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COVID-19 testing

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CDC 2019-nCoV Laboratory Test Kit.jpg
The CDC's 2019-nCoV Laboratory Test Kit

Laboratory testing for SARS-CoV-2 includes methods that detect the presence of virus and those that detect antibodies produced in response to infection.

As of 21 March 2020, the CDC recommends RT-PCR for initial screening.[1] The presence of viruses is generally confirmed by RT-PCR, which detects the coronavirus' RNA. This test detects only the RNA of the SARS-CoV-2 and is used to confirm very recent or active infections.

Detection of antibodies (serology) can be used both for diagnosis and population surveillance. Antibody tests show how many people have had the disease, including those whose symptoms were minor or who were asymptomatic. An accurate mortality rate of the disease and the level of herd immunity in the population can be determined from the results of this test.

Due to limited testing, as of March 2020 no countries had reliable data on the prevalence of the virus in their population.[2] By 23 March, no country had tested more than 3% of their population, and there are variations in how much testing has been done across countries.[3] This variability is also likely to be affecting reported case fatality rates, which have probably been overestimated in many countries, due to sampling bias.[4][5][6]

As of 6 March 2020, WHO listed the development laboratories and protocols for detection of virus[clarification needed][7]
Country Institute Gene targets
China China CDC ORF1ab and nucleoprotein (N)
Germany Charité RdRP, E, N
Hong Kong HKU ORF1b-nsp14, N
Japan NIID Pancorona and multiple targets,
Spike protein (Peplomer)
Thailand National Institute of Health N
United States US CDC Three targets in N gene
France Pasteur Institute Two targets in RdRP

Test methods[edit source | edit]

RT-PCR[edit source | edit]

Using real-time reverse transcription polymerase chain reaction (rRT-PCR)[8] the test can be done on respiratory samples obtained by various methods, including a nasopharyngeal swab or sputum sample.[9] Results are generally available within a few hours to 2 days.[10] The RT-PCR test performed with throat swabs is only reliable in the first week of the disease. Later on the virus can disappear in the throat while it continues to multiply in the lungs. For infected people tested in the second week, alternatively sample material can then be taken from the deep airways by suction catheter or coughing up material (sputum) can be used.[11]

INAA[edit source | edit]

On 27 March 2020, the FDA approved an "automated assay" from Abbott Diagnostics Scarborough "that utilizes isothermal nucleic acid amplification technology".[12] On 13 April, Health Canada approved a similar test from Spartan Bioscience. The benefit of these isothermal tests is that institutions may "test patients" with a handheld DNA analyzer "and receive results without having to send samples away to a [central] lab."[13]

Serology tests[edit source | edit]

Most serology tests are in the research stage of development.[14] As of 10 April, only a single test had been approved for diagnosis in the United States and this is under FDA Emergency Use Authorization (EUA).[14][15] This test, when tested in China, had a specificity of 95.6% and a sensitivity of 93.8%.[14] A highly sensitive test rarely overlooks an actual positive. A highly specific test rarely registers a positive classification for anything that is not the target of testing. Other tests have been approved in other countries.[14]

A number of countries are beginning large scale surveys of their populations using these tests.[16][17]

Part of the immune response to infection is the production of antibodies including IgM and IgG. According to the FDA, IgM antibodies to SARS-CoV-2 are generally detectable in blood several days after initial infection, although levels over the course of infection are not well characterized. IgG antibodies to SARS-CoV-2 become detectable later following infection.[18] Antibody tests can be used to determine the percentage of the population that has contracted the disease and that is therefore immune.

Assays can be performed in central laboratories (CLT) or by point-of-care testing (PoCT). The high-throughput automated systems in many clinical laboratories will be able to perform these assays but their availability will depend on the rate of production for each system. For CLT a single specimen of peripheral blood is commonly used, although serial specimens can be used to follow the immune response. For PoCT a single specimen of blood is usually obtained by skin puncture. Unlike PCR methods an extraction step is not needed before assay.[citation needed]

In late March 2020, a number of companies received European approvals for their test kits. The testing capacity is several hundred samples within hours. The antibodies are usually detectable 14 days after the onset of the infection.[19]

In early April, the UK found none of the antibody test kits it purchased were sufficiently good to use.[20]

Medical imaging[edit source | edit]

