Thursday, June 13, 2024

EID Journal: Multicountry Spread of Influenza A(H1N1)pdm09 Viruses with Reduced Oseltamivir Inhibition, May 2023–February 2024

Credit NIAID


Not quite 20 years ago, we lost our frontline influenza anti-viral drug - Amantadine - after it suddenly lost effectiveness after decades of use (see MMWR Levels of Adamantane Resistance Among Influenza A (H3N2) Viruses and Interim Guidelines for Use of Antiviral Agents --- United States, 2005--06 Influenza Season). 

Amantadine was both cheap and effective, which is why it was allegedly used by Chinese farmers to protect their flocks from avian flu, which is believed to have led growing resistance (see Nature News China's chicken farmers under fire for antiviral abuse).

In January of 2006 the CDC issued a warning to doctors not to rely on Amantadine or Rimantadine to treat influenza. Luckily, there was an alternative - Oseltamivir (aka `Tamiflu') - which had been approved in the late 1990s, although it was far more expensive.  

While occasional instances of Oseltamivir resistance had been observed, in nearly every case, it developed after a person was placed on the drug (i.e. `spontaneous mutations’). 

Although of obvious concern to the patient receiving treatment, it occurred in only about 1% of treated cases, and studies suggested that these resistant strains were `less biologically fit’, and were therefore thought unlikely to spread from human-to-human.

That happy notion was dispelled in 2008, when in the course of a less than a year the H1N1 virus defied all expectations and went from being 99% susceptible to oseltamivir to 99% resistant.  

By the end of 2008, nearly all of the H1N1 samples tested in the United States were resistant to oseltamivir and the CDC was forced to issue major new guidance for the use of antivirals (see CIDRAP article With H1N1 resistance, CDC changes advice on flu drugs).

This resistance was primarily due to an H275Y mutation - where a single amino acid substitution (histidine (H) to tyrosine (Y)) occurs at the neuraminidase position 275 (Note: some scientists use 'N2 numbering' (H274Y)).

Although an influenza antiviral crisis seemed unavoidable, in a Deus Ex Machina moment a new swine-origin H1N1 virus - that happened retain its sensitivity to Tamiflu - swooped in as a pandemic strain in the spring of 2009, supplanting the older resistant H1N1 virus. 

Both incidents remind us that antivirals - much like antibiotics - can lose effectiveness over time, as pathogens evolve and resistant strains emerge. 

Since 2009 flu surveillance centers around the world have been looking for any signs of growing resistance to NAI inhibitors. For the most part, we've seen the same 1% incidence of spontaneous mutations in people receiving the antiviral, although we've seen a few `clusters' of cases.

As added insurance, in 2018 the FDA Approved Xofluza : A New Class Of Influenza Antiviral (aka baloxavir marboxil), but it too has shown signs of resistance (see Eurosurveillance: A community Cluster of Influenza A(H3N2) Virus infection with Reduced Susceptibility to Baloxavir - Japan 2023), particularly in seasonal H3N2.

Three months ago, however, we saw a worrisome report in The Lancet - Global Emergence of Neuraminidase Inhibitor-Resistant Influenza A(H1N1)pdm09 Viruses with I223V and S247N Mutations - which reported a much higher incidence of oseltamivir resistance among samples tested in Hong Kong in 2023 (along with a concurrent rise in GISAID sequences deposited since last summer).

Instead of the H275Y mutation which caused so much trouble in 2008, these viruses carried dual I223V/S247N mutations. Yesterday the CDC's EID journal published a new report which finds this resistance signature has spread from Asia to Europe, which suggests it may be just as `biologically fit' as antiviral susceptible viruses.

Some excerpts from yesterday's report, after which I'll return with a postscript. 

Multicountry Spread of Influenza A(H1N1)pdm09 Viruses with Reduced Oseltamivir Inhibition, May 2023–February 2024

Mira C. Patel1, Ha T. Nguyen1, Philippe Noriel Q. Pascua, Rongyuan Gao, John Steel, Rebecca J. Kondor, and Larisa V. Gubareva
Author affiliation: Centers for Disease Control and Prevention, Atlanta, Georgia, USA

Since May 2023, a novel combination of neuraminidase mutations, I223V + S247N, has been detected in influenza A(H1N1)pdm09 viruses collected in countries spanning 5 continents, mostly in Europe (67/101). The viruses belong to 2 phylogenetically distinct groups and display ≈13-fold reduced inhibition by oseltamivir while retaining normal susceptibility to other antiviral drugs.

