Wednesday, April 06, 2022

WHO Weekly COVID Epi Report (#86) - Update On Emerging Variants (Including Recombinants)


As discussed last week, in WHO COVID Weekly Epi Update #85 - Includes Warning On The Dangers Of Reduced Testing, for a variety of reasons (including political expedience, limited resources & pandemic fatigue), countries around the world are doing far less COVID testing and reporting. 

As a result, our ability to interpret the numbers and trends being presented is increasingly limited.  

This concern is broached once again by this week's WHO Epi report, which - after presenting this week's data - warns:

These trends should be interpreted with caution as several countries are progressively changing their COVID-19 testing strategies, resulting in lower overall numbers of tests performed and consequently lower numbers of cases detected. 

This warning is reprised several times in this 22-page PDF, along with a familiar plea for Member Nations to implement  `. . . continuous, comprehensive, and representative community sampling and sequencing strategies' and to share that data in a `timely manner'.  

I'll have more on this growing problem in a postscript after the break.

Global overview

Data as of 3 April 2022

After the increase observed during the first half of March 2022, the number of new COVID-19 cases has decreased for a second consecutive week, with a 16% decline during the week of 28 March through 3 April 2022 as compared to the previous week (Figure 1). The number of new weekly deaths also decreased sharply (-43%) as compared to the previous week, when an artificial spike in deaths was observed (see WEU 85).

Across the six WHO regions, over nine million new cases and over 26 000 new deaths were reported. All regions reported decreasing trends both in the number of new weekly cases and new weekly deaths (Table 1). As of 3 April 2022, just over 489 million cases and over 6 million deaths have been reported globally.

These trends should be interpreted with caution as several countries are progressively changing their COVID-19 testing strategies, resulting in lower overall numbers of tests performed and consequently lower numbers of cases detected.

At the country level, the highest number of new weekly cases were reported from the Republic of Korea (2 058 375 new cases; -16%), Germany (1 371 270 new cases; -13%), France (959 084 new cases; +13%), Viet Nam (796 725 new cases; -29%), and Italy (486 695 new cases; -3%).

The highest number of new weekly deaths were reported from the United States of America (4 435 new deaths; -10%), the Russian Federation (2 357 new deaths; -18%), the Republic of Korea (2 336 new deaths; -5%), Germany (1 592 new deaths; +5%), and Brazil (1 436 new deaths; -19%).

 This week's report also contains the following update on Variants, including recombinants. 

Special Focus: Update on SARS-CoV-2 variants of interest and variants of concern

WHO, in collaboration with national authorities, institutions and researchers, routinely assesses if variants of SARS-CoV-2 alter transmission or disease characteristics, or impact effectiveness of vaccines, therapeutics, diagnostics or public health and social measures (PHSM) applied to control disease spread. Potential variants of concern (VOCs), variants of interest (VOIs) or variants under monitoring (VUMs) are regularly assessed based on the risk posed to global public health.

The classifications of variants will be revised to reflect the continuous evolution of circulating variants and their changing epidemiology. Criteria for variant classification, and the current lists of VOCs, VOIs and VUMs, are available on the WHO Tracking SARS-CoV-2 variants website. National authorities may choose to designate other variants and are encouraged to investigate and report on the impacts of these variants. When referring to the genomic sequence of SARS-CoV-2 identified from the first cases (December 2019), the term ‘index virus’ should be used.

Geographic spread and prevalence of VOCs

The Omicron variant remains the dominant variant circulating globally, accounting for nearly all sequences recently reported to GISAID. Among the 417 147 sequences uploaded to GISAID with specimens collected in the last 30 days i , 416 175 (99.8%) were Omicron, 141 (<0.1%) were Delta, and 562 sequences were not assigned to a Pango lineage (<0.2%). The total number of submitted Omicron sequences continues to decline, a trend observed for each of the Omicron descendent variants. 

Among the Omicron descendent lineages, the relative proportion of BA.2 has increased to 93.6%, while BA.1.1 accounts for 4.8% and BA.1 and BA.3 account for <0.1% (figure 4, panels A and B) of all Omicron lineages. BA.2 has become dominant in all six WHO regions (figure 4, panel C) and in 68 countries for which sequence data are available. However, there have been subregional differences in the rise of BA.2; notably in South America: BA.2 began to rise later and at a slower rate as compared to other subregions, accounting for 28% of  Omicron lineages in week 11 (14 to 20 March 2022). 

These trends should be interpreted with due consideration of the limitations of surveillance systems, including differences in sequencing capacity and sampling strategies between countries, as well as laboratory turn-around times for sequencing and delays in reporting.

Reduced number of SARS-CoV-2 sequences in publicly available database

Since the first epidemiological week of 2022, when the highest number of weekly sequences was reported in GISAID (284 061 sequences), the number of weekly sequences has declined progressively. During week 12 (21 to 27 March 2022), only 65 381 sequences were collected and submitted to GISAID. There has been an average of 12% reduction in the weekly collection and submission of sequences.

While the decrease in sequences is consistent with the overall trend in new cases observed globally, it may also reflect changes in epidemiological surveillance policies in some countries, including changes in sampling and sequencing strategies, resulting in lower overall numbers of tests performed and consequently lower numbers of cases detected.

Recombinants update

The SARS-CoV-2 virus continues to evolve. Given the current high level of transmission worldwide, it is likely that further variants, including recombinants, will continue to emerge. Recombination is common among coronaviruses and is regarded as an expected mutational event.

WHO is tracking recombinant variants, both recombinants of Delta (AY.4) and Omicron (BA.1) (e.g., XD Pango lineage), as well as recombinants of BA.1 and BA.2 (e.g., XE Pango lineage). The XD recombinant is being tracked as a VUM by WHO, although its spread appears to have remained limited at present (26 sequences in GISAID). Currently available evidence does not suggest that it is more transmissible than other circulating variants. 

The XE recombinant is being tracked as part of the Omicron variant. This recombinant was first detected in the United Kingdom on 19 January and approximately 600 sequences have been reported and confirmed as of 29 March 2022. Early estimates suggest that XE has a community growth rate advantage of 1.1 (which represents a 10% transmission advantage) as compared to BA.2; however, this finding requires further confirmation.

The evolution rate and the risk of the emergence of new variants, including recombinants, is still very high. The implementation of continuous, comprehensive and representative community sampling and sequencing strategies, alongside timely sharing of data by Member States, remain critical for tracking and understanding the behaviour of SARS-CoV-2 (see WEU 85). WHO continues to closely monitor and assess the public health risk associated with recombinant variants, alongside other SARS-CoV-2 variants, and will provide updates as further evidence becomes available.

          (Continue . . . .)

This disturbing tendency to `Don't Test, Don't Tell' is sadly nothing new, and has been the topic of a number past blogs, many written long before this pandemic began.  

Although the new 2005 International Health Regulations (IHR) required – among other things – that countries develop mandated surveillance and testing systems, and that they report certain disease outbreaks and public health events to WHO in a timely manner, after 17 years we still see huge gaps in surveillance and reporting. 

While for some nations, this failure is due to a lack of resources, for others it is deliberate, and based on politics, public relations, or economic concerns (see Adding Accountability To The IHR).

This short list is indicative of a much larger problem.  One which we've discussed often (see Flying Blind In the Age Of Pandemics & Emerging Infectious Diseases).  

Based on what I'm seeing, our `situational awareness' of emerging infectious disease activity around the world appears to be worse than its been in many years.

A failing that could easily come back to haunt us, with very little warning.