June 12, 2020 | The diagnostics community has continued to expand their understanding of COVID-19, observing the high incidence of cases in certain populations, as well as improving blood tests for the virus. Here, we round up the week’s research and industry news for COVID-19.
Literature Updates
Preliminary observations suggest a high incidence of COVID-19 in stroke patients, including younger patients who were otherwise healthy, according to a 14-patient study published in Neurosurgery. Researchers at Thomas Jefferson University and NYU Langone Medical Center in New York noted seeing patients in their 30s, 40s and 50s with massive strokes typically seen in patients in their 70s and 80s. Mortality rate for these COVID-19 stroke patients was 42.8% vs. the typical 5% to 10% for stroke. The incidence of coronavirus in this small patient sample was 31.5% and had an unusual presentation, including stroke in large vessels, in both hemispheres of the brain, and in both arteries and veins of the brain. The authors speculate that the virus may be interfering with the ACE2 receptor’s normal function, which controls blood flow in the brain, in addition to using it as an entry point to the cell. DOI: 10.1093/neuros/nyaa254
More than half of COVID-19 patients admitted to the ICU developed clinically significant blood clots that went undetected using routine screenings in an observational study by researchers at Baylor College of Medicine, who are now recommending that all such patients undergo a thromboelastography (TEG) to test for the risk of their formation. TEG is most used for open heart surgery and trauma patients. It revealed that patients clotting their central intravenous and arterial lines and dialysis catheters had abnormally high clotting function compared to the patients who did not have clotting issues, and the clot breakdown function was significantly higher in patients who were clotting less than others. Findings were based on the experience of 21 patients with confirmed COVID-19 infection admitted to the Baylor St. Luke's Medical Center ICU between March 15 and April 9. Neither their standard clotting profile nor fibrinogen level indicated a problem. Researchers are now looking at whether undetected blood clots could be related to unexplained deaths they are seeing in COVID-19 patients. The study published in JAMA Network Open. DOI: 10.1001/jamanetworkopen.2020.11192
A study coming out of Queen Mary University (London) and Cardiff University (Wales) has demonstrated the effectiveness of the GloBody platform to detect anti-drug antibodies in the blood of patients with multiple sclerosis. Researchers say the platform, which uses a light-producing enzyme called nanoluciferase, has also been applied to COVID-19 for potential use in antibody testing to determine whether someone has previously been infected with the virus. Their study, published in Neurology: Neuroimmunology & Neuroinflammation, focused on the detection of antibodies predicting which MS patients were subsequently likely to fail treatment with Alemtuzumab. But the GloBody platform could be applied to any therapeutic antibody in any clinical condition as well as pre-clinical animal models to save time and effort before moving to clinical trials in humans. In a matter of days, researchers were able to produce enough of the COVID-19 GloBody reagent to potentially test 1.6 million people for COVID-19. If the virus mutates, a new test could be made just as quickly. DOI: 10.1212/NXI.0000000000000767
Universally screening pediatric patients for COVID-19 before they undergo surgical procedures has allowed hospitals to improve safety by identifying all patients who test positive for COVID-19, half of whom have no symptoms, according to research published in JAMA Surgery. The study analyzed universal screening procedures at Children's Hospital of Philadelphia (CHOP), Seattle Children's Hospital and Texas Children's Hospital and included screening data gathered on1,295 patients over a one-month period. Overall incidence of COVID-19 was 0.93%, with significant variation across hospitals. At CHOP, 55.56% of positive patients were from a single township. Researchers noted that symptoms were not useful in differentiating those who tested positive for COVID-19 and those who tested negative. (DOI: 10.1001/jamasurg.2020.2588
In a letter to the editor published in The Journals of Gerontology, Series A, researchers from the University of Connecticut Health and the University of Exeter (U.K.) report that the ApoE e4 genotype predicts severe COVID-19, independent of pre-existing dementia, cardiovascular disease, and type-2 diabetes. The ACE2 receptor the virus used for cell entry is highly expressed in type II alveolar cells in the lungs, where ApoE is one of the highly co-expressed genes. Findings were based on an analysis of UK Biobank data on genetically European ancestry participants. DOI: 10.1093/gerona/glaa131
A narrative review published in the Annals of Internal Medicine has identified key use cases for SARS-CoV-2 antibody detection tests and their application to serologic studies. Researchers discuss currently available assays, highlight key areas of ongoing research, and propose potential strategies for test implementation. They found that despite a rapid increase in the number and availability of serologic assays to test for antibodies against SARS-CoV-2, most have undergone minimal or no external validation or have poorly described validation panels. In addition, interpretation of serologic assays is limited because of critical knowledge gaps. DOI: 10.7326/M20-2854
A report in the New England Journal of Medicine examines challenges and implications of false-negative COVID-19 tests, which are problematic because infected persons who are possibly asymptomatic may not be isolating. Factors contributing to the current limitations of diagnostic tests include variability in test sensitivity and the lack of a standard process for validating test accuracy. The authors cite several large studies whose frequent false-negative results are cause for concern. Measuring the sensitivity of tests in asymptomatic people is an urgent priority, they say, since a negative result on even a highly sensitive test cannot rule out infection if the pretest probability is high. DOI: 10.1056/NEJMp2015897
Researchers in Germany have identified protein biomarkers in the blood of patients with COVID-19 linked to the severity of their disease, according to an article in press with Cell Systems. Using a high-throughput mass spectrometry platform, the team analyzed samples from 31 men and women who were receiving treatment at Charité – Universitätsmedizin (Berlin) for COVID-19 of varying degrees of severity to identify 27 biomarkers. They then validated the molecular signatures by analyzing samples from another group of 17 COVID-19 patients and 15 healthy people. Results lay the foundation for disease prognosis and, to get closer to this goal, researchers will now study how the biomarker signatures change over the course of the disease. Another possible future use would be as an in-hospital diagnostic test, which will require testing the method in a larger number of patients. Some of the blood biomarkers have not previously been linked to an immune response; others include clotting factors and regulators of inflammation (interleukin 6). Several might be suitable targets for treatment, the authors say. DOI: 10.1016/j.cels.2020.05.012
Electrochemiluminescence (ECL) can make serological tests for COVID-19 quicker as well as more cost effective and reliable, report an international team of researchers in Nature Communications. Germany-based Roche Diagnostic and the Japan-based Hitachi High-Tech were involved in the research. The published study showed serological tests with increased sensitivity levels up to 128% more than those currently in use—a new milestone for signal enhancement by ECL-based immunoassays—thanks to highly efficient reactants. ECL relies on an electrochemical reaction producing a light signal, switching on antibodies as if they were lamps. But the molecules able to prompt this reaction are in very low concentrations in the human blood, so highly sensitive techniques are required. DOI: /10.1038/s41467-020-16476-2
A study coming out of France, and published in Clinical Kidney Journal, found that acute renal Fanconi syndrome (at least two tubular abnormalities) in 75% of hospitalized COVID-19 patients. Data from 42 hospitalized COVID-19 patients with no previous kidney disease were analyzed retrospectively. Additional findings were that proteinuria (88%), phosphate loss in urine (55%), increased uric acid excretion (43%) and glycosuria (30%) were the most frequently presented features. ICU patients were more frequently affected (96% vs. 62%) and were also more severely affected by proteinuria and acute kidney injury (AKI). A noteworthy finding was that Fanconi syndrome preceded severe AKI in 88% of the patients. Five of the AKI patients required dialysis; two died (after 13 and 27 days); one patient was dialysis-free after one week and two patients were still on dialysis at the end of the follow-up. A total of 7/42 patients died (including six intensive care patients with AKI), 24/42 could be discharged (including 12 intensive care patients) and 11/42 patients were treated as in-patients for a further 34 (±4.3) days. Proximal renal tubules seem to be a specific target of SARS-CoV-2 and the significance of Fanconi syndrome as a biomarker of tubular cell infection and as a potential predictive prognostic marker deserves systematic investigation. An increased risk of subsequent kidney disease after SARS-CoV-2-associated Fanconi syndrome can also be assumed, researchers say. DOI: 10.1093/ckj/sfaa109
A study on children suffering from severe inflammatory symptoms shows the condition is new and distinct from Kawasaki disease. In a paper published in the Journal of the American Medical Association, researchers have identified the main symptoms and clinical markers of the new syndrome. The study was led by Imperial College Academic Health Science Centre and involved clinicians and academic partners at eight hospitals across England as well as the Kawasaki Disease Research Center at the University of California San Diego. The condition, which the researchers named Paediatric Inflammatory Multisystem Syndrome Temporally associated with SARS-CoV-2 (PIMS-TS), was studied in 58 hospitalized children in England—45 of whom had evidence of current or past COVID-19 infection. PIMS-TS is extremely rare, but it can make a child very ill. It appears to be more likely to affect older children than Kawasaki disease (average nine years old versus four years old, respectively) and presents more often with abdominal pains and diarrhea alongside the common features such as persistent fever. It also appears to affect a higher proportion of black and Asian patients. Blood tests also show different results, with PIMS-TS patients showing more markers of inflammation and cardiac enzymes, which suggest the heart is under strain. DOI: 10.1001/jama.2020.10369
