Thursday, May 13, 2021

ECDC Threat Assessment Brief On COVID Variant B.1.617.x

 

#15,958

While there are many gaps in our understanding of the threats posed by the emerging B.1.617 variant and its sublineages in India, over the past 7 days we've seen acknowledgements of its potential importance from a variety of public health agencies, including:
WHO COVID SitRep: Special Focus On Variant B.1.617.x

UK: 88th SAGE Meeting On COVID - B.1.617 Variant, SitRep & Vaccine Effectiveness

WHO Designates B.1.617 as a Global Variant of Concern

While already dire, pandemic reports coming out of India are believed to be incomplete and substantially underreported (see U.S Consulate & Embassies In India: Messaging On COVID Crisis).  Although there are likely many factors involved, there are growing concerns that the B.1.617 lineage possesses enhanced transmissibility, potentially greater severity, and possibly some ability to evade existing antibodies. 

Two days ago the ECDC published a Threat Assessment Brief on this COVID lineage, which appears to have information current as of May 10th.  They do provide a brief note regarding the recent WHO announcement (above):

Since the publication of the Threat Assessment Brief, WHO announced that viruses within the lineage B.1.617 have been characterized as a Variant of Concern. More details can be accessed in the WHO COVID-19 Weekly Epidemiological Update

While there aren't a lot of answers yet, you will find a good deal of background, and discussion, of these B.1.617.x variants in the following report.   I've reproduced the executive summary below, after which we'll take a closer look at one of the report's graphics. 

Follow the link to down load the full 12-page PDF.
Threat Assessment Brief: Emergence of SARS-CoV-2 B.1.617 variants in India and situation in the EU/EEA
Risk assessment
11 May 2021
  
The aim of this Threat Assessment Brief is to assess potential public health implications of B.1.617 variants for EU/EEA countries, with a focus on lineage B.1.617.2.

Executive summary
  • First reported in India in December 2020, SARS-CoV-2 lineages B.1.617.1, B.1.617.2 and B.1.617.3 have been increasingly detected in other countries.
  • The aim of this Threat Assessment Brief is to assess the potential public health implications of the B.1.617 lineages for EU/EEA countries with a focus on lineage B.1.617.2.
  • Over the past eight weeks India and some surrounding countries have seen a sharp increase in the number of reported SARS-CoV-2 cases and deaths. This has been associated with a rising proportion of sequenced viruses belonging to lineages B.1.617.1 and B.1.617.2.
  • The United Kingdom has seen a rapid increase in detection of lineage B.1.617.1 and, to a greater extent, B.1.617.2, associated with travel to India and onward community transmission. On the 6 May, the United Kingdom (UK) designated lineage B.1.617.2 as a variant of concern.
  • In the EU/EEA there are indications that the frequency of detection of both lineages B.1.617.1 and B.1.617.2 is increasing.
  • Currently described lineages B.1.617.1, B.1.617.2 and B.1.617.3 have distinct mutation profiles and warrant individual assessment. Given the still very limited available data with respect to their transmissibility, disease severity and immune escape potential relative to other co-circulating SARS-CoV-2 variants in the EU/EEA, the full impact of these lineages on public health is not yet possible to assess.
  • At this time, ECDC maintains its assessment of B.1.617.1, B.1.617.2 and B.1.617.3 as variants of interest and will continue to actively monitor the situation.
Options for response
  • In order to better understand and inform assessments of the potential public health implications of these variants, targeted genomic surveillance should be enhanced (including of travel-associated cases, clusters or outbreaks and breakthrough infections) together with antigenic characterisation of SARS-CoV-2 variants and enhanced general surveillance.
  • Diagnostic laboratories should remain vigilant to detect any mismatches of specific RT-PCR assay primers and probes in comparison to circulating virus genomes.
  • COVID-19 vaccination rollout should continue to be a high priority to reduce COVID-19 mortality by vaccinating those at risk of severe illness in the shortest time possible, thereby reducing SARS-CoV-2 transmission, as has recently been documented in Israel and the UK.
  • COVID-19 vaccine coverage remains at low levels in all EU/EEA countries, and as such, ECDC currently advises caution in the relaxation of current non-pharmaceutical measures including those related to travel. The limited information so far regarding these new variants does not change ECDC’s current advice on nonpharmaceutical measures. Greater understanding of the risks related to these B.1.617 lineages is needed before any modification of current measures can be considered.
  • Further characterisation of these lineages is needed to allow a full assessment of their potential public health implications
Threat Assessment Brief: Emergence of SARS-CoV-2 B.1.617 variants in India and situation in the EU/EEA - EN - [PDF-549.49 KB]


One graphic (among many) in this report caught my eye, as it illustrates the rapid rise of the B.1.617.2 variant - going from near obscurity in early March to becoming the dominant variant in India by mid-April - despite competing with the highly transmissible B.1.1.7 variant. 


The report describes this variant's rapid rise:

B.1.617.2 was first detected in India in December 2020, and remained rare in the country until early March 2021, when it started to increase, becoming the dominant variant amongst reported sequences in mid-April 2021 (Figure 2). As of 10 May 2021, it has been detected in the United Kingdom (676), India (290), USA (192), Singapore (91), Australia (58), Germany (31), Japan (20), Denmark (18), Bahrain (13), Belgium (12), France (12), Ireland (12), Switzerland (10), New Zealand (9), Italy (5), Poland (5), China (4), Spain (3), Sweden (3), Indonesia (2), the Netherlands (2), Aruba (1), Austria (1), Canada (1), Greece (1), Hong Kong (1), Luxembourg (1), Norway (1), Romania (1), Slovenia (1), and South Korea (1).

The United Kingdom has seen a rapid increase in the proportion of this variant, associated with travel to India and onward community transmission [9]. There is an increasing trend in some EU/EEA countries, but the variant remains at low levels, with the highest proportions being reported by Ireland (1.5%), France (1.0%), and Belgium (0.8%) in GISAID EpiCoV, for week 16. If these countries would follow the same pattern of increase of B.1.617.2 as the United Kingdom, they are at least two weeks behind in the evolution of the increase (Figure 3). When a variant is associated with travel, its proportion in the community can be overestimated as travellers and their contacts are more likely to be tested than others, so these data should be interpreted with caution.

Regardless of any other potential qualities, B.1.617.2's ability to rout all of the other COVID variants circulating in India over a matter of a few weeks  - combined with its detection in more than 3 dozen countries - should give us pause. 

Stay tuned.

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