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COVID-19 testing

From Wikipedia, the free encyclopedia

Laboratory testing for the respiratory coronavirus disease 2019 (COVID-19) and the associated SARS-CoV-2 virus includes methods that detect the presence of virus and those that detect antibodies produced in response to infection. Detection of antibodies (serology) can be used both for clinical purposes and population surveillance. Antibody tests allow us to find out how many people have had the disease, including those whose symptoms were so minor that they were shrugged off. In this way we can find the true mortality rate of the disease as well as how much herd immunity has been built up in society.

Due to limited testing, as of March 2020 no countries had reliable data on the prevalence of the virus in their population.[1] This variability also affects reported case-fatality rates.

Test methods

As of 6 March 2020, WHO listed the development laboratories and protocols for detection of virus[clarification needed][2]
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

Detection of virus using PCR tests

CDC 2019-nCoV Laboratory Test Kit.jpg
The CDC's 2019-nCoV Laboratory Test Kit
Demonstration of a nasopharyngeal swab for COVID-19 testing
Demonstration of a throat swab for COVID-19 testing

Using real-time reverse transcription polymerase chain reaction (rRT-PCR)[3] the test can be done on respiratory samples obtained by various methods, including nasopharyngeal swab or sputum sample.[4] Results are generally available within a few hours to 2 days.[5]

A thermocycler or thermal cycler, also known as a PCR machine

One of the early PCR tests was developed at Charité in Berlin in January 2020 using real-time reverse transcription polymerase chain reaction (rRT-PCR), and formed the basis of 250,000 kits for distribution by the World Health Organization (WHO).[6] The United Kingdom had also developed a test by 23 January 2020.[7]

The South Korean company Kogenebiotech developed a clinical grade, PCR-based SARS-CoV-2 detection kit (PowerChek Coronavirus) on 28 January 2020.[8][9] It looks for the "E" gene shared by all beta coronaviruses, and the RdRp gene specific to SARS-CoV-2.[10]

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.[11]

In the United States, the Centers for Disease Control and Prevention (CDC) is distributing its 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel to public health labs through the International Reagent Resource.[12] 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.[13] The test was approved by the Food and Drug Administration under an Emergency Use Authorization.[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.[14] Quest Diagnostics similarly made nationwide COVID-19 testing available as of 9 March 2020.[15] No quantity limitations were announced; specimen collection and processing must be performed according to CDC requirements.

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.[16]

On 12 March 2020, Mayo Clinic was reported to have developed a test to detect COVID-19 infection.[17]

On 13 March 2020, Roche Diagnostics received FDA approval for a test which could be performed within 3.5 hours, thus allowing one machine to do approximately 4,128 tests in a 24-hour period.[18]

On 19 March 2020, the FDA issued emergency use authorization (EUA) to Abbott Laboratories for a test on Abbott's m2000 system; the FDA had previously issued similar authorization to Hologic, LabCorp, and Thermo Fisher Scientific.[19] On 21 March 2020, Cepheid similarly received EUA from the FDA for a test that takes about 45 minutes.[20]

A test which uses a monoclonal antibody which specifically binds to the nucleocapsid protein (N protein) of the novel coronavirus is being developed in Taiwan, with the hope that it can provide results in 15 to 20 minutes just like a rapid influenza test.[21]

Detection of virus using non-PCR tests

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

The FDA has approved[22] a new test by Abbott Labs that uses isothermal nucleic acid amplification technology instead of PCR.[23] Since this does not require the time-consuming 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.[24]

Chest CT scans and radiographs

A March 2020 literature review concluded that "chest radiographs are of little diagnostic value in early stages, whereas CT [computed tomography] findings may be present even before symptom onset."[25] Typical features on CT include bilateral multilobar ground-glass opacificities with a peripheral, asymmetric and posterior distribution.[25] Subpleural dominance, crazy paving and consolidation develop as the disease evolves.[26] A study comparing PCR to CT in Wuhan at the epicenter of the current pandemic has suggested that CT is significantly more sensitive than PCR, though less specific, with many of its imaging features overlapping with other pneumonias and disease processes.[27] As of March 2020, the American College of Radiology recommends that "CT should not be used to screen for or as a first-line test to diagnose COVID-19".[28]

