#15,640
While it is too soon to know how much of an impact the recently announced SARS-CoV-2 variant (VUI 202012/01) in the UK will have on the course of the pandemic (see New COVID-19 Variant Up To 70% More Transmissible), there is little doubt that scientists around the world are closely monitoring its spread in both the UK, and a handful of other countries.
The original Asian strain of COVID mutated last winter after it arrived in Europe when it picked up a D614G mutation, which is thought to have made it more transmissible (see Cell Evidence that D614G Increases Infectivity of the COVID19 Virus). Over the summer, we saw another variant (Dubbed 20A.EU1) emerge in Europe, which may have upped the ante once again.
This latest variant supposedly contains a larger number of mutations, and has reportedly increased its transmissibility by up to 70%. For now, there is no evidence this new variant produces any greater severity of disease, or would evade the current vaccine, but investigations are still ongoing.
Evidence of the level of concern this variant has unleashed, several EU countries have banned travel to and from the UK, and earlier today the ECDC published a rapid risk assessment on this new UK variant.
Since information remains scant, this report is short on conclusions, but it does summarize what we know - and the things that need to happen in order to better quantify the threat - in it's 13-page PDF file.
I've reproduced the executive summary below, along with a couple of excerpts from the report. Follow the link to read the full report in its entirety.
Threat Assessment Brief: Rapid increase of a SARS-CoV-2 variant with multiple spike protein mutations observed in the United Kingdom
Risk assessment
20 Dec 2020
The aim of this Threat Assessment Brief is to summarise the findings, assess potential public health implications of this new variant, provide options for response and point out limitations, unknowns and needs for further studies and investigations.
Executive summary
Over the last few weeks, the United Kingdom (UK) has faced a rapid increase in COVID-19 cases in South East England, leading to enhanced epidemiological and virological investigations. Analysis of viral genome sequence data identified a large proportion of cases belonged to a new single phylogenetic cluster. The new variant is defined by multiple spike protein mutations (deletion 69-70, deletion 144, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H) present as well as mutations in other genomic regions.While it is known and expected that viruses constantly change through mutation leading to the emergence of new variants, preliminary analysis in the UK suggests that this variant is significantly more transmissible than previously circulating variants, with an estimated potential to increase the reproductive number (R) by 0.4 or greater with an estimated increased transmissibility of up to 70%.This new variant has emerged at a time of the year when there has traditionally been increased family and social mixing. There is no indication at this point of increased infection severity associated with the new variant. A few cases with the new variant have to date been reported by Denmark and the Netherlands and, according to media reports, in Belgium.
Given that there is currently a lack of evidence to indicate the extent to which the new virus variant is spread outside the UK, timely efforts to prevent and control its spread are needed, and include the following:
- Public health authorities and laboratories are urged to analyse and sequence virus isolates in a timely manner to identify cases of the new variant. People with an epidemiological link to cases with the new variant or travel history to areas known to be affected should be identified immediately to test, isolate and follow up their contacts in order to stop the spread of the new variant.
- If cases infected with this new SARS-CoV-2 variant or other new SARS-CoV-2 variants of potential concern are identified, countries should notify through the Early Warning and Response System of the European Union.
- The importance of strict adherence to non-pharmaceutical interventions according to national policies needs to be communicated to the public, and in particular guidance on the avoidance of non-essential travel and social activities should be stressed.
- Laboratories should review the PCR performance and drop-out of the S-gene. PCR could be used as an indicator for cases with the new variant for further sequencing and investigation.
- Suspected cases of COVID-19 reinfection should be followed up, closely accompanied by sequencing respective virus isolates from these cases. Similarly, cases with treatment failures using convalescent plasma or monoclonal antibodies should be further studied.
- With the implementation of vaccination, close monitoring of COVID-19-vaccinated individuals needs to be ensured to identify possible vaccination failure and breakthrough infections. Virus isolates from these cases should be sequenced and characterised genetically and antigenically.
Download
Rapid increase of a SARS-CoV-2 variant with multiple spike protein mutations observed in the United Kingdom - EN - [PDF-647.35 KB]
COVID-19 GISAID acknowledgement ECDC threat assessment on UK variant - EN - [PDF-88.1 KB]
One of (many) interesting discussions in this report revolve around the large number of mutations in this new variant, and suggests several ways that might have occurred.
(EXCERPT)Possible sources of SARS-CoV-2 virus variants with a high number of mutations in the spike protein
The unusually high number of spike protein mutations, other genomic properties of the variant, and the high sequencing coverage in the UK suggest that the variant has not emerged through gradual accumulation of mutations in the UK.
It is also unlikely that the variant could have arisen through selection pressure from ongoing vaccination programmes as the observed increase does not match the timing of such activities.
- One possible explanation for the emergence of the variant is prolonged SARS-CoV-2 infection in a single patient, potentially with reduced immunocompetence, similar to what has previously been described [17,18]. Such prolonged infection can lead to accumulation of immune escape mutations at an elevated rate.
- Another possible explanation could be adaptation processes in a virus that occur in a different susceptible animal species and is then transmitted back to humans from the animal hosts. This led to the emergence of a variant with multiple spike protein mutations (including RBD mutation Y453F and deletion 69-70) in Denmark during transmission among mink [19]. Several different spike protein mutations associated with mink have also been described in the Netherlands [20]. The UK has reported to ECDC and the WHO Regional Office for Europe that there is no clear epidemiological link to animals for VUI 202012/01, so this explanation is less likely for this variant [1].
- Lastly, it is also possible that the variant has emerged through circulation in countries with no or very low sequencing coverage. This hypothesis is less plausible, however, as random mutations acquired during circulation of the virus would not explain the unusually high proportion of spike protein mutations, and undetected circulation for a long enough time for the high number of mutations to accumulate (around 10 months according to current molecular clock estimates) is also not very likely due to global travel patterns.
South Africa reports through the GISAID EpiCoV database [11] and a public press release [21,22] a similar rapid increase since October of a variant with the spike protein mutation N501Y, two additional RBD mutations and multiple additional spike protein mutations. This variant has no close evolutionary relation to VUI 202012/01 but demonstrates that the emergence of successful variants with similar properties may not be rare.
Their first hypothesis; the potential for seeing rapid mutation of SARS-CoV-2 in immunocompromised patients - particularly those receiving convalescent plasma therapy, steroids, or monoclonal antibodies - is something we looked at in considerable depth a few days ago in:
