Infection Testing & Diagnostics

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WHO List of Protocols for Laboratory Testing

πŸ”—https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance/laboratory-guidance

Technical guidance for laboratories conducting COVID-19 testing.



✏️ Edit this document to make it better ✏️

Guides


COVID-19: how hospital-based healthcare workers can arrange laboratory testing for patients

πŸ‡¬πŸ‡§πŸ”—https://www.gov.uk/government/publications/wuhan-novel-coronavirus-guidance-for-clinical-diagnostic-laboratories/wuhan-novel-coronavirus-who-to-call-to-request-laboratory-testing

Guidance for healthcare professionals from Public Health England on how to request COVID-19 lab tests


UK government test kit regulations

πŸ‡¬πŸ‡§πŸ”—https://www.gov.uk/government/publications/regulatory-approval-for-coronavirus-covid-19-test-kits

UK govt. guide and official submission form for manufacturers of COVID-19 test kits


Testing Resource Center

πŸ”—https://docs.google.com/document/d/1eSFsGVui5JyXvd_0AuVoV0Hd_UxYRufSDiLrXii7TLc/edit?usp=sharing

Curated strategies and best-practices for rolling out and scaling testing


The Crick COVID-19 Consortium

πŸ”—https://www.crick.ac.uk/research/covid-19/covid19-consortium

Francis Crick Institute shares guidance for steps involved in testing using open protocols and avoiding proprietary bottlenecks:


Supplementary Method 2 Chemical inactivation of clinical samples

πŸ”—https://www.crick.ac.uk/sites/default/files/2020-04/Supplementary%20Method%202%20Chemical%20inactivation_wet%20and%20dry%20swabs.pdf

Standard operating procedure on the handling of wet and dry swabs


Reopening Playbook

πŸ”—https://quaranteam.com/

The town of Bolinas, California conducted an ambitious pilot this April and tested every one of its 1845 citizens for COVID-19. Everyone in the population tested negative for active infection. An open-source playbook is underway to empower other communities to take a similar bottom-up approach to clear small populations of COVID. 


Online Questionnaires and Diagnostics

See also:

πŸ”— https://coronavirustechhandbook.com/self-reporting

News

Veterinary scientist hailed for Faroe Islands' lack of COVID-19 deaths

πŸ‡«πŸ‡΄ πŸ”—https://www.theguardian.com/world/2020/apr/08/vetinary-scientist-hailed-faroe-islands-lack-covid-19-deaths

Debes Christiansen adapted his salmon-testing lab to test for disease among humans''


FDA authorizes new test that could detect Coronavirus in about 45 minutes

πŸ”—https://edition.cnn.com/2020/03/21/politics/fda-coronavirus-test/index.html

FDA approves new test that could detect Coronavirus in about 45 minutes


Crowdsourcing against coronavirus: Seattle biologists work on DIY test kit

πŸ”— https://crosscut.com/2020/03/crowdsourcing-against-coronavirus-seattle-biologists-work-diy-test-kit

Crowdsourcing against Coronavirus: Seattle biologists work on DIY test kit

Open Initiatives

OpenCOVID-19 initiative

πŸ”—https://app.jogl.io/project/118#about

JOGL open-source detection protocol. Developing and sharing open source methodologies to safely test for the presence of COVID-19 using multiple approaches.


Biodesign Challenge 2020

πŸ”—https://biodesignchallenge.org/bdc-2020

βœ‰οΈJim Haseloff @ University of Cambridge -

set up an open DIY device and protocol design group under BioDesign2020


Coronavirus Data Hub

πŸ”— https://www.coindesk.com/world-health-organization-teams-with-ibm-oracle-on-blockchain-based-coronavirus-data-hub

Blockchain technology to check the veracity of data relating to the Coronavirus pandemic

Test Systems and Labs

OpenCell

πŸ”—https://www.opencell.bio/coronavirus

Open Cell has developed open-source high-throughput COVID-19 emergency labs


OpenTrons

πŸ”—https://blog.opentrons.com/testing-for-covid-19-with-opentrons/

Automated test system to scale COVID-19 testing to hundreds of thousands of samples per day.


Petro

πŸ”—https://github.com/johnbywater/peto

Peto is a reliable, scalable, event-sourced, open source software system designed to support periodic mass testing for novel infectious diseases such as Coronavirus.