Human readers and artificial intelligence

A small study showed that Chinese radiologists demonstrated 72–94% sensitivity and 24–94% specificity in differentiating COVID-19 from other types of viral pneumonia using CT imaging.[29] Artificial intelligence based convolutional neural networks have also been developed to detect imaging features of the virus both on radiographs[30] and CT with significantly higher specificity.[31]

As of March 2020, the CDC recommends PCR for initial screening[32] because it has higher specificity than CT.[citation needed]

Detection of antibodies

Part of the immune response to infection is the production of antibodies including IgM and IgG. These can be used to detect infection in individuals starting 7 days or so after the onset of symptoms, to determine immunity, and in population surveillance.[citation needed]

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]

On March 26, 2020, the FDA named 29 entities that provided notification to the agency as required and are now therefore able to distribute their antibody tests.[33] One test[34] recently approved by the FDA can give a result in 15 minutes. It has a 91% clinical specificity rate and a 99% clinical sensitivity rate, according to a news release. 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.

In late March 2020, Euroimmun Medical Laboratory Diagnostics and Epitope Diagnostics received European approvals for their test kits, which can detect IgG and IgA antibodies against the virus in blood samples. The testing capacity is several hundred samples within hours and therefore much faster than the conventional PCR assay of viral RNA. The antibodies are usually detectable 14 days after the onset of the infection.[35]

Approaches to testing

Hong Kong has set up a scheme where suspected patients can stay home, "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.[36]

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.[37]

In drive-through testing for COVID-19 for suspected cases, a healthcare professional takes sample using appropriate precautions.[38][39] Drive-through centers have helped South Korea do some of the fastest, most-extensive testing of any country.[40]

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.[41] According to the president of the Robert Koch Institute, Germany has an overall capacity for 160,000 tests per week.[42] As of 19 March drive in tests were offered in several large cities.[43] As of 26 March 2020 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.[44] A first lab survey revealed that as of calendar week 12/2020 a total of at least 483,295 samples were tested up to and including week 12/2020 and 33,491 samples (6.9%) tested positive for SARS-CoV-2.[45]

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.[46][47][48]

In Wuhan a makeshift 2000-sq-meter emergency detection laboratory named "Huo-Yan" (Chinese: 火眼, or "Fire Eye" in English) was opened on 5 February 2020 by BGI,[49][50] which can process over 10,000 samples a day.[51][50] With the construction overseen by BGI-founder Wang Jian and taking 5-days,[52] 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 hadn't come on line.[53] 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.[54]

By March, shortages and insufficient amounts of reagent has become a bottleneck for mass testing in the EU and UK[55] and the US.[56][57] 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.[58][59]

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[60]. 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[61].

Production and volume

Number of tests done per day in the United States.
Blue: CDC lab
Orange: Public health lab
Gray: Data incomplete due to reporting lag

Different testing recipes targeting different parts of the coronavirus genetic profile were developed in China, France, Germany, Hong Kong, Japan, 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 was not available until 28 January, delaying available tests in the U.S.[62]

China[63] and the United States[64] had problems with the reliability of test kits early in the outbreak, and these countries and Australia[65] 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.[66] 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.[67][68]

Effectiveness

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.[69] 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.[70]

Confirmatory testing

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.[71] Out of the 16 reference laboratories, 7 are in Asia, 5 in Europe, 2 in Africa, 1 in North America and 1 in Australia.[72]

Testing statistics by country

In the following chart, the column “Positive/thousand tests” is influenced by the country’s testing policy. A country that only tests people admitted to hospitals will have a higher positive per thousand tests than a country that tests all citizens, whether or not they are showing symptoms, other things being equal.

