Credit WHO Influenza Report #380
#15,560
As we've discussed often over the past 6 months (see here, here & here) - reports of influenza activity dropped off a cliff in the Northern Hemisphere in mid-March with the arrival of COVID-19, and barely made an appearance in the Southern Hemisphere during their winter (June-July-August).
Six weeks ago, in WHO Recommended 2021 Southern Hemisphere Flu Vaccine Composition & Impact Of COVID-19 On Selection, the WHO had this to say about the lack of flu data.
16. What impact has the COVID-19 pandemic had on influenza activity?
The COVID-19 pandemic has had a major impact on influenza activity. Between February and March 2020, influenza activity was elevated in most countries in the northern hemisphere consistent with a typical influenza season. Starting in mid-March, influenza activity decreased sharply, concomitant with the spread of SARS-CoV-2. Implementation of travel restrictions, mitigation strategies and social-distancing measures is likely the reason for decreased influenza activity. Correspondingly, very low levels of influenza detection have been reported globally, including from countries in the temperate zone of the southern hemisphere.
17. How has the COVID-19 pandemic impacted the 2021 southern hemisphere influenza vaccine recommendation?
The amount of genetic and antigenic data available from recently circulating viruses has been significantly lower for this southern hemisphere vaccine recommendation meeting than is typical due to the COVID-19 pandemic. Influenza activity had started in several northern hemisphere countries prior to the emergence of the COVID-19 pandemic, providing a source of viruses collected in 2020, mainly from February and March. While the overall numbers were lower, recent viruses from every WHO region were characterized and the recommendations are based on viruses that are likely to be a fair representation of those that may continue to circulate.
Nevertheless, due to the reduced number of recent viruses circulating and available for characterization, there are uncertainties regarding the full extent of genetic and antigenic diversity. It is unknown what impact the low level of influenza activity will have on forthcoming influenza seasons and which influenza virus types and subtypes will begin to circulate widely when social interactions resume
While less flu is generally considered a good thing, the lack of data (and virus isolates) means we have very little idea what evolutionary changes are occurring in flu strains circulating around the world. When seasonal flu returns - and there is no reason to believe it won't - we may find ourselves dealing with one or more antigenically drifted viruses.
Despite the lack of surveillance data (and antigenic characterization of virus samples), the ECDC continues to publish what little data they have in their (nearly) monthly Influenza Virus Characterization Reports.
These reports are highly technical, and of interest primarily to virologists and epidemiologists. The Executive summary - while hampered by a 97% drop in samples over this time last year - is slightly more accessible.
Influenza virus characterisation, October 2020
Surveillance report
13 Nov 2020
Publication series: Influenza Virus Characterisation
ECDC’s influenza virus characterisation reports are published periodically and give an overview of circulating influenza viruses. They provide details on the current vaccine strains, summarise the development of the viruses since the last report, and closely follow the main developments for the ongoing influenza season. Virus characterisation reports are primarily intended for influenza virologists and epidemiologists.
Executive summary
This is the first report for the 2020–2021 influenza season. As of week 44/2020, only 39 influenza detections across the WHO European Region had been reported to The European Surveillance System (TESSy); 59% type A viruses, with A(H3N2) prevailing over A(H1N1)pdm09, and 41% type B viruses with none having been ascribed to a lineage. This represents a 97% drop in detections compared with the same period in 2019, probably due to the COVID-19 pandemic and measures introduced to combat it.
Since the September 2020 characterisation report1, no shipments of influenza-positive specimens from the European Union/European Economic Area (EU/EEA) countries, or elsewhere, have been received at the London WHO Collaborating Centre, the Francis Crick Worldwide Influenza Centre (WIC). Therefore, this report focuses largely on genetic characterisation of influenza viruses with collection dates prior to week 40, the start of weekly influenza surveillance reporting for the 2020-2021 influenza season.
The vast majority of A(H1N1)pdm09 viruses have continued to fall in genetic subclade 6B.1A5, mostly in the 6B.1A5A group with few in the 6B.1A5B group. 6B.1A5A viruses have continued to evolve and two subgroups have emerged designated 6B.1A5A+187V/A, representatives of which are recommended for use in the northern hemisphere 20202021 season, and 6B.1A5A+156K, an antigenically distinct group representatives of which are recommended for use in the southern hemisphere 2021 season. Following a rise in the number of 6B.1A5A+156K viruses detected, the two subgroups appear to be currently circulating in approximately equal proportions.
Recently circulating A(H3N2) viruses have continued to fall in clades 3C.2a and 3C.3a, with the vast majority of clade 3C.2a viruses being in the 3C.2a1b group which has now been divided into four subgroups designated 3C.2a1b+T131K-A, 3C.2a1b+T131K-B, 3C.2a1b+T135K-A and 3C.2a1b+T135K-B. Antisera raised in ferrets show high levels of clade/group specificity, though there is some subgroup cross-reactivity. Viruses representative of subgroup 3C.2a1b+T135K-B have been recommended for use in influenza vaccines for the northern hemisphere 2020-2021 season and the southern hemisphere 2021 season.
Of four antigenically distinct groups of viruses in the B/Victoria-lineage, only two have circulated recently, small numbers of that designated subclade 1A(2) with a two amino acid deletion in HA1 and that designated subclade 1A(3)B with a three amino acid deletion in HA1 being hugely dominant. Viruses representative of subclade 1A(3)B have been recommended for use in influenza vaccines for the northern hemisphere 2020-2021 season and the southern hemisphere 2021 season.
At the time of writing this report, genetic information for only 70 B/Yamagata-lineage viruses with collection dates in 2020 was available in GISAID. All 67 viruses for which full-length HA sequences were available belong to genetic clade 3 and contain at least two HA amino acid substitutions (HA1 L172Q and M251V) compared to B/Phuket/3073/2013- like viruses which have been recommended for use in quadrivalent influenza vaccines for the northern hemisphere 2020-2021 season and the southern hemisphere 2021 season. The antigenic effects of these amino acid substitutions have been minimal as assessed in earlier reports.
Influenza virus characterisation, October 2020 - EN - [PDF-7.56 MB]
While this year's northern hemisphere flu vaccine is already manufactured, decisions will have to be made in February as to what flu strains to include in next year's (2021-2022) flu vaccine. If this dearth of data continues into the new year, vaccines experts will have very little data to base their decisions on.
Between `viral interference' from SARS-CoV-2, and pandemic inspired social distancing and NPIs (hand hygiene, face covers, etc.), the global `fluscape' has been radically altered since early spring. Exactly what this might mean for the emergence of novel flu viruses is unknown.
But the natural evolution of seasonal flu viruses has also been impacted in ways that we can only begin to envision (see COVID-19, The Next Flu Season, And The Temporary Immunity Hypothesis), and for the most part, this is all happening out of our sight.
Whether seasonal flu returns this winter, next summer - or stays suppressed for a year or longer - we should be prepared for some surprises when it finally does return. If nothing else, community immunity to influenza will likely diminish the longer this lull continues.
Even assuming COVID's impacts can be largely subdued by a vaccine, its knock-on effects may end up being felt for years to come.