List of COVID-19 Testing in the USA

πŸ‡ΊπŸ‡ΈπŸ”—https://docs.google.com/spreadsheets/d/1WtlvoK5UBKmJGE3FgvRC7agacaDRybB2BxUAKOQ3_lo/edit#gid=1808305318

List of COVID-19 testing in the United States (NOT OPENLY ACCESSIBLE, permission must be requested)

Test Kit Developers & Manufacturers

Lists of Test Kit Manufacturers

FIND database of test kit manufacturers

πŸ”—https://www.finddx.org/covid-19/pipeline/

Over 200 manufacturers of test kits listeda


Testing for the Presence of Antibodies

Diazyme

πŸ”—http://www.diazyme.com/diazyme-laboratories-inc-announces-availability-of-covid-19-antibody-tests

Diazyme has developed an antibody-based test kit for COVID-19


Alphabiolabs

πŸ”—https://www.alphabiolabs.co.uk/workplace-testing-services/coronavirus-testing-kit/

Alphabiolabs has developed an antibody-based test kit for COVID-19 (currently out of stock)


ELISA Genie

πŸ”—https://www.linkedin.com/in/therealcolmryan/

We develop innovative reagents for biomarker & drug discovery scientists through our 3 brands ELISA Genie, Assay Genie & Antibody Genie


MoLogic

πŸ‡¬πŸ‡§πŸ”—https://mologic.co.uk/mologic-awarded-c-1-million-by-uk-government-to-develop-rapid-diagnostic-test-for-covid-19/

MoLogic has been awarded Β£1 million by the UK government to develop a new COVID-19 test kit


Euroimmun

πŸ‡©πŸ‡ͺπŸ”—https://www.coronavirus-diagnostics.com/

The complete package for the diagnostic of COVID-19


Testing for the Presence of the Virus (rRT-PCR)

πŸ”—https://res.cloudinary.com/crowdicity-eu-cld/image/upload/NWLP_Heat_Inactivation_Validation_mr7jdp

SARS CoV-2: NWLP Heat inactivation with no extraction Protocol


Charite Test

πŸ‡©πŸ‡ͺπŸ”—https://www.charite.de/en/service/press_reports/artikel/detail/researchers_develop_first_diagnostic_test_for_novel_coronavirus_in_china/

Researchers from the German Center for Infection Research (DZIF) at CharitΓ© β€“ UniversitΓ€tsmedizin Berlinhave developed a new laboratory assay to detect the novel Chinese Coronavirus. The assay protocol has now been published by WHO as a guideline for diagnostic detection. The new assay enables suspected cases to be tested quickly.


The University of the Basque Country

πŸ‡ͺπŸ‡ΈπŸ”—https://www.ehu.eus/en/web/campusa-magazine/-/alternative-covid-19-rt-pcr-detection-test-validated-by-basque-country-s-scientific-personnel

Basque scientists validate alternative RT-PCR test for COVID-19 detection. Researchers from the University of the Basque Country (UPV/EHU), Ikerbasque, Achucarro and the Biofisika Bizkaia Foundation, in collaboration with Osakidetza, the Basque Public Health Service, are participating in the project.


KogeneBiotech

πŸ‡°πŸ‡·πŸ”—http://www.kogene.co.kr/eng/about_us/news/listbody.php?h_gcode=board&h_code=7&po_no=288

PowerCheck 2019-nCoV Real-time PCR Kit provides the fast and accurate testing solution for Coronavirus, targeting the E gene for beta Coronavirus and the RdRp gene for COVID-19 specifically. Contracted by the South Korean government.


Seegene

πŸ‡°πŸ‡·πŸ”—http://www.seegene.com/

Flexible PCR setup solution. Contracted by the South Korean government.


BGI

πŸ‡¨πŸ‡³πŸ”—https://www.bgi.com/global/company/news/bgi-develops-real-time-dna-based-kit-for-detecting-the-2019-novel-coronavirus/

BGI Develops Real-Time Fluorescent RT-PCR kit for detecting the 2019 Novel Coronavirus


LabCorp

πŸ‡ΊπŸ‡ΈπŸ”—https://ir.labcorp.com/news-releases/news-release-details/labcorp-launches-test-coronavirus-disease-2019-covid-19

LabCorp’s test has been validated for use with respiratory samples, including nasopharyngeal (NP) or oropharyngeal (OP) aspirates or washes, NP or OP swabs, and broncheoalveolar lavage (BAL). The test is a qualitative assay using PCR technology.


Abbott

πŸ‡ΊπŸ‡ΈπŸ”—https://abbott.mediaroom.com/2020-03-27-Abbott-Launches-Molecular-Point-of-Care-Test-to-Detect-Novel-C OK oronavirus-in-as-Little-as-Five-Minutes

Abbott has developed a PCR-derivative blood test with results in ~5 minutes

Some kind of PCR derivative based on video on this page.


