#16,146
Although there is currently very little influenza being reported around the world, for the second year in a row we are faced with the possibility of seeing a `twindemic' of both COVID and Flu this fall or winter. Last year, between social distancing and face masks - and likely some degree of `viral interference' from COVID - influenza remained a no-show.
Hopefully we'll get lucky again this year.
But we've already seen some signs of increased RSV transmission in the United States (see CDC HAN: Increased RSV Reports Across The Southern United States) and around the globe (see here and here), and some reports of influenza outbreaks (see Influenza cases rising amid Covid-19 pandemic - The Kathmandu Post).
Six weeks ago, in UK Academy Of Medical Sciences: Looking Ahead To COVID-19 Over Winter 2021/22 & Beyond, we looked at a lengthy (133 page PDF) report on what this fall and winter - and beyond - might look like with both COVID-19 and other respiratory illnesses concurrently spreading in the community.
The report outlined three key challenges the UK will face this winter and beyond:
● A resurgence of respiratory infectious diseases, including COVID-19, influenza and respiratory syncytial virus (RSV). Our modelling suggests that there will be a third peak of COVID-19 infections over the summer of 2021, although the timing and magnitude of the peak are uncertain. Mortality may be less severe than last winter but a rise in infections will put pressure on the health service and lead to higher levels of long COVID. The possibility of a further new variant is also of concern. Outbreaks of RSV in the autumn and influenza in the winter could be around twice the magnitude of a ‘normal’ year, and might overlap (at least partially) with a peak in COVID-19 infections.● Wider health and wellbeing impacts of the pandemic, including long COVID, mental and physical deconditioning, and the impact of delays in diagnosis and disease management during the pandemic. During the winter months, noncommunicable diseases (NCDs) such as asthma, chronic obstructive pulmonary disease (COPD), ischaemic heart disease, myocardial infarction and stroke are likely to be exacerbated.● Continued disruption to health and social care service delivery, including managing the backlog of treatment and diagnosis, incorporating IPC measures, and the financial precariousness of social care. By the winter, staff across the sectors will have been responding to a prolonged pandemic for over 18 months, with many directly affected by COVID-19, thereby compounding issues of staff capacity and vacancies.
Added to these, ongoing uncertainties remain over the: duration of post-vaccination immunity in different groups (and safety in children); likelihood of and impact of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants, including the possibility of vaccine-resistant variants. This is in addition to the development and availability of treatments and prophylaxis for COVID-19; and prevalence, duration, severity and ability to treat, long COVID
Influenza is still out there, of course, and continues to evolve. But since March of 2020 we've had extremely limited real-world data, making this fall's flu shot - whose components were selected last February - perhaps an even longer-shot of matching this year's flu (assuming it arrives) than usual.
Complicating matters even further, with almost no influenza exposure for 18 months, community immunity to influenza - which is expected to decline over time - is likely lower than we've seen in years (see COVID-19, The Next Flu Season, And The Temporary Immunity Hypothesis).
I'll still get the flu shot this fall, because even a little protection beats no protection at all. And once again, maybe we'll get lucky, and whatever flu does appear is covered by this year's vaccine.
Besides, there is some evidence (see PLoS One: Potential Benefits of the Influenza Vaccine Against SARS-CoV-2 (Retrospective Cohort Analysis) that the flu shot may help ramp up our immune system against other viruses as well.
The ECDC has continued to produce monthly Influenza Characterization reports, based on limited viral submissions, over the summer. How probative they will be for this year's influenza season is unknown, but we have to go with the data we have - not the data we wished we had.
Influenza virus characterisation - Summary Europe, July 2021
Systematic review
23 Aug 2021
Publication series: Influenza Virus Characterisation
This is the ninth report for the 2020-2021 influenza season. As of week 28 /2021, only 943 influenza detections across the WHO European Region had been reported to the European Surveillance System (TESSy); 51% type A viruses, with A(H3N2) and A(H1N1)pdm09 being approximately equally represented, and 49% type B viruses with only 16 having been ascribed to a lineage, 13 B/Victoria and three B/Yamagata.This represents a 99.4% drop in detections compared with the same period in 2020, probably due to measures introduced to combat the COVID 19 pandemic.Executive summary
Since the June 2021 characterisation report report, one shipment from an EU/EEA country (France) containing six virus isolates was received at the London WHO Collaborating Centre, the Francis Crick Worldwide Influenza Centre (WIC): virus characterisation of these six viruses is ongoing. This report therefore focuses on genetic characterisation of the HA genes of seasonal influenza viruses submitted and/or released in GISAID during July 2021, together with sequences recently determined at the WIC. The data continue to show extremely low levels of influenza detections globally.
