What the Covid-19 tests should look like

As the pandemic heads to an unenviable two-year milestone, the Otago Institute of Global HealthThe Covid-19 masterclass series brings together a network of experts to discuss key Covid-19 topics. We will be running an article every day until December 5th.

James Ussher and Philip Hill assess our current testing options and what’s available around the world – and make some suggestions on what paths we should take

Diagnostic testing is crucial in the response to Covid-19, but adequate testing capacity and turnaround times fast enough to get results are major challenges globally.

People who show symptoms of Covid-19 should be tested as soon as possible. If they are looking for a test and the result is available quickly, public health teams have the opportunity to find their contacts and stop the transmission of SARS-CoV-2.

Covid-19 is highly infectious even up to two days before an infected person becomes symptomatic, requiring surveillance testing of asymptomatic people in particular situations.

As the pandemic continues, many businesses and organizations will develop testing strategies. These should be developed with health experts, taking into account the following questions:

How to estimate the performance of tests for Covid-19?

The properties of tests provide information on how we use them. We estimate their sensitivity (percentage of those who have the virus who test positive) and specificity (percentage of those who do not have the virus who test negative). When a test has low specificity, it will give too many false positive results.

We also estimate predictive values ​​- positive predictive value tells you what percentage of those who test positive have the virus; The negative predictive value tells you what percentage of those who test negative do not have the virus.

The predictive values ​​change with the prevalence of infection in a population. For example, if a test is 80% sensitive and 98% specific (like the current rapid antigen tests described below), at a community prevalence of 1% of Covid-19, the positive predictive value is less than 30% .

With SARS-CoV-2, tests often detect both viable and non-viable viruses, making it difficult to interpret the results.

What tests have been developed?

Tests for Covid-19 that require a lab tend to use high throughput polymerase chain reaction (PCR) machines and have high sensitivity (over 90 percent) and extremely high specificity (almost 100 percent). ). Two key sampling methods for these tests are the nasopharyngeal swab and the saliva sample.

The sensitivity of the best saliva tests reached levels similar to those of nasopharyngeal tests. However, transportation to the lab, processing multiple samples, batch testing, and reporting to the patient can often combine with waiting more than 24 hours for a result.

There are machines that perform PCR testing after placing a sample in a cartridge, with a result available in less than an hour, but they can only process a few cartridges at a time and the availability of cartridges is severely limited in the field. world.

Another simplification of these methods for detecting viral RNA is isothermal loop-mediated amplification (LAMP), which does not require a laboratory and provides a result in less than half an hour. Few studies have evaluated the performance of LAMP tests so far and they appear to be less sensitive than PCR tests.

Rapid turnaround antigen testing (RAT) for Covid-19 is increasingly available. RATs detect the presence of the virus’ “spike protein”. They tend to use nasal swab samples, with few large-scale studies so far evaluating saliva as a sample.

RATs vary widely in their performance properties and turnaround time, and typically can only process one sample at a time. There are differences in sensitivity in symptomatic people (around 65% on average) compared to asymptomatic people (around 55% on average).

The reported sensitivity estimates are often inflated by calculating the percent positive agreement with PCR testing. Sensitivity also varies at different stages of the disease, averaging around 70 percent in the first week compared to around 45 percent in the second week. The specificity is often very high (around 100 percent) with many better quality antigen tests.

Some of those with higher sensitivity (around 90%) may have a small drop in specificity of up to 97%. At a low prevalence of infection, this can lead to the majority of positive tests being false positive.

Other diagnostic tests in development use technologies such as microfluidics, holographic microscopes to examine nanoscale structures, and gas chromatography. Breath tests and trained sniffer dogs show promise.

Wastewater sampling PCR-based testing is hampered by the variation in the number of cases that shed the virus in their stool, the dilution of the virus, and the inability to distinguish between viable and non-viable viruses.

What testing strategies should I use?

While many countries have struggled to establish testing capacities large enough to respond effectively to epidemics, the lack of strategic use of large testing capacities has led to severe inefficiencies in other countries and failure. later to contain epidemics.

Symptomatic cases are much more contagious than those that never become symptomatic, and testing on asymptomatic people can lead to deflecting testing from symptomatic people.

Additionally, since people who never have symptoms are likely to play a minor role in overall transmission, a large number of positive results from these people can lead to unnecessary work on the health response.

We can think of at least five different groups of people when it comes to testing:

1. Symptomatic people in the community should be able to be tested. Nasopharyngeal swabs and saliva PCR tests should be available to maximize absorption.
2. Everyone entering the country should go through a test plan, with a mix of pre-departure, arrival and post-arrival testing adjusted with expert guidance over time.
3. Symptomatic and asymptomatic people admitted to risky situations (eg hospitals) should be subject to a screening plan to protect vulnerable people. It may not be possible to filter visitors or even all emergency service participants.
4. Symptomatic and asymptomatic individuals who attend large events that are at risk for super-spread are candidates for self-test using RAT prior to participation and requirements may be influenced by immunization status.
5. Outbreaks will vary depending on the strategic use of the tests. Screening for asymptomatic occasional contacts can be avoided to maximize the value of limited laboratory resources.

* Conflict of Interest Statement: Associate Professor James Ussher is employed by Southern Community Laboratories in Dunedin, which performs Covid-19 testing. Professor Philip Hill has served on four ministerial advisory committees for COVID-19.