Tests performed: Haemostatic tests ristocetin-induced platelet aggregation plasma VWF antigen VWF risocetin cofactor VWF FVIII-binding capacity VWF multimers and FVIII activity DDAVP test Concentration timecourses

sequencing from genomic DNA performed and reported in 2011

cDNA analysis

Real-time-PCR analysis

long PCR

Ellman assay (quantifying sulfhydryls)

Dynamic light scattering measurements

circular dichroism

ADAMTS13 proteolysis assay

ADAMTS13-VWF binding assay

Useful discussion on the pros and cons!

See notes in this section for restriction digestion tips

NEB says

Digestion is recommended whenever DNA input is greater than 75 ng Source

NEB says that biorad recommends these enzymes: AluI, CviQI, HaeIII, HindIII-HF, MseI

More guidelines

• Assemble ddPCR reactions at room temperature, this allows the restriction enzyme to digest the gDNA during the reaction set-up period
• Prepare reaction mixes as you would for a standard ddPCR reaction. Add 0.5–1 μL of each restriction enzyme (5–20 units, depending on enzyme concentration) to the reaction mixture
• After set-up, simply continue droplet generation as normal
• Restriction enzyme will be inactivated during first PCR denaturation step

Refer to this protocol mentioned in the BioRad page, annotation

Bird banding is one technique used to monitor migratory flock patterns and given the infection rate of HPAIV A/H5N1 is near 100% the virus can be understood as endemic in all migratory waterfowl so tracking their movements is an effective method for tracking the transmission dynamics of the virus itself.

Nova might be better to have for 1-step ddPCR applications where the BHQ quenchers are unstable due to reduction of the N=N azo bond by the DTT additive

Pritchard, E., Matthews, P. C., Stoesser, N., Eyre, D. W., Gethings, O., Vihta, K.-D., Jones, J., House, T., VanSteenHouse, H., Bell, I., Bell, J. I., Newton, J. N., Farrar, J., Diamond, I., Rourke, E., Studley, R., Crook, D., Peto, T. E. A., Walker, A. S., & Pouwels, K. B. (2021). Impact of vaccination on new SARS-CoV-2 infections in the United Kingdom. Nature Medicine, 1–9. https://doi.org/10.1038/s41591-021-01410-w

Lenhardt, S. (2021, November 30). Labore am Limit: Bei PCR-Tests kommt es zu Engpässen. tagesschau.de. https://www.tagesschau.de/wirtschaft/labore-corona-pcr-test-101.html

Barnes, O., & Payne, S. (2021, October 15). Covid testing suspended at private UK lab over potentially inaccurate results. Financial Times. https://www.ft.com/content/bee7bdde-e37b-4411-afd5-1e8ceacfa5f8

Dixon, B. C., Fischer, R. S. B., Zhao, H., O’Neal, C. S., Clugston, J. R., & Gibbs, S. G. (2021). Contact and SARS-CoV-2 Infections Among College Football Athletes in the Southeastern Conference During the COVID-19 Pandemic. JAMA Network Open, 4(10), e2135566. https://doi.org/10.1001/jamanetworkopen.2021.35566

Beecher, J. (2021, October 30). I raised an early alarm on PCR test scandal but authorities ignored me. OpenDemocracy. https://www.opendemocracy.net/en/ournhs/i-raised-an-early-alarm-on-pcr-test-scandal-but-authorities-ignored-me/

Kissane, E. (2021, December 23). We’re About to Lose Track of the Pandemic. The Atlantic. https://www.theatlantic.com/ideas/archive/2021/12/were-about-to-lose-track-of-the-pandemic/621097/

Thomas, T., & Duncan, P. (2021, December 23). If Omicron is the dominant variant in UK, why is the number of confirmed cases so low? The Guardian. https://www.theguardian.com/world/2021/dec/23/if-omicron-is-the-dominant-variant-in-uk-why-is-the-number-of-confirmed-cases-so-low

