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Fast sequencing and sewage samples to keep closer eye on variants

Fast sequencing and sewage samples to keep closer eye on variants

Tuesday 11 May 2021

Fast sequencing and sewage samples to keep closer eye on variants

Jersey will be ramping up its testing for variants of covid that may be more transmissible or resistant to the vaccine as it loosens its borders this summer, the island’s top pandemic medic has said.

Dr Ivan Muscat said the island had been speaking to a provider that would be able to turn around variant tests within 48 hours.

He also said an 'emergency brake' system, which would see travel rapidly banned in areas with high levels of covid or concerning variants, would also be a protection against new variants arriving in Jersey, and noted that the island is now conducting sewage sampling to help identify early warning signs of more cases or variants emerging locally.

The Deputy Medical Officer for Health’s assurances came in response to questions from Express at a press conference on the Government’s new approach to travel this summer.

Yesterday, it was announced that fully vaccinated passengers arriving from green or amber areas of the UK would not need to isolate upon arriving in Jersey this summer, while England, Scotland, Wales, Northern Ireland and the Crown Dependencies will move to national rather than regional classifications.

While regional classification for France and Ireland was due to be reintroduced from 17 May, it has been pushed back to 28 May to coincide with the other changes.

Video: The summer travel policy was unveiled at a press conference yesterday.

With some areas in the UK still showing as red under the current system, including several parts of the Yorkshire and the Humber region, there were concerns about the risk travel from these areas might pose to the island, especially given the possibility of new variants emerging.

Dr Muscat explained that, according to providers, the vaccines that are currently available should provide protection against the more transmissible Kent and Indian variants of covid. However, he did not mention the variants discovered in South Africa and Brazil, which may resist antibodies.

As a way of mitigating the risk from variants potentially arriving in Jersey, Dr Muscat said that the new travel policy includes an “emergency brakes” or “red card” system, allowing the Medical Officer for Health, Public Health or STAC to ban travel from a particular area.

“If we note that there is an increase in the number of variant concerns in a particular part of the UK, such that it has led to surge testing over there, then we would apply the emergency brake to entrance from that area to Jersey in order to safeguard Jersey,” he said.

“We would also be looking at an emergency brake in relation to higher numbers of infection. A higher number of infections may be due to a new variant, for example, that is more transmissible than previous variants.

“We would bear that in mind as well when thinking about our emergency brake because as you know there are two variants: variants of concern that you already know about and emerging variants that you only work out are variants of concern after the event and increasing number of infections will tell us that.”


Pictured: Dr Muscat said the Government is seeking to "expedite" the results from tests on variants.

He also said the Government is also looking into how it could identify any potential variants in the island quicker.

Last December, the Government started sending off weekly samples to the UK to test for any new variants but results took many weeks to come back - the Kent variant was identified in early February from samples that had been sent off in January.

“We are seeking to expedite the sequencing result we get from viruses in Jersey and last week we had discussions with a particular provider with a view to getting results for S variants - variants in the spike genes - within 48 hours or so of sending them away,” Dr Muscat said.

Public Health has also been working with the Infrastructure, Housing and Environment (IHE) department on a new covid-19 sewage sampling project to monitor local case rates and variants.

As part of the project, raw sewage and faeces have been extracted from treatment works around the island and sent off to the London School for Hygiene and Tropical Medicine, which has designed a system to detect cases of covid-19 from sewage.

laboratory sample analysis

Pictured: Sewage samples are also being analysed.

The first samples were sent last week and results are expected within the next fortnight. The survey will continue until November and it is hoped it will provide the Government with early warning signs of any increase in cases and any variants that could be in the island as well as help advise the Government on what steps islanders can take to reduce the risk of a third wave.

“Covid is also excreted through the gut and therefore finds its way in sewage,” Dr Muscat said. “There are systems that allow for analysis of sewage to see if covid is there and it can pick up 1 in 10,000 individuals with covid, so if one individual in an area with 10,000 people in it has covid, it will be picked up, so it’s very sensitive. Additionally it can sequence it as well.

“We will be getting results, monitoring results on a weekly basis going forward. Additionally, we have stored samples, frozen down to minus 70 to go back to analyse further should we need to do so.

“Starting where we are now is a good place to start because of our very low baseline levels so if we see those levels starting to go up it will start to tell us that something is happening within the community and we need to be perhaps a bit more cautious and undertake more testing and so forth. It’s yet another tool.”

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