacked markers associated with mammalian adaptation. Collectively, epidemiologic, and viral genomic analyses found that this case represents a single zoonotic event and while the HA lacked changes likely to enhance transmission to mammals, it did acquire substitutions in PB2 likely to enhance replication in mammals, which illustrates that we have to remain vigilant and characterize zoonotic viruses.