ReconfigBehSci. (2021, December 11). RT @DrEricDing: DOUBLING % in one day: The spike of probable #Omicron variant in Scotland🏴󠁧󠁢󠁳󠁣󠁴󠁿 has critically surged—Now at 13.3%, up fro… [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1469596523222781954

ReconfigBehSci. (2021, December 22). RT @chrischirp: Positivity rising steeply too—There are definitely many more people we aren’t catching https://t.co/4xDPwYQtrx [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1473695678610214927

1. Managing COVID at home, isolation and protecting your household: an overview

ReconfigBehSci [@SciBeh]. (2021, November 26). RT @timcolbourn: @kallmemeg so no cases of B.1.1.529 cases in UK as of Mon 22nd Nov? Do you know when the S-gene drop out PCR results for… [Tweet]. Twitter. https://twitter.com/SciBeh/status/1464320681315905542

ReconfigBehSci [@SciBeh]. (2021, November 28). RT @CiesekSandra: Servicetweet für Labore: #Omicron wird auch von 3 PCR Systemen in den angegebenen Genen detektiert. Https://t.co/x3gZEP2r… [Tweet]. Twitter. https://twitter.com/SciBeh/status/1464991380628021254

Sebastian Rushworth M.D. (2021, January 25). This graph shows the share of the Swedish population testing positive to antibodies against covid week on week. The results are pretty startling. Https://t.co/rye4WImrvl [Tweet]. @sebrushworth. https://twitter.com/sebrushworth/status/1353775606274654208

Sample, I., & Walker, P. (2021, December 7). Scientists find ‘stealth’ version of Omicron that may be harder to track. The Guardian. https://www.theguardian.com/world/2021/dec/07/scientists-find-stealth-version-of-omicron-not-identifiable-with-pcr-test-covid-variant

Mia Malan. (2021, November 25). [Thread] What is the potential impact of the new B.1.1.529 #COVID19 variant? @rjlessells: 1. It’s relatively simple to detect some B.1.1.529 cases, as it’s possible to use PCR tests to do this in some cases 2. B.1.1.529 = has many mutations across different parts of the virus https://t.co/ytktqLzJUi [Tweet]. @miamalan. https://twitter.com/miamalan/status/1463846528578109444

Camero, K. (n.d.). If You Think You Have COVID But Your Rapid Test Is Negative, Here’s Why. BuzzFeed News. Retrieved February 4, 2022, from https://www.buzzfeednews.com/article/katiecamero/negative-covid-test

Covid-19: Cutting self-isolation to five days would be helpful, Nadhim Zahawi says. (2022, January 9). BBC News. https://www.bbc.com/news/uk-59925702

Scientists try to pinpoint why rapid Covid tests are missing some cases. (2022, January 6). STAT. https://www.statnews.com/2022/01/06/scientists-try-to-pinpoint-why-rapid-covid-tests-are-missing-cases/

NSW records 22 deaths, 91,928 COVID-19 cases as rapid tests added to daily infection tallies. (2022, January 12). ABC News. https://www.abc.net.au/news/2022-01-13/nsw-records-22-deaths-and-91928-covid-cases/100753504

Cutler, S. (2022, January 13). Cutting the Covid isolation period to five days is foolhardy and dangerous. The Guardian. https://www.theguardian.com/commentisfree/2022/jan/13/cutting-covid-isolation-period-five-days-foolhardy-dangerous

Pathology insider describes unworkable conditions in SydPath PCR labs. (2022, January 10). ABC News. https://www.abc.net.au/news/2022-01-10/pathology-insider-describes-unworkable-conditions/100744536

Yoni Freedhoff 🟣, MD. (2022, January 5). Good lord! The percent positivity rate in #Ottawa LTC’s PCR tests was 🚨83.72%🚨 yesterday (while Ottawa large was 50%)! [Tweet]. @YoniFreedhoff. https://twitter.com/YoniFreedhoff/status/1478832524533116931

Eric Topol. (2021, November 27). View of key mutations of Omicron’s 50, with 30 in the spike protein, 15 in its receptor binding domain https://ft.com/content/42c5ff3d-e676-4076-9b9f-7243a00cba5e http://covariants.org @EllingUlrich @_b_meyer https://t.co/onMoNFVLFJ [Tweet]. @EricTopol. https://twitter.com/EricTopol/status/1464452102382448643

Arieh Kovler. (2021, November 26). Israel has identified four cases of the B.1.1.529 variant, all recent travellers. One case, a 32-year-old woman returning from South Africa, was triple vaccinated with Pfizer and had her 3rd dose just two months ago. [Tweet]. @ariehkovler. https://twitter.com/ariehkovler/status/1464190991204859919

Tom Moultrie. (2021, December 17). A 1-figure Gauteng update, bringing in data through Wednesday 15/12 (PCR only; by date of collection). The turn continues. On similar metrics (not shown) ALL northern provinces (NW, GT, MP, LP) seem to have now turned. Https://t.co/6Bh3kZsooK [Tweet]. @tomtom_m. https://twitter.com/tomtom_m/status/1471723711287996416

Jay Varma. (2021, December 16). Um, we’ve never seen this before in #NYC. Test positivity doubling in three days 12/9—3.9% 12/10—4.2% 12/11—6.4% 12/12—7.8% Note: Test % is only for PCR & NYC does more per capita daily than most places ~67K PCR/day + 19K [reported] antigen over past few days (1/2) https://t.co/PhxsZq55jn [Tweet]. @DrJayVarma. https://twitter.com/DrJayVarma/status/1471485885447389186

An Omicron cluster in diplomats and an outbreak at a Steps concert: The variant’s timeline is shifting. (2021, December 5). ABC News. https://www.abc.net.au/news/2021-12-06/omicron-netherlands-origins-and-strategy-to-control-it/100668682

Mahase, E. (2021). Covid-19: Do vaccines work against omicron—and other questions answered. BMJ, 375, n3062. https://doi.org/10.1136/bmj.n3062

Omicron cases may be far higher than currently confirmed, variant marker analysis reveals. (2021, December 8). Inews.Co.Uk. https://inews.co.uk/news/health/omicron-covid-cases-may-be-seven-times-higher-than-confirmed-1341156

Why Is It So Hard to Get a Rapid Covid Test in the U.S.? (2021, November 23). Bloomberg.Com. https://www.bloomberg.com/opinion/articles/2021-11-23/why-is-it-so-hard-to-get-a-rapid-covid-test-in-the-u-s

Follmann, D., & Fay, M. (2021). Vaccine Efficacy at a Point in Time (p. 2021.02.04.21251133). https://doi.org/10.1101/2021.02.04.21251133

Covid: Lateral flow tests more accurate than first thought, study finds—BBC News. (n.d.). Retrieved October 15, 2021, from https://www.bbc.co.uk/news/health-58899612

ReconfigBehSci. (2021, July 6). RT @mvankerkhove: I’m struggling with how best to stress how fragile the global situation is, so I’ll be blunt: Each week >2.6 million cas… [Tweet]. @SciBeh. https://twitter.com/SciBeh/status/1412416348676820992

How contagious is Delta? How long are you infectious? Is it more deadly? A quick guide to the latest science—ABC News. (n.d.). Retrieved October 3, 2021, from https://www.abc.net.au/news/2021-09-29/covid-delta-variant-what-the-science-says/100497804?utm_campaign=abc_news_web&utm_content=twitter&utm_medium=content_shared&utm_source=abc_news_web

Beauté, J., Adlhoch, C., Bundle, N., Melidou, A., & Spiteri, G. (2021). Testing indicators to monitor the COVID-19 pandemic. The Lancet Infectious Diseases, 0(0). https://doi.org/10.1016/S1473-3099(21)00461-8

Kraemer, M. U. G., Hill, V., Ruis, C., Dellicour, S., Bajaj, S., McCrone, J. T., Baele, G., Parag, K. V., Battle, A. L., Gutierrez, B., Jackson, B., Colquhoun, R., O’Toole, Á., Klein, B., Vespignani, A., Consortium‡, T. C.-19 G. U. (CoG-U., Volz, E., Faria, N. R., Aanensen, D., … Pybus, O. G. (2021). Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence. Science. https://doi.org/10.1126/science.abj0113

Kissler, S., Fauver, J. R., Mack, C., Tai, C. G., Breban, M. I., Watkins, A. E., Samant, R. M., Anderson, D. J., Ho, D. D., Grubaugh, N. D., & Grad, Y. (2021). Densely sampled viral trajectories suggest longer duration of acute infection with B.1.1.7 variant relative to non-B.1.1.7 SARS-CoV-2. https://dash.harvard.edu/handle/1/37366884

Covid Data Science. (2021) ‘UK Variant B.1.1.7 becoming the dominant strain in the USA - what does it mean for Spring/Summer?’. Accessed 26 March 2021. https://www.covid-datascience.com/post/uk-variant-b-1-1-7-becoming-the-dominant-strain-in-the-usa-what-does-it-mean-for-spring-summer

de Oliveira T, Lutucuta S, Nkengasong J, Morais J, Paixao JP, Neto Z, Afonso P, Miranda J, David K, Ingles L, Amilton P A P R R C, Freitas H R, Mufinda F, Tessema K S , Tegally H, San E J, Wilkinson E, Giandhari J, Pillay S, Giovanetti M, Naidoo Y, Katzourakis A, Ghafari M, Singh L, Tshiabuila D, Martin D, Lessells R. (2021) A Novel Variant of Interest of SARS-CoV-2 with Multiple Spike Mutations Detected through Travel Surveillance in Africa. medRxiv. https://www.krisp.org.za/publications.php?pubid=330. Accessed 26 March 2021.

Volz, E., Mishra, S., Chand, M. et al. Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature (2021). https://doi.org/10.1038/s41586-021-03470-x

Varsavsky, Thomas, Mark S. Graham, Liane S. Canas, Sajaysurya Ganesh, Joan Capdevila Pujol, Carole H. Sudre, Benjamin Murray, et al. ‘Detecting COVID-19 Infection Hotspots in England Using Large-Scale Self-Reported Data from a Mobile Application: A Prospective, Observational Study’. The Lancet Public Health 6, no. 1 (1 January 2021): e21–29. https://doi.org/10.1016/S2468-2667(20)30269-3.

Here’s a graph they don’t want you to see. (2021, January 25). Sebastian Rushworth M.D. https://sebastianrushworth.com/2021/01/25/heres-a-graph-they-dont-want-you-to-see/

There is no way to know how many times a target has been copied.

This seems like it would more accurate than just about any other test.

[[Z: The number of PCR cycles has not been standardized, and is usually not even mentioned to the doctor]]

[[Z: A positive PCR should be followed by a viral culture test to see if you're dealing with a live infection]]

After a positive PCR test, you don't know if the virus is alive or not. To find this out you can add it to respiratory cells (in the case of a respiratory virus) and see if they start producing virus particles).

[[Z: Viral culture tests are rarely used in clinical practice]]

Positive diagnoses of COVID-19 are done base on PCR only.

PCR only tells you if you're detecting sequences of the viral genome. It doesn't tell you that what you're finding is live virus or not.

Surkova, E., Nikolayevsskyy, V., Drobniewski, F. (2020). False-positive COVID-19 results: hidden problems and costs. The Lancet Respiratory Medicine. https://doi.org/10.1016/S2213-2600(20)30453-7

Take Away: This is an incorrect usage of the term "false positive." A positive PCR test result from a recovered infection is a valid and true positive.

Claim: PCR tests for SARS-CoV-2 give false positive results when there is no active virus.

Evidence: The diagnostic PCR tests currently in widespread use are designed to detect the presence of the SARS-CoV-2 viral RNA in a clinical sample. The RNA is only a part of the complete virus and is not infectious on its own. Research has shown that viral RNA can be detected in some samples up to 12 weeks after onset of symptoms (1). In other words, this is like testing if an oven is warmer than the room temperature - it could be hot even after it has been turned off.

By definition, in the context of SARS-CoV-2 PCR tests, a "false positive" means that a test result is deemed positive when in reality there was no viral RNA in the sample. If a person is recovering from an infection, gets tested, and then is given a positive test result, that is a true positive regardless of whether they are infectious or not.

Sources: 1) https://www.cdc.gov/coronavirus/2019-ncov/hcp/duration-isolation.html

Take Away: Diagnostic tests are most useful when they are both sensitive and rapid. The sensitivity of SARS-CoV-2 PCR tests is not the issue, but rather the time it takes to get a result. Additionally, the "90%" statistic is likely misleading due to the data source and not generalisable to all testing results.

The Claim: The usual PCR diagnostic tests may be too sensitive and too slow, with up to 90% of positive cases due to trace amounts of virus.

The Evidence: Polymerase Chain Reaction (PCR)-based tests, which are currently in the most widespread use for detection of SARS-CoV-2 RNA, involves a molecular process that amplifies target DNA sequences in repeated temperature-dependent cycles. The amount of target DNA is measured after each cycle and the number of the cycle when the target can be reliably detected is often referred to as the cycle threshold (Ct). The Ct value is proportional to the amount of starting DNA in the sample and can be used to estimate the viral load of a patient. In some ways this is like a teacher making photocopies of a chapter from a textbook until they have enough for all their students.

However, Ct values are relative measurements and need to be directly compared to controls for every sample - a Ct value taken alone can be meaningless. For instance, consider an infected patient who is tested twice: the first time they are gently swabbed and the sample is relatively dilute, the second time they are vigorously swabbed and the sample is relatively concentrated. The resulting Ct values could be drastically different. Therefore, Ct values need to be considered carefully in the proper context for making medical or policy decisions. The FDA also recommends that a PCR result alone should not be used to determine infection status.

Positive results are indicative of the presence of SARS-CoV-2 RNA; clinical correlation with patient history and other diagnostic information is necessary to determine patient infection status. (1)

Current PCR test results are generally given as a binary positive/negative based on a cutoff value for Ct. The cutoff needs to be determined based on the performance of each individually developed SARS-CoV-2 test, of which there are currently over 160 that have been granted emergency use authorization by the FDA (2). Based on unpublished data from the CDC, setting a stringent Ct cutoff of 30 could return negative results in patients who are both infected and potentially infectious (3 Fig 5). Furthermore, a 30 cycle cutoff would return invalid results for samples which are too diluted. Based on the same CDC data, up to 30% of potentially infectious patients would get invalid results and need to be re-swabbed, thereby extending the time between getting infected and getting a positive result.

The period of time when RNA from SARS-CoV-2 can be detected (and a positive PCR test result returned) may extend up to 12 weeks after recovery, with Ct values trending higher over time (3,4). According to The New York Times article, they looked at Ct values from people who tested positive in Massachusetts in July and found 85-90% of results had Ct values greater than 30. The epidemiology of COVID-19 is highly time and region dependent. Massachusetts had a peak in COVID-19 hospitalizations on April 21 (5), which is 9-12 weeks prior to the testing data analyzed by The NY Times. Therefore, the detection of a large proportion of people with lingering viral RNA is not surprising. These results are likely not universal and can not be applied to other regions, especially where community spread is still significant.

Sources:

(1) https://www.fda.gov/media/135900/download

(2) https://www.fda.gov/medical-devices/coronavirus-disease-2019-covid-19-emergency-use-authorizations-medical-devices/vitro-diagnostics-euas

(3) https://www.cdc.gov/coronavirus/2019-ncov/hcp/duration-isolation.html

(4) Li N, Wang X, Lv T. Prolonged SARS-CoV-2 RNA Shedding: Not a Rare Phenomenon. J Med Virol 2020 Apr 29. doi: 10.1002/jmv.25952.

