For our March webinar, we discussed CoV 2 Testing & Research and looked at how the new variants will change our approach to diagnosis, researching and tackling Covid-19. This webinar featured presentations by Neil Bentley from cog and ProLabs very own Charlotte Duncan.
Our first presentation was presented by Niel Bently from Cog. Cog is made up of 16 regional university sequencing sites and covers the whole of the UK. It includes the four public health agencies of England, Scotland, Wales and Northern Ireland.
As of March 2021, the Cog network has screened and sequenced 392487 genomes and that’s just the ones that have been uploaded into the climb database. Studies covered by the cog network include:
The HOCI study is the hospital-onset of infection study, to investigate how implementing real-time genomics can impact on the infection control to prevent spread within hospitals. It is for patients and staff within the hospital and has over 2000 participants in over 15 hospitals. Early results show that rapid sequencing does enable identification of the source of hospital outbreaks in real-time and fast enough to inform changes in infection in control practice and therefore reduce the spread of the virus.
This study is simply to see if healthy people can be protected with vaccines and do, they invoke an immune response.
“It’s been wildly published in the press that the vaccines do work, and they do evoke an immune response obviously its early days and we don’t know how long that response lasts for but the studies are ongoing”
The genomics study is a larger study than just SARSCOV2 and it’s been running since 2016 when we were looking at emerging infections within hospitals for example SARS, MERS and Flu variants and the study is to recruit sick people with sepsis and other critical illnesses to try and understand their genomic picture by sequencing both the human genome in the patent and also the viral genome or the microbial genome and linking it to the sequence as well as including metadata for example for example age, sex, postcode, ethnicity etcetera and bringing all that together to look genomicly at the outcomes and if there are any associations with the disease. The study suggests that’s there’s an insight into how the patent and the virus genomicly act together to influence patients and it will help with future outbreaks and with the understanding of why certain people are more prone to disease than others.
The REACT study looks at real-time assessments of community transmissions and this uses home testing techniques to improve our understanding of how the pandemic is progressing across England. It’s the largest population study going at the moment and it involves over 15000 participants each month and the findings provide the government with a better understanding of how the bug works and transmits and the risk associated with different population groups.
The Office of National Statistics is looking at the population survey and is trying to understand how many people of different age groups in the UK have covid at any one time. You’ll see the difference between the government figures and the ONS studies because as we know with this disease a lot of people are symptomless so it informs the status both within the NHS and possible disease trends and were looking at both the antigen and the antibody in this study and it will be running for a year.
The SIREN study looks into the immunity reinfection rates across the whole of the UK to see whether a prior infection protects against any future infection of the virus and what impact is detectable in any antibody in the disease in health care workers and initially, we found that every period of 5 months saw around 83% protection in this group against infection.
The VIVALDI study looks at how the virus is transmitting within the care home setting with both care home staff and residents and is to inform future practice and there is 6500 staff being screened and over 5000 residents across 100 care homes and they are looking for both past infection, current infection and also looking at antibodies over time ad well as the reinfection rates.
All of the studies and reports being curated by cog are uploaded to climb where you can read the results.
ProLabs technical manager Charlotte Duncan gave a presentation on the COVID-19 variants and how we are planning to develop a kit capable of detecting variants.
I find it quite useful to get back to basics because we can get so caught up in the science of it all. We all know DNA is made up of nucleotides – we have bases, and the bases form a pair. A always binds with T, T always binds with G.
When we’re talking about mutilations there are three main types that we need to be mindful of and the reason that they’re relevant is that they tend to affect a codon which is a sequence of 3 bases that determines an amino acid subsequently that amino acid combination determines the proteins that form.
So, when we’re talking about these particular mutations there are inherent errors and oftentimes, they don’t confer any benefit to the virus, they are either non-mutations or they’re actively deselected because they don’t do the virus any favours in terms of pathogenicity or infectivity.
So, the ones that do tend to be conserved and spread to become potential future wild type strains you have substitutions, deletions and insertions and they each affect the codons in different ways, so substitution is when a base is replaced with an alternative base.
Often to create a different amino acid and then you have deletions and insertions, and you’ll have a frameshift effect when you have those mutations. These are often the mutations that cause more negative effects on the virus because you end up with a whole shift of every single codon downstream or upstream of translations.
With the genome of SARSCOV2 the mutations of interest are around the spike protein, this is because the spike protein is where the virus binds to the H2 receptor and infects hosts cells.
In terms of variant kit options, we’re still not completely sure about what the policy is going to be but we are ploughing ahead to create something that we hope might be a useful solution we have an improved covid kit called the SUK2 which is the same as our current VIASURE COVID kit in that it has the ORF1ab and N genes of the Wuhan wild type it also has the s gene with the 69-70 deletion which is the indication of the Kent variant it makes it the equivalent of what you observe with the taqpath S gene drop out and it has the endogenous control of RNAse P.
We are developing a specific variant detection kit so this is a multiplex single tube same format as all the other VIASURE kits so it’s going to be lyophilized room temperature storage runs from the same elute as your first line COVID test and it runs in exactly the same way as all other VIASURE kits so it’s completely open to be being put on any thermal cycle and very similar prep so it is microlitres of mass that makes 5 microlitres of extracted sample and we’ve decided to go for four mutations of interest.
The reason that we’ve done that is if you take a look at the analysis of the variants of concern and variants of interest the route that we’ve decided to go down is to not say we have a kit for the Brazil variant or we have a kit for the South African variant but rather we have a kit that detects key mutation and based in interpretation you can then essentially identify particular variants.