Avian Flu Diary: A Disturbing Dearth Of Data

#15,398

I get it. It's hard to worry about the creek rising when your house in on fire. And right now the flames of COVID-19 have everyone's attention.

But our world doesn't stop just simply because we are embroiled in a pandemic.

The seasons inexorably change, migratory birds make their twice annual flight to and from their high latitude roosting areas, natural disasters occur, viruses and bacteria mutate and adapt, and some may even jump species or acquire increased virulence or transmissibility along the way.

In the best of times, our visibility of what is going on with infectious diseases is limited.

Despite the long-standing IHR 2005 international Health Regulations agreement where WHO member countries pledged to develop mandated surveillance and testing systems, and to report certain disease outbreaks and public health events in a timely manner - fewer than half the countries of the world self-report having met the core requirements.

And even those countries capable of reporting sometimes find economic or political reasons to hold back (or delay releasing) disease outbreak information - or refuse to share virus samples - violating both the letter and the spirit of this agreement (see Adding Accountability To The IHR).

But over the past 6 months, even the normally reliable surveillance and reporting systems around the globe have diverted their attentions away from old threats like seasonal influenza, MERS-CoV, avian flu, Monkeypox, and a host of other emerging infectious diseases.

The graphic at the top of this blog compares the early August Influenza reporting by the WHO for 2019 vs. 2020. Except for North America, the 2020 map is blank. Some of this is undoubtedly due to reduced influenza transmission around the world, due to COVID-19 social distancing, but certainly not all.

From yesterday's bi-weekly flu report.

Influenza update - 373
03 August 2020 - Update number 373, based on data up to 19 July 2020

Information in this report is categorized by influenza transmission zones, which are geographical groups of countries, areas or territories with similar influenza transmission patterns. For more information on influenza transmission zones, see the link below:

Influenza Transmission Zones pdf, 659kb

Open map in new window png, 268kb

Summary
The current influenza surveillance data should be interpreted with caution as the ongoing COVID-19 pandemic might have influenced to varying extents health seeking behaviours, staffing/routines in sentinel sites, as well as testing priorities and capacities in Member States. The various hygiene and physical distancing measures implemented by Member States to reduce SARS-CoV-2 virus transmission might also have played a role in mitigating influenza virus transmission.
Globally, influenza activity was reported at lower levels than expected for this time of the year. In the temperate zones of the southern hemisphere, the influenza season has not commenced.
In the temperate zone of the northern hemisphere, influenza activity remained at inter-seasonal levels.
In the Caribbean and Central American countries, sporadic influenza detections were reported in most reporting countries. Severe acute respiratory infection (SARI) activity remained elevated in some reporting countries.
In tropical South American and tropical Africa, there were no or sporadic influenza virus detections across reporting countries.
In Southern Asia and South East Asia, no influenza detections were reported.
Worldwide, seasonal influenza A viruses accounted for the majority of detections.
National Influenza Centres (NICs) and other national influenza laboratories from 59 countries, areas or territories reported data to FluNet for the time period from 06 July 2020 to 19 July 2020 (data as of 2020-07-31 04:23:14 UTC). The WHO GISRS laboratories tested more than 302586 specimens during that time period. A total of 45 specimens were positive for influenza viruses, of which 26 (57.8%) were typed as influenza A and 19 (42.2%) as influenza B. Of the 7 sub-typed influenza A viruses, 100% were influenza A(H1N1)pdm09. Of the 2 characterized B viruses, 100% belonged to the B-Victoria lineage.

WHO encourages the testing of routine influenza surveillance samples from sentinel and non-sentinel sources for SARS-CoV-2 virus where resources are available and invites all countries/areas/territories to report this information (ideally indicating which data are from sentinel sites) to routine, established regional and global platforms. (See the Operational considerations for COVID-19 surveillance using GISRS guidance)

(Continue . . . )

In the corresponding 2019 report (Aug 5th), 4322 positive influenza samples were submitted, 75 times greater than was submitted in this report.

