Infection Testing & Diagnostics

๐Ÿ’ฌ WhatsApp Chat for Testing section ๐Ÿ’ฌ


Link Drop

Got another link for this section? Put it here.

๐Ÿ”—https://res.cloudinary.com/crowdicity-eu-cld/image/upload/NWLP_Heat_Inactivation_Validation_mr7jdp
SARS CoV-2: NWLP Heat inactivation with no extraction
Protocol

WHO List of Protocols for Laboratory Testing

๐Ÿ”—https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance/laboratory-guidance
Technical guidance for laboratories conducting COVID-19 testing.


โœ๏ธ Edit this document to make it better โœ๏ธ

Guides

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

๐Ÿ‡ฌ๐Ÿ‡ง๐Ÿ”—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

๐Ÿ‡ฌ๐Ÿ‡ง๐Ÿ”—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

๐Ÿ”—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

๐Ÿ”—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

๐Ÿ”—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

Online Questionnaires and Diagnostics

See also:

๐Ÿ”— https://coronavirustechhandbook.com/self-reporting

๐Ÿ‡ฌ๐Ÿ‡ง๐Ÿ”— NHS 111 Online - About coronavirus (COVID-19)
๐Ÿ—ฃ https://www.nhs.uk/contact-us/
Tool from the NHS to give advice on what to do next based on your symptoms.
Github:

111 Online

๐Ÿ”— https://github.com/111Online
NHS Digital 111 Online Program Public Repo's

๐Ÿ”—Solvโ€™s COVID-19 response: Free telemedicine for providers on the front lines of care

๐Ÿ‡บ๐Ÿ‡ธ๐Ÿ”—https://medium.com/solv/solvs-covid-19-response-free-telemedicine-for-providers-on-the-front-lines-of-care-4d03a7939918
An article from Solv Health discussing how they are providing free telemedicine for providers during the COVID-19 pandemic.

Coronavirus disease (COVID-19)

๐Ÿ‡จ๐Ÿ‡ฆ๐Ÿ”—https://www.canada.ca/en/public-health/services/diseases/coronavirus-disease-covid-19.html
Self-assessment by government of Canada. Includes information on how apply for benefits.

COVID-19 Screeningย Tool

๐Ÿ‡บ๐Ÿ‡ธ๐Ÿ”—http://apple.com/covid-19
Screening tool from Apple to work out whether symptoms are COVID-19 related or not.

COVID-19 CHECK

๐Ÿ”—https://chat.mybingli.com/#/covid
COVID-19 pre-triage module. With the help of a few simple questions filled in by the patient at home, the app determines whether the patient should contact a doctor or go to the hospital, or not. This pre-triage is available free of charge in 10 languages.

News

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

๐Ÿ‡ซ๐Ÿ‡ด ๐Ÿ”—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

๐Ÿ”—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

๐Ÿ”— 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

๐Ÿ”—https://app.jogl.io/project/118#about
Collaboration to develop Opensource bio test.

Biodesign Challenge 2020

๐Ÿ”—https://biodesignchallenge.org/bdc-2020
โœ‰๏ธJim Haseloff @ University of Cambridge -
set up an open DIY device and protocol design group under BioDesign2020

Coronavirus Data Hub

๐Ÿ”— 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

๐Ÿ”—https://www.opencell.bio/coronavirus
Open Cell has developed open-source high-throughput COVID-19 emergency labs

OpenTrons

๐Ÿ”—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

๐Ÿ”—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

๐Ÿ‡บ๐Ÿ‡ธ๐Ÿ”—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

๐Ÿ”—https://www.finddx.org/covid-19/pipeline/
Over 200 manufacturers of test kits listeda

Testing for the Presence of Antibodies

Diazyme

๐Ÿ”—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

๐Ÿ”—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

๐Ÿ”—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

๐Ÿ‡ฌ๐Ÿ‡ง๐Ÿ”—https://mologic.co.uk/mologic-awarded-c-1-million-by-uk-government-to-develop-rapid-diagnostic-test-for-covid-19/
MoLogic has been awarded ยฃ1 million by the UK government to develop a new COVID-19 test kit

Euroimmun

๐Ÿ‡ฉ๐Ÿ‡ช๐Ÿ”—https://www.coronavirus-diagnostics.com/
The complete package for the diagnostic of COVID-19

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

Charite Test

๐Ÿ‡ฉ๐Ÿ‡ช๐Ÿ”—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) atย Charitรฉย โ€“ย Universitรคtsmedizin 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

๐Ÿ‡ช๐Ÿ‡ธ๐Ÿ”—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

๐Ÿ‡ฐ๐Ÿ‡ท๐Ÿ”—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

๐Ÿ‡ฐ๐Ÿ‡ท๐Ÿ”—http://www.seegene.com/
Flexible PCR setup solution. Contracted by the South Korean government.

