Covid-19 testing: ‘We should have been ready for this’

By Monday morning, GPs’ WhatsApp groups were buzzing with worrying signs of what would become apparent to the rest of the country the following evening. The number of people looking for a test for Covid-19 was surging. It was only a matter of time before positive cases would follow. “It’s starting to feel like March,” one GP said on Twitter.

The volume of potential cases escalated to "extraordinary levels", says Dr Mary Favier, the head of the Irish College of General Practitioners. Her three-GP practice in Cork had made 25 Covid referrals before lunch on Monday. "Even at the height of everything, we never made this number of referrals," she noted.

She texted the deputy chief medical officer, Ronan Glynn, to report what she was seeing. "I hope we've got capacity," she wrote.

The same concerns were being reflected in GP practices around the country. In total, on Monday, 13,000 people were referred for a test, double the figure for the previous week. Eight thousand more followed on Tuesday. The majority were schoolchildren and people in north Dublin.

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Prof Sam McConkey makes the analogy of “the frog in boiling water. Now we’re getting community transmission numbers of between 30 and 40 a day; we’re getting total numbers between 100 and 200 a day. We’re seeing so many outbreaks that the contact tracers and public health doctors are struggling to keep on top of them”.

The number of Covid-19 cases in Dublin could double every 14 days unless the public makes urgent changes to behaviour, was the stark warning from Dr Ronan Glynn this week. The most pressing question now is whether our system of test, trace and isolate – still the best toolkit in our armoury in the battle against Covid – will be able to rise to the challenge.

According to Health Protection Surveillance Centre (HPSC) figures, the number of tests completed on Monday was 6,253 (4,089 in labs and 2,164 in hospitals). Tuesday’s total figure was 5,387. On Wednesday, the number of tests jumped to 10,700. A record 12,000 tests were scheduled in labs for Thursday and a further 3,000 were due to take place in hospitals, the HSE said. The overall number of tests completed for the seven days prior was 71,910.

All these figures fall within the range of the HSE’s goal of 14,200 tests per day, or 100,000 per week. So why, some experts are asking, did the HSE make the decision on Wednesday to postpone serial testing in meat plants?

"While we have the 100,000 capacity, we have to address what comes at us on a daily basis… It's about treating the symptomatic people, and prioritising that," HSE chief executive Paul Reid said at a briefing on Thursday morning.

Others believe that, if the capacity is there, we should be using it now, instead of holding it in reserve. "We've never been consistently near our capacity, which is amazing, because we clearly should have been doing serial testing in meat plants and other high-risk areas" earlier, says Dr Tomás Ryan, associate professor in the School of Biochemistry and Immunology and Institute of Neuroscience at Trinity College.

“We were expecting that they would build [capacity] up in the background over the summer. I hoped that as soon as cases started to rise again that we would see a much slicker operation ready and waiting to pounce on outbreaks and contact chains. And the opposite has happened.”

‘So frustrating’

Is it the case that the weekly testing goal of 100,000 isn't enough to cope with the winter onslaught, if serial testing has to be interrupted so early in the season? Reid said on Thursday that if capacity needed to be increased, the HSE would seek that. Three additional pop-up swabbing centres opened this week in Limerick, Tallaght and Carlow-Kilkenny.

In terms of overall numbers of testing, Ireland compares well internationally, points out Prof Paul Moynagh, director of the Kathleen Lonsdale Institute for Human Health Research at Maynooth University. "But the efficiencies around the system need to be addressed and improved."

This week, Reid said 14,000 tests were being processed on some days, and the “median end-to-end testing turnaround from referral to contact tracing complete time” was 2.1 days. All contact tracing was completed within a median of one day, he added.

The HSE didn’t respond to a question from The Irish Times about the turnaround time for community tests conducted in labs only, as distinct from the figure for hospitals.

Testing in hospital settings tends to be “very, very efficient”, says Moynagh. For a non-scientist, it’s easy to underestimate the degree of complexity of what happens after a swab is taken – from the logistics of collecting and couriering samples to centralised labs; to sorting, date-stamping, checking samples; to running samples through an analyser; to dealing with occasional breakdowns; to manually inputting some of the data. “The problems really lie in community testing,” he suggests.