Chest CT scans may be helpful to diagnose COVID-19 in individuals with a high clinical suspicion of infection based on risk factors and symptoms but is not recommended for routine screening.[21][22] Typical features on CT initially include bilateral multilobar ground-glass opacities with a peripheral, asymmetric and posterior distribution.[22] Subpleural dominance, crazy paving, and consolidation may develop as the disease evolves.[22][23]

Approaches to testing[edit source | edit]

A sample collection kiosk for COVID-19 testing in India
Timeline of Number of tests per million people in different countries.[24]

Hong Kong has set up a scheme where suspected patients can stay home, "[the] emergency department will give a specimen tube to the patient", they spit into it, send it back and get a test result a while after.[25]

Several countries are aiming to conduct 100,000 tests per day – Germany by mid-April, the United Kingdom by the end of April and France by the end of June. Germany has a large medical diagnostics industry, with over 100 testing labs that provided the technology and infrastructure to enable rapid increases in testing. The UK sought to diversify its life sciences companies into diagnostics to scale up testing capacity.[26]

By the start of April, the United Kingdom was delivering around 10,000 swab tests per day. It set a target for 100,000 per day by the end of April, eventually rising to 250,000 tests per day.[26] The British NHS has announced that it is piloting a scheme to test suspected cases at home, which removes the risk of a patient infecting others if they come to a hospital or having to disinfect an ambulance if one is used.[27]

In drive-through testing for COVID-19 for suspected cases, a healthcare professional takes sample using appropriate precautions.[28][29] Drive-through centers have helped South Korea do some of the fastest, most-extensive testing of any country.[30]

In Germany, the National Association of Statutory Health Insurance Physicians said on 2 March, that it had a capacity for about 12,000 tests per day in the ambulatory setting and 10,700 had been tested in the prior week. Costs are borne by the health insurance when the test is ordered by a physician.[31] According to the president of the Robert Koch Institute, Germany has an overall capacity for 160,000 tests per week.[32] As of 19 March drive in tests were offered in several large cities.[33] As of 26 March, the total number of tests performed in Germany was unknown, because only positive results are reported. Health minister Jens Spahn estimated 200,000 tests/week.[34] A first lab survey revealed that as of the end of March a total of at least 483,295 samples were tested and 33,491 samples (6.9%) tested positive for SARS-CoV-2.[35]

In Israel, researchers at Technion and Rambam Hospital developed and tested a method for testing samples from 64 patients simultaneously, by pooling the samples and only testing further if the combined sample is found to be positive.[36][37][38]

In Wuhan a makeshift 2000-sq-meter emergency detection laboratory named "Huo-Yan" (Chinese: 火眼, "Fire Eye") was opened on 5 February 2020 by BGI,[39][40] which can process over 10,000 samples a day.[41][40] With the construction overseen by BGI-founder Wang Jian and taking 5-days,[42] modelling has show cases in Hubei would have been 47% higher and the corresponding cost of the tackling the quarantine would have doubled if this testing capacity had not come into operation.[citation needed] The Wuhan Laboratory has been promptly followed by Huo-Yan labs in Shenzhen, Tianjin, Beijing, and Shanghai, in a total of 12 cities across China. By 4 March 2020 the daily throughput totals were 50,000 tests per day.[43]

Open source, multiplexed designs released by Origami Assays have been released that can test as many as 1122 patient samples for COVID19 using only 93 assays.[44] These balanced designs can be run in small laboratories without the need for robotic liquid handlers.

By March, shortages and insufficient amounts of reagent has become a bottleneck for mass testing in the EU and UK[45] and the US.[46][47] This has led some authors to explore sample preparation protocols that involve heating samples at 98 °C (208 °F) for 5 minutes to release RNA genomes for further testing.[48][49]

On 31 March it was announced United Arab Emirates was now testing more of its population for Coronavirus per head than any other country, and was on track to scale up the level of testing to reach the bulk of the population.[50] This was through a combination of drive-through capability, and purchasing a population-scale mass-throughput laboratory from Group 42 and BGI (based on their "Huo-Yan" emergency detection laboratories in China). Constructed in 14 days, the lab is capable of conducting tens of thousands RT-PCR tests per day and is the first in the world of this scale to be operational outside of China.[51]

Production and volume[edit source | edit]

