Monday, March 18, 2024

The Lancet Correspondence: Global Emergence of Neuraminidase Inhibitor-Resistant Influenza A(H1N1)pdm09 Viruses with I223V and S247N Mutations

Credit NIAID










#17,953

Twenty years ago Amantadine was the preferred influenza antiviral. It was cheap, plentiful, and worked reasonably well as both a treatment, and a preventative.  

It was so popular it was allegedly used by Chinese farmers to protect their flocks from avian flu, which is believed led to growing resistance (see Nature News China's chicken farmers under fire for antiviral abuse). 
By late 2005 Amantadine was beginning to lose its effectiveness against the H3N2 seasonal flu virus and some strains of the H5N1 bird flu. In January of 2006 the CDC issued a warning to doctors not to rely on Amantadine or Rimantadine to treat influenza.
Tamiflu (Oseltamivir) - an NAI (neuraminidase inhibitor) - was approved for use in the U.S. in 1999. While far more expensive, it became the new treatment standard.  

While occasional instances of Oseltamivir resistance were recorded prior to 2007, 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.

Which of course, is exactly what they did do. Between 2007 and 2008, the incidence of resistant seasonal H1N1 viruses literally exploded around the globe. 

So much so, that 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)). 

It seemed as if antiviral crisis was inevitable, when 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 showed 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.

The CDC's most recent FluView report (see below) - based on roughly 2,600 viruses tested since October 1st - finds very low levels of NAI resistance in our armamentarium of influenza antiviral drugs. 

  • One A(H1N1)pdm09 virus had NA-H275Y amino acid substitution and showed highly reduced inhibition by oseltamivir and peramivir.
  • One (H1N1)pdm09 virus had NA-I223V and NA-S247N amino acid substitutions and showed reduced  inhibition by oseltamivir.
  • One A(H3N2) virus had PA-I38T amino acid substitution and showed reduced susceptibility to baloxavir.

While this is exactly what we would hope to find, we've a correspondence from researchers at the University of Hong Kong  - published last week in The Lancet - of 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). 

While the numbers are still relatively small, this is not a trend we'd want to see continue. 

First the gist of the correspondence (follow the link for supplementary information), after which I'll have a brief postscript.  


Rhoda Cheuk-Ying Leung, Jonathan Daniel Ip, Lin-Lei Chen , Wan-Mui Chan, Kelvin Kai-Wang To
Open Access Published: March 14, 2024 
DOI:https://doi.org/10.1016/S2666-5247(24)00037-5

Neuraminidase inhibitors (NAIs), such as oseltamivir and zanamivir, serve as the primary treatment for influenza virus infection. NAI-resistant influenza A(H1N1) strains were widespread during the 2008–09 influenza season, especially in Japan, where 100% of the strains were resistant to oseltamivir.1
However, after the NAI-susceptible 2009 pandemic subtype (A[H1N1]pdm09) replaced the previous seasonal A(H1N1) subtype in 2009, the incidence of A(H1N1)pdm09 with reduced inhibition (10-fold to 100-fold) or highly reduced inhibition (>100-fold) was only approximately 1% in the 2019–20 influenza season.2
After a period of quiescence during the COVID-19 pandemic, the incidence of influenza has increased following the relaxation of physical distancing measures. In Hong Kong, the resurgence of the influenza virus occurred in 2023 following the relaxation of all COVID-19 restriction measures, with a peak in the spring, predominantly driven by A(H1N1)pdm09 in April, 2023.3 
We have successfully sequenced the influenza neuraminidase gene in 92 individuals with A(H1N1) infection in Hong Kong in 2023. Among them, four individuals (4·35%) carried at least one mutation known to confer reduced susceptibility to the NAIs oseltamivir or zanamivir (appendix p 3).4 Notably, three of ten (30%) A(H1N1)pdm09 strains collected in October, 2023, harboured both I223V and S247N mutations.
To ascertain the global incidence of A(H1N1)pdm09 strains with I223V or S247N mutations, or a combination of both, we conducted a comprehensive analysis of A(H1N1)pdm09 strains available in the Global Initiative on Sharing All Influenza Data (GISAID) repository collected between January, 2016, and November, 2023 (appendix p 4).
The incidence of strains with I223V or S247N mutations, or both, increased in the fall of 2023. The incidence of the I223V mutation increased from fewer than 1200 per 100 000 individuals before August, 2023, to 1250–4972 per 100 000 individuals between August and November, 2023, whereas that of the S247N mutation increased from fewer than 1200 per 100 000 individuals before September, 2023, to 1775–2500 per 100 000 individuals between September and October, 2023.
None of the strains collected before July, 2023, harboured dual I223V/S247N mutations; however, since July, 2023, nine of 1023 strains (880 per 100 000 individuals) harboured dual I223V/S247N mutations, with the highest incidence in October, 2023 (five of 169 strains [2959 per 100 000 individuals]).
Of the nine strains with dual I223V/S247N mutations, five were collected from Europe (two from the Netherlands and one each from Norway, Sweden, and France), and four were collected from Oman. Additionally, among these nine strains, three were clustered under clade 6B.1A.5a.2a, and the remaining six were clustered within clade 6B.1A.5a.2a.1 (appendix pp 1–2).
Previous studies have shown that mutations at neuraminidase amino acid residue 223 are associated with an 11–28-fold increase in the half-maximal inhibitory concentration (IC50) for oseltamivir, whereas mutations at residue 247 are linked to a six-fold increase in the oseltamivir IC50, compared with the reference median IC50 values.2,5
However, investigations into such associations for dual I223V/S247N mutations have not been reported. Therefore, in this study, we assessed the susceptibility of a strain with dual I223V/S247N mutation (HKU-231217-085) to neuraminidase inhibitors using a chemiluminescent neuraminidase inhibition assay (appendix p 7).
The IC50 value for HKU-231217-085 was 10·63-fold higher (from 0·429 nM to 4·563 nM) against oseltamivir and 3·38-fold higher (from 0·924 nM to 3·120 nM) against zanamivir than the average IC50 value for the three A(H1N1) strains (HKU-231217-099/2023, HKU-231217-100/2023, and 415742/2009) without the dual mutation (appendix p 5). Hence, strains harbouring dual I223V/S247N mutations can be considered as having reduced inhibition, as per the WHO definition.
In summary, the findings highlight the global emergence of NAI-resistant A(H1N1)pdm09 strains with dual I223V/S247N mutations. These results emphasise the importance of continual monitoring of antiviral resistance in influenza viruses.

While the recent appearance of dual I223V/S247N mutations in A(H1N1)pdm09 sequences are  concerning, it isn't clear whether these are spontaneous mutations occurring people receiving oseltamivir, or if they represent biologically `fit' viruses actually spreading in the wild. 

Of course, in 2008 we saw H1N1 resistance go from one extreme to the other in the space of a little more than a year, so we'll definitely want to keep an eye out for future reports. 

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.


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