Report

Report 12: 15th October 2020 – COVID-19 Genomics UK (COG-UK) Consortium

Please Note: This report is provided at the request of SAGE and includes information on the ongoing state of the research being carried out. It should not be considered formal or informal advice. The conclusions of the ongoing scientific studies may be subject to change as further evidence becomes available and as such any firm conclusions would be premature.

Executive Summary

  • COG-UK genome sequence data and tools have been used in more than 120 retrospective and live public health outbreak investigations in the UK since March 2020.
  • A viral lineage carrying a mutation, N439K, a probable antigenic variant owing to its location in the receptor binding motif of the SARS-CoV-2 spike protein, is now spreading in Europe (including 500+ infections in the UK). While there is no evidence that this variant will affect the efficacy of vaccines currently in development, it does highlight the need to establish a systematic approach for monitoring the appearance and spread of all variants and prioritising mutations of interest for further characterisation, in particular when selective pressure from mass vaccination programmes begins.

 

COG-UK summary

As described in COG-UK Report #11, in addition to retrospective investigations, the consortium has been providing crucial support for the genomic surveillance of active SARS-CoV-2 outbreaks. An email survey of COG-UK site leads was used to collate information on the number of outbreaks in which investigations by the consortium using genomics have added value (Table 1). In total, COG-UK data and tools have been used in 120-166 live and retrospective SARS-CoV-2 outbreak investigations in public health and hospital settings in the UK to date.

Table 1: A summary of live and retrospective outbreaks in the UK for which COG-UK and PHA researchers have used consortium genomic data and tools. Exceedance describes defined outbreaks, for instance in a workplace. Surveillance programmes describe requests to look at everything in a local authority area, school, care home etc. Ranges are reported as some sites were only able to provide estimates.

For a description of specific examples of the value added through the use of genomics by consortium members during outbreak investigations see ‘COG-UK genomic surveillance in action’, COG-UK Report #11.

As the transition to a new operational phase continues through late 2020 and into 2021, COG-UK will provide large scale genomic surveillance service to support the investigation of a growing proportion of live outbreaks in the UK.

As described in the recent NERVTAG paper to SAGE, co-authored by COG-UK (Is there evidence for genetic change in SARS-CoV-2 and if so, do mutations affect virus phenotype?), there is increasing interest in monitoring mutations arising in the SARS-CoV-2 genome and determining whether these mutations have an impact on the biology of the virus, its transmission and the severity of the disease that it causes (See also ‘A preliminary analysis of SARS-CoV-2 spike protein N439K lineages and surveillance of receptor binding mutations.’ below). A COG-UK working group is being established to ensure that new and existing mutations are monitored in a systematic manner and that mutations of particular interest are prioritised for in depth analysis.

As the speed and scale of SARS-CoV-2 genome sequencing increases, the ability to use genomic data to investigate a wide range of scientific and public health questions is also growing. Accordingly, COG-UK is strengthening its interactions with other SAGE sub-groups, research consortia and public health bodies in the UK, and globally, so that the opportunities provided by integrating genomics can be realised. Dr Andrew Page of the Quadram Institute, Norwich has recently agreed to represent COG-UK on the SAGE sub-group focussed on social care homes. Dr Ewan Harrison of the Wellcome Sanger Institute represents the consortium on the sub-group focussed on ethnicity, and  Professor Judith Breuer of University College London on the nosocomial infection sub-group.

All five Health and Social Care Trusts in Northern Ireland are joining the SIREN study (the PHE priority study to determine if prior SARS-CoV-2 infection in health care workers confers future immunity to re- infection), and the Belfast Health and Social Care Trust is expected to join COG-UK’s Hospital-Onset COVID-19 Infections study. Northern Ireland will therefore be represented in both of these important UK-wide studies, with viral genome sequencing/analysis via COG-UK.


 

Analysis updates

A preliminary analysis of SARS-CoV-2 spike protein N439K lineages and surveillance of receptor binding domain mutations.

Study leads

David L Robertson1, Sebastian Maurer-Stroh2, Ana da Silva Filipe1 and Emma C Thomson1
1. MRC-University of Glasgow Centre for Virus Research;
2. Bioinformatics Institute, Agency for Science, Technology and Research, Singapore

Question addressed

SARS-CoV-2 is continually accruing mutations as it replicates and transmits among the human population. While the majority of observed mutations have no effect on the biological properties of the virus and the rate of change is relatively slow, it is important that there is a systematic approach to identify new genetic changes and to assess their biological significance. While much attention has been focussed on the SARS-CoV-2 spike protein D614G mutation (See COG-UK report #6, report #9 and Ref 1), other mutations in the spike protein may be of epidemiological and clinical relevance. This analysis describes the assessment of transmission and likely biological significance of one such mutation: N439K in the spike receptor binding motif is an example of a stable and circulating mutation in the receptor binding motif that binds to the ACE2 receptor on the surface of host cells to enable viral entry.