COVID-19 testing statistics

Country or region Tests Positive As of
Tests /
million
people
Positive /
thousand
tests
Ref.
Argentina 4,843 966 31 Mar 107 199 [73]
Armenia 3,603 663 2 Apr 1,221 74 [74]
Australia 268,168 5,136 2 Apr 10,558 19 [75]
Austria 92,190 10,877 2 Apr 10,355 108 [76]
Azerbaijan 30,000 273 30 Mar 3,031 9 [77]
Bahrain 33,852 268 31 Mar 21,569 8.8 [78]
Bangladesh 1602 54 1 Apr 10 33.7 [79]
Barbados 382 45 1 Apr 1,331 118 [80]
Belarus 31,000 300 2 Apr 3,161 5.1 [81]
Belgium 18,360 1,486 18 Mar 1,594 81 [82][83]
Bolivia 591 97 19 Mar 52 164 [84]
Bosnia and Herzegovina 4,051 529 2 Apr 1,175 131 [85][86]
Brazil 54,824 6,880 1 Apr 218 9.4 [87]
Canada 268,154 11,131 1 Apr 6,780 38 [88]
Canada: AB 57,096 968 2 Apr 12,938 17 [89]
Canada: BC 44,639 1066 1 Apr 8,734 24 [90]
Canada: MB 10,044 127 1 Apr 7,291 12.6 [91]
Canada: NB 3,234 68 30 Mar 4,146 21 [92]
Canada: NL 2,333 135 30 Mar 4,475 63 [93]
Canada: NT 833 1 30 Mar 18,551 1.2 [94]
Canada: NS 5,172 127 30 Mar 5,291 25 [95]
Canada: ON 57,874 2,392 1 Apr 3,934 41 [96]
Canada: PE 608 18 30 Mar 3,844 30 [97]
Canada: QC 74,542 5,518 2 Apr 8,731 74 [98]
Canada: SK 10,528 193 1 Apr 8,909 18 [99]
Canada: YT 598 5 30 Mar 14,558 8.4 [100]
Chile 35,142 2,738 31 Mar 1,843 78 [101]
China: Guangdong 320,000 20 Feb 2,820 1.4 [102]
Colombia 21,129 1,161 2 Apr 438 55 [103]
Costa Rica 3,845 347 31 Mar 769 90 [104]
Croatia 8,352 1,011 2 Apr 2,049 121 [105]
Czechia 60,990 3,589 1 Apr 5,727 59 [106]
Denmark 35,473 3,573 2 Apr 5,983 101 [107]
Ecuador 9,604 3,163 2 Apr 562 329 [108]
Estonia 15,725 858 2 Apr 11,838 55 [109]
Finland 24,200 1,446 1 Apr 4,374 60 [110][111]
France 101,046 20,068 24 Mar 1,508 199 [112]
Germany 918,460 64,906 29 Mar 11,046 71 [45]
Greece 15,961 1,212 30 Mar 1,482 76 [113]
Grenada 18 0 19 Mar 162 0 [114]
Hong Kong 90,000 682 30 Mar 12,028 8 [115]
Hungary 16,401 585 2 Apr 1,678 36 [116]
Iceland 20,930 1,319 2 Apr 57,459 63 [117]
India 47,951 1,637 1 Apr 35 34 [118]
Indonesia 7,193 1,790 2 Apr 27 249 [119]
Iran 80,000 21,638 22 Mar 962 270 [120]
Ireland 30,213 3,235 30 Mar 6,345 107 [121]
Israel 87,108 6,808 2 Apr 9,494 78 [122]
Italy 581,232 115,242 2 Apr 9,636 198 [123]
Italy: Emilia-Romagna 60,507 15,333 2 Apr 13,568 253 [123]
Italy: Liguria 12,069 3,782 2 Apr 7,783 313 [123]
Italy: Lombardy 128,286 46,065 2 Apr 12,751 359 [123]
Italy: Marche 12,943 4,098 2 Apr 8,486 317 [123]
Italy: Piedmont 32,100 10,353 2 Apr 7,368 323 [123]
Italy: Tuscany 40,724 5,273 2 Apr 10,919 129 [123]
Italy: Veneto 120,320 10,111 2 Apr 24,526 84 [123]