Number of tests done per day in the United States.
Blue: CDC lab
Orange: Public health lab
Gray: Data incomplete due to reporting lag
Not shown: Testing at private labs; total exceeded 100,000 per day by March 26[52]

Different testing recipes targeting different parts of the coronavirus genetic profile were developed in China, France, Germany, Hong Kong, Japan, the United Kingdom, and the United States. The World Health Organization adopted the German recipe for manufacturing kits sent to low-income countries without the resources to develop their own. The German recipe was published on 17 January 2020; the protocol developed by the United States Centers for Disease Control (CDC) was not available until 28 January, delaying available tests in the U.S.[53]

China[54] and the United States[55] had problems with the reliability of test kits early in the outbreak, and these countries and Australia[56] were unable to supply enough kits to satisfy demand and recommendations for testing by health experts. In contrast, experts say South Korea's broad availability of testing helped reduce the spread of the novel coronavirus. Testing capacity, largely in private sector labs, was built up over several years by the South Korean government.[57] On 16 March, the World Health Organization called for ramping up the testing programmes as the best way to slow the advance of COVID-19 pandemic.[58][59]

High demand for testing due to wide spread of the virus caused backlogs of hundreds of thousands of tests at private U.S. labs, and supplies of swabs and chemical reagents became strained.[60]

Available tests[edit source | edit]

PCR based[edit source | edit]

Public Health England developed a test by 10 January,[61] using real-time RT-PCR (RdRp gene) assay based on oral swabs.[62] The test detected the presence of any type of coronavirus including specifically identifying SARS-CoV-2. It was rolled out to twelve laboratories across the United Kingdom on February 10.[63] Another early PCR test was developed at Charité in Berlin in January 2020 using rtRT-PCR, and formed the basis of 250,000 kits for distribution by the World Health Organization (WHO).[64]

The South Korean company Kogenebiotech developed a clinical grade, PCR-based SARS-CoV-2 detection kit (PowerChek Coronavirus) on 28 January 2020.[65][66] It looks for the "E" gene shared by all beta coronaviruses, and the RdRp gene specific to SARS-CoV-2.[67]

In China, BGI Group was one of the first companies to receive emergency use approval from China's National Medical Products Administration for a PCR-based SARS-CoV-2 detection kit.[68]

In the United States, the CDC distributed its SARS-CoV-2 Real Time PCR Diagnostic Panel to public health labs through the International Reagent Resource.[69] One of three genetic tests in older versions of the test kits caused inconclusive results due to faulty reagents, and a bottleneck of testing at the CDC in Atlanta; this resulted in an average of fewer than 100 samples a day being successfully processed throughout the whole of February 2020. Tests using two components were not determined to be reliable until 28 February 2020, and it was not until then that state and local laboratories were permitted to begin testing.[70] The test was approved by the FDA under an EUA.[citation needed]

US commercial labs began testing in early March 2020. As of 5 March 2020 LabCorp announced nationwide availability of COVID-19 testing based on RT-PCR.[71] Quest Diagnostics similarly made nationwide COVID-19 testing available as of 9 March 2020.[72]

In Russia, the COVID-19 test was developed and produced by the State Research Center of Virology and Biotechnology VECTOR. On 11 February 2020 the test was registered by the Federal Service for Surveillance in Healthcare.[73]

On 12 March 2020, Mayo Clinic was reported to have developed a test to detect COVID-19 infection.[74]

On 19 March 2020, the FDA issued EUA to Abbott Laboratories[75] for a test on Abbott's m2000 system; the FDA had previously issued similar authorization to Hologic[76], LabCorp,[77] and Thermo Fisher Scientific.[78][79] On 21 March 2020, Cepheid similarly received an EUA from the FDA for a test that takes about 45 minutes on its GeneXpert system; the same system that runs the GeneXpert MTB/RIF.[80][81]

Isothermal nucleic amplification[edit source | edit]

US President Donald Trump displays a COVID-19 testing kit from Abbott Laboratories in March 2020

The FDA has approved a test by Abbott Laboratories that uses isothermal nucleic acid amplification technology instead of PCR.[12] Since this does not require a series of alternating temperature cycles this method can deliver positive results in as little as five minutes and negative results in 13 minutes. There are currently about 18,000 of these machines in the U.S. and Abbott expects to ramp up manufacturing to deliver 50,000 tests per day.[82]

Accuracy[edit source | edit]

In March 2020 China[54] reported problems with accuracy in their test kits.