Methodology

Preliminary assessment of sampling proportions, phylogenetic distribution and the relationship between N/K at position 439 of the spike protein.

Findings

N439K was initially identified in a single lineage first detected in March 2020 and until recently was almost unique to Scotland where it infected more than 500 individuals (Figure 1).

Figure 1: Phylogenetic tree of 5000 Scottish SARS-CoV-2 genomes from COG-UK dataset (17/07/20) highlighting D614G lineages (left panel) and N439K lineages (right panel). Note that the K-439 lineage and most N-439 lineages are also G-614.

This lineage also carries the D614G variant that has been associated with an increase in frequency among the population.

In line with the cessation in viral transmission in Scotland coincident with the lockdown in spring 2020, this UK lineage is now extinct and has not been observed since the 20th June in South Lanarkshire. However, N439K has now been identified in another fast growing lineage that has been sampled between late June and mid-August in Romania, Norway, Switzerland, Ireland, Belgium, Germany and now in all parts of the UK (Figure 2). The apparent sudden rise in August/September appears to be linked to relaxation of  control measures, the degree of sampling in these countries and its recent emergence in the UK with a high sampling rate. N439K has also been detected in four linked infections in the US and sporadically in genome data from elsewhere.

Figure 2: A) Phylogenetic tree of SARS-CoV-2 genomes from the COG-UK data in the context of the GISAID dataset highlighting the original Scottish N439K lineage and the more recent and currently spreading European N439K lineage associated with multiple UK lineages. B) Number of weekly cases and country location of the two N439K lineages from mid-March to 02/10/2020.

Investigation of clinical outcomes from >1600 Scottish patients infected with either the lineage defined by 439K versus the wild-type lineage (439N) showed no significant difference in disease severity. Phylodynamic analysis demonstrated that the Scottish N439K lineage has a relatively fast growth rate in spreading through the population (analysis by Sam Lycett, Roslin Institute), but this is likely due to the D614G background  of this lineage (Ref 1). Competitive virus growth experiments of these different mutants are underway at the MRC-University of Glasgow Centre for Virus Research.

Investigation of clinical outcomes from >1600 Scottish patients infected with either the lineage defined by 439K versus the wild-type lineage (439N) showed no significant difference in disease severity. Phylodynamic analysis demonstrated that the Scottish N439K lineage has a relatively fast growth rate in spreading through the population (analysis by Sam Lycett, Roslin Institute), but this is likely due to the D614G background of this lineage (Ref 1). Competitive virus growth experiments of these different mutants are underway at the MRC-University of Glasgow Centre for Virus Research.

Key Conclusions

While SARS-CoV-2 genetic variation is accumulating, it is relatively constrained for an RNA virus.

Some spike amino acid replacements do seem to be changing the biology of the virus (e.g. D614G), although there is no current evidence that N439K, or other variants in the receptor binding motif (such as T478I and V483I, shown to have antigenic significance) have increased the potential for transmission or altered disease severity.

Importantly, these spike receptor binding domain variants appear to be relatively stable amino acid replacements that are not detrimental to viral fitness and are well tolerated in circulating lineages in the UK. This is a potential concern as vaccination programmes designed using these regions as targets begin to apply selective pressure on these lineages (see below for further discussion).

Discussion

In addition to N439K, other mutations are being observed in the spike receptor binding motif: S477N (>300 UK sequences), T478I (>100), S494P (>20), E484Q (>10), S477I (>10), E484Q (>10) and others at lower frequencies (Figure 3).

Figure 3. Receptor binding surveillance for UK complete genomes. Mutations resulting in amino acid replacements in or near SARS-CoV-2’s spike receptor binding motif that have been observed by 2020-10-06 are shown. Replacements occurring at least twice are listed (top).

Collectively these demonstrate that mutations in the spike receptor binding motif are tolerated. The circulation of the N439K lineages demonstrates these viruses do not necessarily exhibit any apparent fitness cost. This is potentially concerning as this region is soon to be under selective pressure from a range of vaccine programmes.

Some of the mutations in the receptor binding domain have been documented to confer resistance to neutralising antibodies and to influence interactions with the ACE2 receptor, which may facilitate the evolution of additional mutations in the surrounding region that can lead to viruses able circumvent the impact of those neutralizing antibodies. Support for this concern has been provide by laboratory experiments showing that it is possible to select for SARS-CoV-2 spike protein mutations in the receptor-binding domain (including N439K) that remain functional and able to bind ACE2 receptors but can confer resistance to monoclonal neutralising antibodies or convalescent plasma (Refs 2 and 3).