Whole regions of the world have apparently stopped submitting flu reports. The WHO EMRO Influenza weekly update from the Eastern Mediterranean region - which normally reports 52 weeks a year - last submitted a report in early March.

All of this matters because less than two weeks ago, in ECDC: Influenza virus characterisation - Summary Europe, June 2020, we saw the first antigenic analysis of flu samples in the EU since March, which suggested increasing poor reactivity to the 2019-2020 H1N1 vaccine virus, jumping from 9% of samples reported last March to 22% (22 of 99) in this month's report.

Similarly, 25% of the (69) Influenza B/Victoria viruses tested were not well recognized by antiserum raised against the vaccine virus for last year's northern hemisphere influenza season.

How much of a factor seasonal flu will be this fall is anyone's guess, but it is risky to take our eyes off the ball, particularly since decisions must be made in September for next year's Southern Hemisphere flu vaccine.

But it isn't just seasonal flu.

Saudi Arabia hasn't updated their MERS-CoV surveillance page since late May, when they were reportedly dealing with a hospital outbreak (see WHO DON: Middle East respiratory syndrome coronavirus (MERS-CoV) – Saudi Arabia).

No other Middle Eastern countries have reported any MERS-CoV cases since March. While it is possible MERS-CoV activity has vanished, it isn't terribly likely.

Reports of novel flu around the world have declined since the pandemic began as well. We've seen a handful of avian H9N2 cases reported in China, and a small number of swine variant flu infections (Brazil, Germany & Hawaii), but no H5Nx or H7N9 cases in 2020.

If countries aren't robustly testing for seasonal flu - which they don't appear to be right now - they are unlikely to pick up very many novel flu infections.

Only occasionally do we see bird flu reports, such as the recent H7N7 outbreak in Victoria Australia, or this report yesterday from Chelyabinsk Oblast, Russia describing bird deaths from H5N8.

Avian influenza was registered in the Chelyabinsk region

The Rosselkhoznadzor Administration for the Chelyabinsk region informs that an outbreak of bird flu has been registered in the region. The Rosselkhoznadzor Directorate and the Veterinary Directorate of the Regional Ministry of Agriculture are taking all measures to prevent the spread of this dangerous disease. The diagnosis made by the staff of the Uvelskaya Interdistrict Veterinary Laboratory and the Chelyabinsk Testing Laboratory was confirmed by the specialists of the Federal Center for Animal Health (FGBI ARRIAH) in Vladimir: the genetic material of the avian influenza virus subtype H5N8 was identified.

The bodies of birds found were examined (1 wild duck, 2 domestic and 2 domestic geese), selected on the shores of Peschanoe and Tabinsha lakes, Uvelsky district. All samples revealed material from the avian influenza virus subtype H5N8. In this regard, a registration of birds was carried out in these settlements. On the territory of disadvantaged settlements located near these lakes, quarantine has been established, epizootic foci and threatened zones have been identified. In disadvantaged areas, activities are carried out in accordance with the rules for combating avian influenza.

While not particularly ominous, over the winter of 2016/2017 a reassorted, and revitalized HPAI H5N8 virus arrived in Europe following a reassortment event the previous summer in Qinghai/ Ubsu-Nur, (see EID Journal: Reassorted HPAI H5N8 Clade 2.3.4.4. - Germany 2016), sparking perhaps the largest avian epizootic in European history.

A study, published in 2016 (see Sci Repts.: Southward Autumn Migration Of Waterfowl Facilitates Transmission Of HPAI H5N1), suggests that waterfowl pick up new HPAI viruses in the spring (likely from poultry or terrestrial birds) on their way to their summer breeding spots - where they spread and potentially evolve - and then redistribute them on their southbound journey the following fall.

Meaning that what we see this fall and inter could well depend upon what avian viruses have been circulating among birds in the high latitudes over the summer, and will be carried south by migratory birds for the winter (see WHO: Migratory Birds & The Potential Spread Of Avian Influenza).