Three classes of direct-acting antivirals targeting the influenza virus matrix protein 2 (M2) ion channel, neuraminidase (NA), or polymerase cap-dependent endonuclease (CEN) are approved to treat influenza in many countries (1). Although most seasonal influenza viruses are susceptible to NA and CEN inhibitors, emergence of antiviral-resistant variants is a public health concern because of widespread resistance to M2 inhibitors and possibilities of similar resistance developing for other antiviral drugs (2).
Oseltamivir, an NA inhibitor, is the drug most prescribed for influenza (2). The NA amino acid substitution H275Y, acquired spontaneously or after drug exposure, confers resistance to oseltamivir. Oseltamivir-resistant influenza A(H1N1) viruses with H275Y emerged first in Europe during 2007–2008 and rapidly spread worldwide (3). However, they were displaced by influenza A(H1N1)pdm09 (pH1N1), the swine-origin virus that caused the 2009 pandemic (4).

Monitoring oseltamivir susceptibility is a priority for the World Health Organization Global Influenza Surveillance and Response System (WHO-GISRS). In addition to H275Y, many NA substitutions in N1 subtype viruses are suspected of reducing oseltamivir susceptibility (5). Although there are no established criteria for determining clinically relevant oseltamivir resistance based on phenotypic testing, for surveillance purposes, influenza A viruses tested in NA inhibition assays are classified as displaying reduced inhibition if they have a 50% inhibitory concentration (IC50) 10-100–fold higher or as highly reduced inhibition if IC50 >100-fold higher than that of a reference (6).



We report the emergence and intercontinental spread of pH1N1 viruses displaying reduced susceptibility to oseltamivir resulting from acquisition of NA-I223V + S247N mutations. Emergence of the dual mutants was also recently noticed by researchers in Hong Kong (10). The dual mutants that we tested retained susceptibility to other approved influenza antiviral drugs, including baloxavir. Analysis of available sequence data revealed that dual mutants have been in global circulation since May 2023; overall detection frequency was low (0.67%, 101/15,003). However, those data may not necessarily represent the actual proportion of what was in circulation because of differences in surveillance and sequencing strategies in each country.

Substitutions at residues 223 or 247 were previously reported and occurred spontaneously in circulating viruses (5,11,12). pH1N1 viruses with S247N circulated in several countries during 2009–2011 (11), and influenza B viruses with I223V (I221V in B numbering) were found in several US states during 2010–2011 (12). Isoleucine at 223 is a highly conserved framework residue in the NA active site. The S247N substitution may alter the hydrogen bonding network of the active site and the conformation of the residue E277 side chain, thereby weakening oseltamivir binding (11). Changes at 223 or 247 are monitored because they can enhance drug resistance by combining with mutations at other residues (11,13,14).

Rapid spread of dual mutants to countries on different continents suggests no substantial loss in their replicative fitness and transmissibility. I223V was shown to alter NA activity (14), and change at 247 may produce a similar effect, which warrants the question whether signature substitution(s) of NA subclade C.5.3 and of the branch to which the dual mutants belong (i.e., S200N, S366N) could serve as prerequisites for emergence of dual mutants. 

All group 1 dual mutants had an additional substitution R257K, which was previously associated with restoring NA activity of viruses with the H275Y substitution (15). Conversely, most group 2 viruses acquired HA from subclade 5a.2a.1_C.1.1.1 by reassortment, which may have helped to restore the functional HA and NA balance. Acquisition of the antigenically distinct HA could further enhance the spread of group 2 dual mutants. Our study highlights the need to closely monitor evolution of dual mutants because additional changes may further affect susceptibility to antiviral drugs or provide a competitive advantage over circulating wild-type viruses.

Dr. Patel is a senior service fellow in the Influenza Division, National Center for Immunization and Respiratory Diseases, CDC, Atlanta. Her research interests are respiratory viruses and antiviral therapeutics targeting viral or host proteins, and her research focuses on influenza viruses, molecular characterization of antiviral resistance mechanisms, and development of in vitro assays for monitoring drug susceptibility.

So far, detections of these resistant H1N1 viruses remain rare, and most influenza A infections will still respond positively to Oseltamivir.   

The constant evolution and global shifts in H1N1 make it impossible to predict whether these viruses will gain momentum during the upcoming flu season, or if they simply fade away. 

Antivirals, antibiotics, and most anti-fungal medicals all share the same weakness. Over time, and particularly if they are used often enough, the pathogens (viruses, bacteria, or fungi) they were designed
to suppress can evolve or mutate enough to render them ineffective

Making both improved surveillance, and better stewardship, crucial going forward.