Being able to feed back this type of information has been crucial in helping to manage the spread between workforces, according to Dr Smith. She says Public Health has been liaising with employment agencies to identify the links between staff who typically move between workplaces to help stop possible transmission.
“A business may only have told us about their main substantive workforce, so it reminds us to ask, ‘what about your temporary, agency-based staff?’” she explains.
“The obvious place to go to is the employer’s recruitment agent, because often they’re placing people for shifts in different factories and on different days of the week. Then we start to find links between [for example] abattoirs and care homes, simply because people… are working in different businesses.”
Genomic epidemiology has confirmed not only the presence of the virus but informed public health officials as to whether control measures are working in care settings. In one case, the Quadram was able to confirm the lineages were only present in care workers and not their patients – meaning, as Dr Page explains, that “all the basics, such as masks and hand-washing” were working.
It is not the only instance in which science has provided reassurance. When Ipswich Hospital was worried about a possible transmission in the wards, Prof O’Grady was able prove otherwise.
“What we found out was that they had multiple lineages in the wards which were very similar to what was circulating in the community,” he says.
“That basically meant people who were testing positive in the hospital had come in with the virus, not because they all got it from each other in the [wards]. It put the hospital’s mind at ease that their infection control processes were working appropriately – in that case, they were getting it right.”
“The COG-UK initiative to provide whole genome sequencing of SARS-CoV-2 provides improvement in hospital functioning by aiding Infection Prevention and Control efforts and clarifying intra-hospital transmission events as well as reduction of transmission of the virus from hospitals to the community” says Dr Samir Dervisevic, consultant virologist at NNUH.
Quadram and NNUH are now looking at using genomics to identify hospital spread of SARS-CoV-2 within 24 hours.
“The rapid deployment of genome sequencing in outbreak situations would greatly aid the effort to reduce the risk of the spread of infection amongst our vulnerable patients as well the staff,” he adds.
“This type of intervention would not only help patient management but would provide as accurate as possible analysis of intra-hospital transmission.”
The Quadram has not only identified new lineages and clusters of the virus into the region, but also instances in which they have disappeared completely – another form of reassurance. By August, the number of lineages had reduced from 100 to one because the virus had been unable to thrive, says Dr Page.
“A lot disappeared totally because [areas] had been in lockdown and the virus couldn’t infect anyone. So, we do know that some measures were extremely successful,” he explains.
Furthermore, Quadram has found no evidence of secondary infections, adds Prof O’Grady. What continues to be rewarding is the application of their work to help get the virus under control.
“The hospital finds it extremely useful; Test and Trace finds it extremely useful; Public Health finds it extremely useful,” says Prof O’Grady. “But what’s really great is to see direct translation of science – we do a lot of scientific research and it’s not every day that your science is translated into something useful. Doing something in the lab at the bench and then two days later seeing that information being utilised to help control the spread of the virus – that is very satisfying.”