Sense Biodetection

πŸ‡¬πŸ‡§πŸ”—https://www.sense-bio.com/news/2020/3/31/sense-accelerates-instrument-free-molecular-diagnostic-test-for-covid-19

Sense Biodetection Ltd is developing a test kit for COVID-19

Some technical details: it's equivalent to PCR using proprietary chemistry and device technology that is ultra rapid and low cost allowing for a single-use product that can be used anywhere"


Diagnostics for the Real World

πŸ‡¬πŸ‡§πŸ”—https://www.cam.ac.uk/research/news/rapid-covid-19-diagnostic-test-developed-by-cambridge-team-to-be-deployed-in-hospitals

Uses SAMBA II machines, PCR based, 90 minutes


ID NOW

πŸ”— https://www.alere.com/en/home/product-details/id-now-covid-19.html

The ID NOWβ„’ COVID-19 assay is now available for use on the ID NOW platform under U.S. Food and Drug Administration Emergency Use Authorization (EUA). The ID NOWβ„’ COVID-19 rapid test delivers high-quality molecular positive results in as little as 5 minutes, targeting the coronavirus (COVID-19) RdRp Gene.  


Detection Using AI

Scripps Research

πŸ”—https://detectstudy.org/

Downloadable app to wearables from Apple, Fitbit, Garmin, etc. monitors your heart beats. Faster than usual, it can mean that you’re coming down with a cold, flu, Coronavirus, or other viral infection.


XRayCOVID-19

πŸ”— http://tools.atislabs.com.br/covid

XRayCovid-19 is an embryonic project that uses Artificial Intelligence to assist the health system in the COVID-19 diagnostic process. It is characterized by easy use; efficiency in response time and effectiveness in the result.


Covid-cxr

πŸ”— https://github.com/aildnont/covid-cxr

An open source explainable deep CNN model for predicting the presence of COVID-19 in chest X-rays

Source of sample

Link Drop for "Source of sample"

πŸ”—The clinical effectiveness of tests to detect the presence of SARS-CoV-2 virus, and antibodies to πŸ”—SARS-CoV-2, to inform COVID-19 diagnosis

πŸ”—https://jcm.asm.org/content/early/2020/03/27/JCM.00310-20

πŸ”—https://www.journalofinfection.com/article/S0163-4453(20)30139-0/pdf

πŸ”—https://www.rcpath.org/profession/coronavirus-resource-hub/covid-19-pandemic-video-based-learning.html

Saliva sampling for Covid-19 testing

General notes

  • most studies have been done on severely diseased patients. These results may not generalise to those with mild symptoms.
  • most studies done on initial admission to hospital. Results change over time (seem to become negative) even if patient is still severely unwell. Perhaps due to other infections taking over.

Terms:

  • nasopharyngeal aspirates (NPAs)
  • direct immunofluorescence (DFA)


Papers

Azzi et al.2020 Saliva is a reliable tool to detect SARS-CoV-2

n=25, of severe or very severe disease patients.

Source: drooled or if patient intubated then aspirated using pipette if possible

When: ?when sample taken vs hospitalisation / symptoms?

Preprocess: ? into VTM or lysis or ? if nasopharyngeal vs saliva processed differently ?

Detection: ?what RNA purification and RT-qPCR system was used.?

Control: ?what positive control was used if any?

Result: All showed positive RT-qPCR of saliva. Two patients were -ve from nasopharyngeal but +ve from saliva (1 patient for 1 day and another for 2 days).

Saliva Ct always under 33 cycles (range 18.12–32.23, mean 27.16 +/βˆ’ 3.07).


Hospital now only discharge when negative on 2 nasopharyngeal and 1 saliva


Kai-Wang To et al. 12 February 2020

πŸ”—Consistent Detection of 2019 Novel Coronavirus in Saliva

n=12 hospitalised patients

Source: Saliva was "coughed" out of throat. Possible contamination with sputum.

When: On first day of hospitalisation all 12 patients were positive from nasopharyngeal or sputum but 11/12 positive from saliva.

Preprocess: sample put into 2 ml VTM

Detection: S gene of 2019-nCoV with QuantiNova SYBR Green RT-PCR Kit (Qiagen)

Control: ?what detection positive control was used if any?

Result: But 11/12 patients then drop to 0 detectable in saliva day 9 after hospitalisation.


Also mentions n=33 whose nasopharyngeal specimens tested negative and all saliva specimens also tested negative.



πŸ”—(2017) Additional molecular testing of saliva specimens improves the detection of respiratory viruses

"In some patients, Coronavirus was detected only in saliva but not in nasopharyngeal aspirate"


Is for a range of non SARS-2 viruses.

n=159

Source: saliva

When: Not clear when sample taken vs hospitalisation / symptoms  Most (146/159) of the saliva specimens were collected <2 days after the collection of the NPA sample. So introduces error making comparison less fair.