Jamaica 442 44 1 Apr 162 100 [124]
Japan 34,508 2,178 1 Apr 274 63 [125]
Japan: Tokyo 3,027 521 31 Mar 217 172 [126]
Kazakhstan 5,093 13 Mar 276 [127][128]
Kosovo 1267 112 31 Mar 700 88 [129]
Kyrgyzstan 8,186 107 31 Mar 1,281 13 [130][131]
Latvia 16,834 458 2 Apr 8,768 27 [132]
Lithuania 15,635 649 2 Apr 5,595 42 [133]
Malaysia 45,378 3,116 2 Apr 1,385 69 [134]
Malta 4,462 139 27 Mar 9,040 31 [135]
Mexico 9,481 1,049 28 Mar 75 111 [136]
Montenegro 1063 144 2 Apr 1,632 136 [137]
Nepal 1185 6 2 Apr 42 5 [138]
Netherlands 46,810 7,705 26 Mar 2,686 165 [139]
New Zealand 26,015 723 2 Apr 5,232 28 [140]
North Macedonia 4,117 384 2 Apr 1,982 93 [141]
Norway 94,265 4,876 1 Apr 16,812 49 [142]
Pakistan 14,748 1,625 30 Mar 69 110 [143]
Palestine 2,519 16 Mar 499 [144]
Panama 7,333 1,317 1 Apr 1,756 180 [145]
Peru 12,669 852 27 Mar 386 67 [146]
Philippines 4,726 2,633 2 Apr 47 557 [147]
Poland 61,178 2,633 2 Apr 1,594 43 [148]
Portugal 52,086 7,443 31 Mar 5,068 143 [149]
Romania 28,483 2,738 2 Apr 1,468 96 [150]
Russia 536,669 1,836 30 Mar 3,657 3.4 [151][152]
Scotland 17,007 2,310 1 Apr 3,127 136 [153]
Serbia 5,008 1,171 2 Apr 719 234 [154]
Singapore 39,000 558 25 Mar 6,838 14 [155]
Slovakia 9,097 400 31 Mar 1,669 44 [156]
Slovenia 24,857 911 1 Apr 11,870 37 [157]
South Africa 44,292 1,380 1 Apr 754 31 [158]
South Korea 431,743 9,976 2 Apr 8,349 23 [159]
Spain 355,000 24,926 21 Mar 7,596 70 [160][161]
Sweden 36,900 4,435 31 Mar 2,859 102 [162]
Switzerland 139,330 18,267 2 Apr 16,258 131 [163]
Taiwan 31,800 322 31 Mar 1,337 10.1 [164]
Thailand 17,829 1,524 30 Mar 257 85 [165]
Trinidad and Tobago 595 90 1 Apr 436 151 [166]
Turkey 125,556 18,135 2 Apr 1,510 144 [167]
Ukraine 3,834 804 2 Apr 91 210 [168]
United Arab Emirates 220,000 570 29 Mar 22,918 2.6 [169][170]
United Kingdom 152,979 29,474 1 Apr 2,265 193 [171]
United States (unofficial) 1,329,660 238,892 2 Apr 4,051 180 [172]
United States: CA 90,100* 8,155 1 Apr 2,280 91 [173]
United States: FL 78,604 8,010 2 Apr 3,660 102 [174]
United States: IL 43,656 7,695 2 Apr 3,445 176 [175]
United States: LA 51,086 9,150 2 Apr 10,963 126 [176]
United States: NY 238,965 92,381 2 Apr 12,284 387 [177]
United States: NJ 59,110 25,590 2 Apr 6,655 433 [178]
United States: MI 18,391 6,498 31 Mar 1,835 353 [179]
United States: TX 50,679 4,669 2 Apr 1,748 92 [180]
United States: WA 74,798 5,984 1 Apr 9,823 80 [181]
Uruguay 1,538 189 24 Mar 443 123 [182]
Vietnam 67,456 218 1 Apr 701 3.4 [183]

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