The 60 A(H1N1)pdm09 HA sequences derived from viruses detected in 2021 as deposited/released in GISAID during July, all originated in Togo and were subgroup 6B.1A5A+187V/A , represented by the vaccine virus for the northern hemisphere 2020 2021 season, A/Guangdong Maonan/SWL1536/2019 . Most of these sequences (35) encoded additional HA1 amino acid substitutions of I166T and A186T.
All 57 HA sequences that became available in July for A(H3N2) viruses , detected in fell in subgroup 3C.2a1b+T131K A. The viruses in this subgroup split into two antigenically distinguishable clusters originally defined by viruses from Cambodia ( n = 1 3 : with HA1 amino acid substitutions of G186S, F193S, Y195F and S198P, many also having K171N ) and Bangladesh n = 4 4 : with HA1 amino acid substitutions of Y159N, T160I (loss of a glycosylation site), L164Q, G186D, D190N, F193S and Y195F) with Bangladesh-like viruses showing the greatest geographic spread. The seven viruses from EU/EEA countries were Bangladesh like. An A/Cambodia/e0826360/2020 like virus (subgroup 3C.2a1b+T131K A) has been recommended for use in the 2021 2022 northern hemisphere influenza season.
The 45 B/Victoria lineage HA sequences derived from viruses collected in 2021 that became available in July were subclade 1A( 3)B Of these, 10 from Kenya were equally split between groups defined by HA1 G133R substitution or HA1 K75E, E128K, T155A, G230N and I267V substitution. All other sequences were from N150K group viruses with HA1 amino acid substitutions of N150K, G184E, N197D (loss of a glycosylation site) and R279K. N150K group sequences split into two subgroups one of which, defined by HA1 substitutions V220M and P241Q, was confined to viruses detected in China (n = 2) while the second (n = 33 sequences), defined by HA1 substitutions A127T, P144L, and K203R (with two having additional substitutions of T182A, D197E and T221A), showed significant geographic spread. The four viruses detected in EU/EEA countries all fell in the latter subgroup but lacked the additional amino acid substitutions, as was the case for a set of 19 viruses collected in Singapore in June.
Antigenically, viruses in subgroups of the N150K group differ and show some loss of reactivity with post-infection ferret antisera raised against the B /Washington/02/2019 vaccine virus (recommended for inclusion in influenza vaccines for the 2020-2021 and 2021-2022 northern hemisphere seasons and 2021 southern hemisphere season). This was clearly the case for the three N150K group viruses from Sweden characterised by HI in the June report.
No B/Yamagata-lineage HA sequences from clinical specimens collected in 2021, and none with collection dates after March 2020, were available. All of the 77 sequences from viruses detected in 2020, inclusive of 12 from EU/EEA countries, belong to genetic clade 3 and carry three HA1 amino acid substitutions (L172Q, D229N and M251V) compared with B/Phuket/3073/2013-like viruses which have been recommended for use in quadrivalent influenza vaccines for the 2020-2021 and 2021-2022 northern hemisphere seasons and 2021 southern hemisphere season. The antigenic effects of these amino acid substitutions have been minimal, as assessed in earlier reports.
Influenza virus characterisation Summary Europe, Juy 2021 - EN - [PDF-1.95 MB]
Whether we see a little flu this year, or a lot, any flu on top of COVID will make things tougher this winter. Both for healthcare delivery, and for anxious, mildly symptomatic patients who will need to be tested to rule out COVID.
I'm continually hearing of long waits for beds in hospitals, ERs and ICUs either at capacity or on divert, and the terms `COVID Positive' and `Isolation Alert' fill the airwaves. Some EMS and public safety response times are suffering, as there are times when no units are immediately available to respond.As I mentioned a couple of weeks ago in Through A Scanner Darkly, EMS traffic in central Florida in the middle of August is already heavier than you'd expect during the height of a bad flu season.
This is not only a bad time to have COVID, it is a bad time to have a heart attack, a stroke, or a car accident, as emergency services are stretched thin. And barring some kind of miracle, things will probably get worse this fall and winter.
Hopefully, with all the challenges we have facing us already, we won't add a novel or particularly virulent seasonal flu virus to the list.