Preprocess:

Detection:

Control:

Result: all nasopharyngeal +ve for some virus (not sars-2)

Generally NPA viral load significantly greater than saliva (7.23 vs 5.30 log10 copies per mL)

27/159 (17%) saliva had higher viral load than NPA

Does it state how many had no load?


n=99

Source: saliva

When: Not specified but NPA and saliva taken at the same time

Preprocess:

Detection: multiplex PCR using the Luminex NxTAG Respiratory Pathogen Panel

Control:

Result: detected viruses in both NPA and saliva, some only in NPA, some only in saliva. Of corona viruses (Coronavirus OC43, Coronavirus 229E) one was detected in NPA and not saliva and one in saliva and not NPA (Table 4)


πŸ”—Wang et al. 2004 Detection of SARS-associated coronavirus in throat wash and saliva in early diagnosis

"SARS-CoV can be detected in saliva at high titers"

n=17

Source: saliva and throat wash (by gargling 10 mL normal saline)

Performed RT-PCR on throat wash supernatant (S), N-acetyl-L-cysteine treated supernatant (M, mucus-associated), and cellular fractions (C).

When: sampling day varied from day 2 to day 9 after onset of fever, with a median of day 4.

Preprocess: -80 oC storage until use. But showed similar RNA levels in non-frozen and frozen then thawed samples.

Detection: n/a but Qiagen RNA purification followed by Taqman assay design (Applied Biosystems)

Control:

Result: saliva had x30 more than throat wash: throat wash median 3.56 x 10^3 copies/mL, saliva median 9.92 x 10^4 copies/mL


πŸ”—Kojima et al. 15 April 2020 Self-Collected Oral Fluid and Nasal Swabs Demonstrate Comparable Sensitivity to Clinician Collected Nasopharyngeal Swabs for Covid-19 Detection

n=45, 29 +ve, samples collected at home

Source:

  • self-collected oral fluid swab specimens with and without clinician supervision
  • clinician-supervised self-collected mid-turbinate (nasal) swab specimens
  • clinician-collected nasopharyngeal swab specimens

Preprocess: DNA/RNA Shieldβ„’ solution, Zymo Research

Detection:  lysed and extracted with RNA purification kit (Norgen Biotek). RT-PCR single colour TaqMan probe, N1, N2 primer/probe assay (US CDC), N3 (Integrated DNA Technologies)

Control:

Result:

  • 90% clinician-supervised self-collected oral fluid swab specimens
  • 85% clinician-supervised self-collected mid-turbinate (nasal) swab specimens
  • 79% clinician-collected posterior nasopharyngeal swab specimens
  • 66% unmonitored self-collected oral fluid swab specimens detected

(without feedback, some unsupervised patients did not cough before self-collecting their sample)


πŸ”— Wyllie et al. April 22 2020 Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs

n=44, severely diseased

Source: self collected saliva or clinical administered nasopharyngeal swabs

Detection: US CDC SARS-CoV-2 RT-PCR

Result:

  • higher titre in saliva
  • detected SARS-CoV-2 from saliva but not nasopharyngeal swabs from eight matching samples
  • nasopharyngeal swabs and not saliva from three matched samples


πŸ”— Comparison of different samples for 2019 novel coronavirus detection by nucleic acid amplification tests



πŸ”— Saliva as a diagnostic specimen for testing respiratory virus by a point-of-care molecular assay: a diagnostic validity study



πŸ”— Respiratory virus infection among hospitalized adult patients with or without clinically apparent respiratory infection: a prospective cohort study

"Saliva has also been used in screening respiratory viruses among hospitalized patients without fever or respiratory symptoms"


πŸ”— The Presence of SARS-CoV-2 RNA in Feces of COVID-19

Accuracy Issues

πŸ”— 80% of Rapid COVID-19 Tests the Czech Republic Bought From China are Wrong

πŸ‡¨πŸ‡³πŸ‡¨πŸ‡ΏπŸ”—https://www.praguemorning.cz/80-of-rapid-covid-19-tests-the-czech-republic-bought-from-china-are-wrong/

80% of all the test bought by Czech republic from China are wrong.