BGI

๐Ÿ‡จ๐Ÿ‡ณ๐Ÿ”—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

๐Ÿ‡บ๐Ÿ‡ธ๐Ÿ”—https://ir.labcorp.com/news-releases/news-release-details/labcorp-launches-test-coronavirus-disease-2019-covid-19
LabCorpโ€™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

๐Ÿ‡บ๐Ÿ‡ธ๐Ÿ”—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

๐Ÿ‡ฌ๐Ÿ‡ง๐Ÿ”—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

๐Ÿ‡ฌ๐Ÿ‡ง๐Ÿ”—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

๐Ÿ”—ย https://www.alere.com/en/home/product-details/id-now-covid-19.html
The ID NOWโ„ข 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 NOWโ„ข COVID-19 rapid test delivers high-quality molecular positive results in as little as 5 minutes, targeting the coronavirus (COVID-19) RdRp Gene.ย ย 

Home Testing Kits

Everlywell

๐Ÿ‡บ๐Ÿ‡ธ๐Ÿ”—https://www.everlywell.com/blog/news-and-info/our-commitment-to-fighting-covid-19/
US company provides a home testing kit. Samples are collected at home then sent to a lab for analysis. Have announced that they are making their test available for the medical workers first.

Scanwell Health

๐Ÿ‡บ๐Ÿ‡ธ๐Ÿ”—https://www.scanwellhealth.com
Scanwell is working on getting at-home serological testing available in the US.ย 

NURX

๐Ÿ‡บ๐Ÿ‡ธ๐Ÿ”— https://www.nurx.com/coronavirus-testing/
NURX has launched the first at-home COVID-19 test. You can get a home test kit delivered overnight, use a throat swab to take a sample, send it back to them and get results within 48 hours.

Detection Using AI

Scripps Research

๐Ÿ”—https://detectstudy.org/
Downloadable app to wearables from Apple, Fitbit, Garmin, etc. monitors your heart beats. Faster than usual, it can mean that youโ€™re coming down with a cold, flu, Coronavirus, or other viral infection.

XRayCOVID-19

๐Ÿ”— 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

๐Ÿ”— 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"

๐Ÿ”—The clinical effectiveness of tests to detect the presence of SARS-CoV-2 virus, and antibodies to ๐Ÿ”—SARS-CoV-2, to inform COVID-19 diagnosis
๐Ÿ”—https://jcm.asm.org/content/early/2020/03/27/JCM.00310-20
๐Ÿ”—https://www.journalofinfection.com/article/S0163-4453(20)30139-0/pdf
๐Ÿ”—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:ย 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 usedย 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 18.12โ€“32.23, mean 27.16 +/โˆ’ 3.07).




Kai-Wang To et al. 12 February 2020

  • ๐Ÿ”—
















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







  • ๐Ÿ”—


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

Is for a range of non SARS-2 viruses.


159
Source: saliva
When: Not clear when sample taken vs hospitalisation / symptoms ย 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:
  • some

(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





Source: saliva
When:ย 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)




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:ย 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

๐Ÿ”—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 Shieldโ„ข solution, Zymo Research
Detection: ย lysed and extracted with RNA purification kit (Norgen Biotek). RT-PCRย 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)

๐Ÿ”— 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


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๐Ÿ”— 80% of Rapid COVID-19 Tests the Czech Republic Bought From China are Wrong





Heartbreak in the Streets of Wuhan






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





  • C


Britain has millions of Coronavirus antibody tests, but they donโ€™t work









































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







o






























  • ๐Ÿ”—

























Centers for Disease Control and Prevention






The Guardian






The Government of the Republic of Korea

๐Ÿ‡ฐ๐Ÿ‡ท๐Ÿ”— 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

๐Ÿ”—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).