In the United States, the test kits developed by the CDC had "flaws;" the government then removed the bureaucratic barriers that had prevented private testing.[55]

Spain purchased test kits from Chinese firm Shenzhen Bioeasy Biotechnology Co Ltd, but found that results were inaccurate. The firm explained that the incorrect results may be a result of a failure to collect samples or use the kits correctly. The Spanish ministry said it will withdraw the kits that returned incorrect results, and would replace them with a different testing kit provided by Shenzhen Bioeasy.[83]

80% of test kits the Czech Republic purchased from China gave wrong results.[84][85]

Slovakia purchased 1.2 million test kits from China which were found to be inaccurate. Prime Minister Matovič suggested these be dumped into the Danube.[86]

Ateş Kara of the Turkish Health Ministry said the test kits Turkey purchased from China had a "high error rate" and did not "put them into use."[87][88]

The UK purchased 3.5 million test kits from China but in early April 2020 announced these were not usable.[89][90]

Confirmatory testing[edit source | edit]

WHO recommends that countries that do not have testing capacity and national laboratories with limited experience on COVID-19 send their first five positives and the first ten negative COVID-19 samples to one of the 16 WHO reference laboratories for confirmatory testing.[91][92] Out of the 16 reference laboratories, 7 are in Asia, 5 in Europe, 2 in Africa, 1 in North America and 1 in Australia.[93]

WHO Emergency Use Listing[edit source | edit]

Diagnostic tests accepted by the WHO for procurement
Date listed Product name Manufacturer
03/4/2020 Cobas SARS-CoV-2 qualitative assay for use on the cobas 6800/8800 Systems Roche Molecular Systems
07/4/2020 Coronavirus (COVID-19) genesig rtPCR assay Primerdesign

As of 7 April 2020, the WHO had accepted two diagnostic tests for procurement under the Emergency Use Listing procedure (EUL) for use during the COVID-19 pandemic, in order to increase access to quality-assured, accurate tests for the disease.[94] Both in vitro diagnostics, the tests are genesig Real-Time PCR Coronavirus (COVID-19) manufactured by Primerdesign, and cobas SARS-CoV-2 Qualitative assay for use on the cobas® 6800/8800 Systems by Roche Molecular Systems. Approval means that these tests can also be supplied by the United Nations and other procurement agencies supporting the COVID-19 response.

Effectiveness[edit source | edit]

Testing, followed with quarantine of those who tested positive and tracing of those with whom the SARS-CoV-2 positive people had had contact, resulted in positive outcomes[clarification needed].

Italy[edit source | edit]

Researchers working in the Italian town of , the site of the first COVID-19 death in Italy, conducted two rounds of testing on the entire population of about 3,400 people, about ten days apart. About half the people testing positive had no symptoms, and all discovered cases were quarantined. With travel to the commune restricted, this eliminated new infections completely.[95]

Singapore[edit source | edit]

With aggressive contact tracing, inbound travel restrictions, testing, and quarantining, the 2020 coronavirus pandemic in Singapore has proceeded much more slowly than in other developed countries, but without extreme restrictions like forced closure of restaurants and retail establishments. Many events have been cancelled, and Singapore did start advising residents to stay at home on 28 March, but schools reopened on time after holiday break on 23 March.[96]

Others[edit source | edit]

Several other countries, such as Iceland[97] and South Korea[98], have also managed the pandemic with aggressive contact tracing, inbound travel restrictions, testing, and quarantining, but with less aggressive lock-downs. A statistical study has found that countries that have tested more, relative to the number of deaths, have much lower case fatality rates, probably because these countries are better able to detect those with only mild or no symptoms.[4]

Virus testing by country[edit source | edit]

The column “Positive / million people” is influenced by the country's testing policy. A country that only tests people admitted to hospitals will have a higher positive / million people than a country that tests all citizens whether or not they are showing symptoms, assuming the populations of the two countries have the same infection rate. Template:COVID19Testing

Research and development[edit source | edit]

A test which uses monoclonal antibodies which bind to the nucleocapsid protein (N protein) of the SARS-CoV-2 is being developed in Taiwan, with the hope that it can provide results in 15 to 20 minutes just like a rapid influenza test.[99] The World Health Organization raised concerns on April 8 that these tests need to be validated for the disease and are in a research stage only.[100]

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