(5) https://www.bostonherald.com/2020/05/22/massachusetts-finally-seeing-downward-coronavirus-trends/

Take away: The claim that virus can be detected for a long time but is not infectious needs further clarification. This claim was based on a Lancet article (1). Within the Lancet article, some of the studies cited detected RNA in stool/blood/seminal fluid samples instead of nasal swabs. Other studies cited did not test infectious nature of virus detected by PCR. It is several logic steps to travel from detecting virus in stool/blood/seminal fluid in Lancet article to concluding that PCR of nasal swabs for COVID-19 results in large numbers of false positives.

The claim: RNA from coronavirus is present and can be detected for a long time but may not be infectious.

The evidence: The Spectator article links to the article "SARS-CoV-2 shedding and infectivity" in the Lancet (1). This article cites seven articles to support the statement that RNA persists long after virus is not infectious. Of these articles, only one reports that virus was detected at ~30 days but could not be cultured beyond three weeks (2). This article also states that detection was easier in stool samples than nasal samples after the first five days. Several articles cited by source 1 did not report infectivity of virus detected (3, 4, 5, and 7). Of the two remaining articles, virus was detected in serum/blood (6 and 8). In the serum study, 58% of tested specimens were infectious (6).

Source:

1 https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30868-0/fulltext

2 https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(03)13412-5/fulltext

3 https://pubmed.ncbi.nlm.nih.gov/15030700/

4 https://pubmed.ncbi.nlm.nih.gov/27682053/

5 https://pubmed.ncbi.nlm.nih.gov/29648602/

6 https://www.thelancet.com/journals/langlo/article/PIIS2214-109X(16)30243-1/fulltext

7 https://pubmed.ncbi.nlm.nih.gov/28195756/

8 https://pubmed.ncbi.nlm.nih.gov/22872860/

Primer Weekly Briefing 01/05/20

Mei, X., Lee, H.-C., Diao, K., Huang, M., Lin, B., Liu, C., Xie, Z., Ma, Y., Robson, P. M., Chung, M., Bernheim, A., Mani, V., Calcagno, C., Li, K., Li, S., Shan, H., Lv, J., Zhao, T., Xia, J., … Yang, Y. (2020). Artificial intelligence for rapid identification of the coronavirus disease 2019 (COVID-19). MedRxiv, 2020.04.12.20062661. https://doi.org/10.1101/2020.04.12.20062661

Fenton, N., Hitman, G. A., Neil, M., Osman, M., & McLachlan, S. (2020). Causal explanations, error rates, and human judgment biases missing from the COVID-19 narrative and statistics [Preprint]. PsyArXiv. https://doi.org/10.31234/osf.io/p39a4

Shweta, F., Murugadoss, K., Awasthi, S., Venkatakrishnan, A., Puranik, A., Kang, M., Pickering, B. W., O’Horo, J. C., Bauer, P. R., Razonable, R. R., Vergidis, P., Temesgen, Z., Rizza, S., Mahmood, M., Wilson, W. R., Challener, D., Anand, P., Liebers, M., Doctor, Z., … Badley, A. D. (2020). Augmented Curation of Unstructured Clinical Notes from a Massive EHR System Reveals Specific Phenotypic Signature of Impending COVID-19 Diagnosis [Preprint]. Infectious Diseases (except HIV/AIDS). https://doi.org/10.1101/2020.04.19.20067660

Viehweger, A. (2020). Phiweger/clonepool [TeX]. https://github.com/phiweger/clonepool (Original work published 2020)

Viehweger, A., Kühnl, F., Brandt, C., & König, B. (2020). Increased PCR screening capacity using a multi-replicate pooling scheme. MedRxiv, 2020.04.16.20067603. https://doi.org/10.1101/2020.04.16.20067603