It is therefore essential that a systematic approach is taken to identify and assess new genetic changes, in particular in regions important for host infection, viral transmission and for antigenicity. Whilst limited genomic diversity has emerged to date, this may change in the next phase of the epidemic as selective pressures exerted by vaccines, treatments and non-pharmaceutical interventions increases. As such, it is particularly important that surveillance of antigenic change is established in the lead up to the roll out of a vaccination program in the UK, since many of the vaccines under development target the spike protein.

Accordingly COG-UK has established a working group to establish a mechanism to ensure that new and existing mutations are monitored in a systematic manner and that mutations of particular interest are prioritised for in depth genomic, phylodynamic and virological analyses.

References

1. Volz, E. M, et al. Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity (2020) medRxiv, doi: https://doi.org/10.1101/2020.07.31.20166082.

2. Weisblum, Y., Schmidt, F., et al. Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants. (2020) bioRxiv, doi: https://doi.org/10.1101/2020.07.21.214759.

3. Li, Q. et al. The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity. (2020) Cell, doi: https://doi.org/10.1016/j.cell.2020.07.012


 

COG-UK recent publications

Large scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management

MedRxiv – doi: https://doi.org/10.1101/2020.09.28.20201475

Authors:

Andrew J Page, Alison E Mather, Thanh Le Viet, Emma J Meader, Nabil-Fareed J Alikhan, Gemma L Kay, Leonardo de Oliveira Martins, Alp Aydin, David J Baker, Alexander J. Trotter, Steven Rudder, Ana P Tedim, Anastasia Kolyva, Rachael Stanley, Maria Diaz, Will Potter, Claire Stuart, Lizzie Meadows, Andrew Bell, Ana Victoria Gutierrez, Nicholas M Thomson, Evelien M Adriaenssens, Tracey Swingler, Rachel AJ Gilroy, Luke Griffith, Dheeraj K Sethi, Rose K Davidson, Robert A Kingsley, Luke Bedford, Lindsay J Coupland, Ian G Charles, Ngozi Elumogo, John Wain, Reenesh Prakash, Mark A Webber, SJ Louise Smith, Meera Chand, Samir Dervisevic, Justin O’Grady, The COVID-19 Genomics UK (COG-UK) consortium

Summary:

Between March and August 2020, over 3,200 COVID-19 cases were reported in Norfolk. 1565 positive clinical samples from 1376 cases were collected in four major hospitals, multiple minor hospitals, care facilities and community organisations within Norfolk and the surrounding area were collected and subjected to whole genome sequencing. 1035 cases resulted in genomes of sufficient quality for phylogenetic analysis, which revealed the presence of 26 distinct global lineages and 100 distinct UK lineages, with local evolution at a rate of 2 SNPs per month. Sequence data was combined with clinical metadata to understand the origin, genetic variation, transmission and spread of SARS-CoV-2 within the region. Highlights from this county-level analysis included the identification of a single sub-lineage associated with cases in 6 care facilities; confirming an outbreak at a food-processing facility; the ruling out of a nosocomial origin for another outbreak; and the identification of 16 lineages in health care workers not present in patients, demonstrating the effectiveness of infection control measures. The analysis also found that the D614G spike protein variant dominated in the samples, while longitudinal samples showed no evidence of reinfection.


 

Respiratory disease in cats associated with human-to-cat transmission of SARS-CoV-2 in the UK

BioRxiv – doi: https://doi.org/10.1101/2020.09.23.309948

Authors:

Margaret J Hosie, Ilaria Epifano, Vanessa Herder, Richard J Orton, Andrew Stevenson, Natasha Johnson, Emma MacDonald, Dawn Dunbar, Michael McDonald, Fiona Howie, Bryn Tennant, Darcy Herrity, Ana Da Silva Filipe, Daniel G Streicker, Brian J Willett, Pablo R Murcia, Ruth F Jarrett, David L Robertson, William Weir, the COVID-19 Genomics UK (COG-UK) consortium

Summary:

During the COVID-19 pandemic, naturally occurring infections following transmission have been reported in domestic and non-domestic cats, dogs and mink. In this study, two cats from different COVID-19-infected households in the UK were shown to be infected with SARS-CoV-2 from humans. Infection was demonstrated using a range of approaches, including immunofluorescence, in situ hybridization, PCR testing. Post-mortem tissue samples for cat 1 displayed pathological and histological findings consistent with viral pneumonia, while cat 2 presented with rhinitis and conjunctivitis. Whole genome sequencing and analysis of the virus from cat 2 revealed five single nucleotide polymorphisms (SNPs) compared to the nearest sequenced UK human SARS-CoV-2 isolate (from the same UK county), although comparison with genomes from 9 other feline SARS-CoV-2 isolates revealed no shared cat-specific mutations. At present, there is no evidence of cat-to-human transmission or that cats, dogs or other domestic animals play any appreciable role in the epidemiology of human infections with SARS-CoV-2.


 

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