Heartbreak in the Streets of Wuhan

πŸ‡¨πŸ‡³πŸ”—https://www.bloomberg.com/news/articles/2020-03-12/heartbreak-in-the-streets-of-wuhan

Unreliability of test results has caused many patients to be excluded during the early weeks of the outbreak in China


Coronavirus test kits purchased from China are unreliable, says Science Committee member

πŸ‡¨πŸ‡³πŸ‡ΉπŸ‡·πŸ”—https://www.duvarenglish.com/health-2/coronavirus/2020/03/27/coronavirus-test-kits-purchased-from-china-are-unreliable-says-science-committee-member/

Turkey did not use the rapid Coronavirus kits procured from China after tests suggested they had a low accuracy level, Prof. Dr. Ateş Kara, a member of the Health Ministry’s Coronavirus Science Committee, said on March 26. 


Britain has millions of Coronavirus antibody tests, but they don’t work

πŸ‡¬πŸ‡§πŸ”—https://www.thetimes.co.uk/article/britain-has-millions-of-coronavirus-antibody-tests-but-they-don-t-work-j7kb55g89

Britain has millions of Coronavirus antibody test, but they don't work.

Research papers

Mammoth Biosciences

πŸ”—https://mammoth.bio/2020/02/15/white-paper-a-protocol-for-rapid-detection-of-sars-cov-2-using-crispr-sars-cov-2-detectr/

Paper from Mammoth Biosciences describing a CRISPR protocol for detection of COVID-19

Isothermal LAMP PCR + CRISPR Cas12 DETECTR

Needs RNA extraction step

protocol


Icahn School of Medicine at Mount Sinai

πŸ”—https://www.medrxiv.org/content/10.1101/2020.03.17.20037713v1

A serological assay to detect SARS-CoV-2 seroconversion in humans


Broad Institute

πŸ”—https://www.broadinstitute.org/news/enabling-coronavirus-detection-using-crispr-cas13-open-access-sherlock-research-protocols-and

Paper from the Zhang lab at MIT and Harvard on a CRISPR protocol for COVID-19 detection

Isothermal PCR CRISPR Cas13 SHERLOCK

protocol


How Broad Institute converted a clinical processing lab into a large-scale COVID-19 testing facility in a matter of days

πŸ”—https://www.broadinstitute.org/news/how-broad-institute-converted-clinical-processing-lab-large-scale-covid-19-testing-facility

How Broad Institute converted a clinical processing lab into a large-scale COVID-19 testing facility in a matter of days


BOMB Bio

πŸ”—https://bomb.bio/forums/topic/bomb-protocol-8-1-rna-extraction-from-mammalian-cells-using-tri-reagent/

Open-source BOMB Protocol for RNA isolation


Balachandran lab at Brunel University

πŸ”—https://www.brunel.ac.uk/news-and-events/news/articles/Manufacturers-needed-for-rapid-roll-out-of-Coronavirus-test

A lab at Brunel University London has developed a COVID-19 test and is looking for manufacturing partners


Wang, Xu, Gao, et al

πŸ”—https://jamanetwork.com/journals/jama/fullarticle/2762997

Detection of SARS-CoV-2 in Different Types of Clinical Specimens: finds that COVID-19 may be transmitted by the fecal route

πŸ”— https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciaa149/5734265?searchresult=1

Coronavirus (2019-nCoV) was detected in the self-collected saliva of 91.7% (11/12) of patient

Data

See also:

πŸ”— https://coronavirustechhandbook.com/data


Testing location maps

πŸ‡ΊπŸ‡ΈπŸ”—www.Openhealth.cc

Map of all current testing locations.


Safecast

πŸ”—https://covid19map.safecast.org/

Map of people who have self-reported as having been tested or having been refused testing.

Commentary

Tony Blair Institute

πŸ”—https://institute.global/tony-blair/covid-19-testing-uk-primer

Summary on the UK position from the Tony Blair Institute


Centers for Disease Control and Prevention

πŸ‡ΊπŸ‡ΈπŸ”—https://www.cdc.gov/coronavirus/2019-ncov/symptoms-testing/testing.html

Information from CDC on who should be tested


The Guardian

πŸ‡¬πŸ‡§πŸ”—https://www.theguardian.com/world/2020/apr/09/uk-government-urged-to-abandon-poor-finger-prick-antibody-tests-coronavirus

UK government urged to abandon finger pricking tests


The Government of the Republic of Korea

πŸ‡°πŸ‡·πŸ”— http://www.korea.kr/common/download.do?fileId=190536078&tblKey=GMN

How South Korea responded to a pandemic using ICT, report including testing


The role of CRP testing in Coronavirus management in China

πŸ”—https://www.abacusdx.com/biochemistry/crp-is-an-important-marker-in-the-prediagnostics-and-treatment-follow-up-of-the-new-coronavirus-2019-ncov/

Abacus DX blog: CRP is an important marker in the prediagnostics and treatment follow up of the new Coronavirus (2019-nCoV).