A 2.1-day turnaround wasn't the experience for everyone this week. Secondary school teacher Fiona Cullen was one of those trying to get an appointment on Monday in north Dublin for her two-year-old son. He had developed a cough and a temperature over the weekend and, after "a very bad night" on Saturday, she was worried enough to call the out-of-hours GP service on Sunday. She was told he would need a Covid test, and that the rest of the family should restrict their movements until a negative result came through.

On Monday, when she still hadn’t got a date for a test, she called the HSE helpline three times, conscious that while she was self-isolating her Leaving Cert students were without a teacher.

“It’s so frustrating. I’m literally back in the door, and now I’m out again. We’ve got the digital platform so there’s learning happening, but it can’t in any way replace the face to face contact,” she says.

Cullen’s son eventually got an appointment for Wednesday afternoon at 2pm, three days after she made the initial call. With the results likely to take between 24 and 72 hours, she was not expecting to make it back to the classroom this week. Priority testing for teachers as well as students is one of the issues that needs to be addressed, she believes.

One suggestion to improve efficiency in community testing is that GPs could be taken out of the system, and individuals allowed to self-refer for testing. Under a system like this, Cullen would have been able to make an appointment herself, or even take her son directly for a test on Sunday at a drive-thru centre.

Ryan points out that the vast majority of patients who go for testing are not really sick, so shouldn’t need to go through a GP. “A small minority of positive people will be sick to the degree that they will need medical attention. So everyone going through their GP does not make sense. We need drive-in test centres. We need a 24/7 phone line and a website that you can book your appointment. It’s a no-brainer. It would save us time and money.”

But while Favier says self-referral would significantly reduce the burden on general practice, taking GPs out of the system raises questions about the clinical governance of those who do become very sick.

Saliva swabbing

Even before this week, there were signs of strain in some parts of the system. One woman in Waterford who contacted The Irish Times said she called her GP with upper respiratory symptoms, including a persistent cough, on Thursday August 20th. She was given a test on Sunday (August 23rd) and got her result on Tuesday. It was negative – but if she had been positive, contact tracing would have taken another day, bringing the total turnaround time to almost a week.

Rapid turnaround times, especially as people have to go back for tests again and again over the winter, will become increasingly important, says Favier. “The shorter it is, the fewer people have to self-isolate, the more tolerant they’ll be of recurrent testing, because it won’t interfere with work and childcare.”

Some experts believe a lot of these issues could have been addressed with a more proactive approach earlier in the crisis. “We should not have been caught off guard. We should have been ready for this,” says Ryan.

A white paper by a taskforce on SARS-Cov-2 Testing – which included Moynagh, Ryan and others – was presented to the National Public Health Emergency Team in April, and subsequently released to Jack Horgan-Jones of The Irish Times under Freedom of Information. One of its recommendations was for greater private-sector involvement and use of university labs and “human resources, expertise, know-how and infrastructure”.

That recommendation was not implemented, but there is still an economic argument for using university labs for testing, says Moynagh, who points out that the cost to the State of achieving the HSE’s target of 100,000 tests a week is about €400 million per year.

“All along, I think what’s been missing is a long-term strategy in terms of how we were going to deal with testing and tracing over a prolonged time period, not just for three or six months,” says Moynagh.

The arrival of cheaper rapid testing kits, like the Covid test cards produced by Abbott, which plans to scale up to 50 million units in October, could help alleviate the strain on the system. In the meantime, both Moynagh and Ryan would like to see Ireland move towards less invasive saliva swabbing instead of the current nasal pharyngeal swabs. The HSE planned to introduce a new nasal-only test for children this week, and the National Virus Reference Laboratory (NVRL) is investigating saliva testing.

Ryan also believes that public health campaigns should stress the importance of reporting symptoms earlier; and that smartphones should be provided to people who can’t afford them to aid uptake of the Covid Tracker app.

McConkey would like to see teams of community contact tracers doing what he calls “shoe leather contact tracing” where there are community outbreaks, in a bid to stop the spread.

Another suggestion to improve efficiency and bring down costs is pool testing – where samples from 10 different people in areas where there are outbreaks would be tested together, and only if a pooled sample tests positive would individual testing be required. This is advocated by all three scientists who spoke to The Irish Times.

For now, the mood among GPs facing into winter, says Favier, is one of trepidation. “Most GPs described being very busy over the summer. Burnout is a real issue. The sheer volume of work is going to be an issue. And then obviously we’re going to have some GPs who may get sick themselves. It’s a very delicate tipping point.”