Patients with SARS-CoV-2 infection can present with gastrointestinal symptoms with possible fecal-oral route of transmission due to the presence of viral RNA in the stool, according to research published in JAMA Network Open. The systematic review and meta-analysis of 23 published and six preprint studies found that approximately 12% of patients with SARS-CoV-2 infection reported gastrointestinal symptoms, including diarrhea, nausea and vomiting. Liver enzyme levels outside reference ranges were observed in 15% to 20% of patients, and SARS-CoV-2 RNA shedding in stool was detected in up to 41% of patients. DOI: 10.1001/jamanetworkopen.2020.11335
Johns Hopkins researchers have found that testing people for SARS-CoV-2 too early in the course of infection is likely to result in a false negative test, even though they may eventually test positive for the virus. Findings published in the Annals of Internal Medicine. Patients who have a high-risk exposure should be treated as if they are infected, particularly if they have symptoms consistent with COVID-19. This means communicating with patients about the tests' shortcomings. The researchers reviewed RT-PCR test data from seven prior studies, including two preprints and five peer-reviewed articles covering 1,330 respiratory swab samples from a variety of subjects. From this data, they have calculated daily false-negative rates and made their statistical code and data publicly available so results can be updated as more data are published. Those tested with SARS-CoV-2 in the four days after infection were 67% more likely to test negative, even if they had the virus. When the average patient began displaying symptoms of the virus, the false-negative rate was 38%. The test performed best eight days after infection (on average, three days after symptom onset), but still had a false negative rate of 20%, meaning one in five people who had the virus had a negative test result. DOI: 10.7326/M20-1495
Researchers at York University (Canada) also put COVID-19 tests to the “test” and found seven out of 27 published methods (including those recommended by WHO) had potential sequence mismatch issues that may lead to underperforming or false-negative results. Many of the tests were developed early in the outbreak and the virus may have since mutated. Assays mismatched due to genetic variability in the viral genome raises the concern that the tests may not be detecting all the circulating variants of the virus. Correcting any mismatches may help to improve the sensitivity and accuracy of some of the diagnostic tests. Results published in Royal Society Open Science. DOI: 10.1098/rsos.200636
The steps manufacturers are taking to ensure COVID-19 antibody tests are accurate and available are detailed in an article in Chemical & Engineering News. The FDA has issued several emergency use authorizations to companies for the blood-based tests, allowing them to be used during the pandemic. Tests vary in their mechanisms for detecting antibodies, but all separate antibody-containing plasma from red blood cells and then determine whether the antibodies "stick" to specific COVID-19 proteins. That binding action is detected with fluorescent or other readout methods. While some of the early tests had questionable accuracy, much progress has been made in recent months with some manufacturers reporting sensitivities and specificities near 100%. Experts believe that humans can produce large amounts of SARS-CoV-2 antibodies, and the virus is slow to mutate, which bodes well for long-term protection. VOLUME 98, ISSUE 22
Updates from Industry
Illumina has been issued an Emergency Use Authorization by FDA for the COVIDSeq Test, a high-throughput, sequencing-based, in vitro diagnostic workflow enabling the detection of SARS-CoV-2. COVIDSeq uses upper respiratory specimens, including a nasopharyngeal or oropharyngeal swab, and delivers sample receipt to result in 24 hours using the NovaSeq 6000 Sequencing System. The differentiated diagnostic design includes 98 amplicons that target the full SARS-CoV-2 genome, creating accurate detection and high sensitivity. The workflow accommodates up to 3,072 samples per NovaSeq run leveraging the S4 flow cell, and includes steps for viral RNA extraction, RNA-to-CDNA conversion, PCR, library preparation, sequencing and report generation. The key components leveraged include the NovaSeq 6000, coupled with Illumina Tagmentation library preparation technology, and the DRAGEN COVIDSeq Test Pipeline for rapid reporting. COVIDSeq is currently available to a limited number of early access sites and is expected to be more broadly available this summer. Press release.
The Virginia Coronavirus Serology Project will test the blood of 5,000 patients for COVID-19 antibodies to determine if they have or have had the virus. This will help the Virginia Department of Health (VDH) estimate how many people have had the virus without showing symptoms, or went untested, and better predict how COVID-19 may affect the state in the future. While the blood samples will be collected across Virginia, all the testing will be performed at UVA Health. To launch the initiative, VDH partnered with a health system in each of the state's five health planning regions. Each region will collect 1,000 blood samples in June and July from patients, age 18 or older, who agree to the testing during regular outpatient clinic visits. Participants will also complete a short questionnaire. Press release.
Scientists at University Hospital of Siena (Italy) report that they have identified the genetic and molecular basis of COVID-19 susceptibility as well as to the possibility of contracting a more severe form of the disease. The news broke at last weekend’s 53rd annual conference of the European Society of Human Genetics. The team used whole exome sequencing to study data from 130 COVID-19 patients from Siena and other Tuscan institutions. They suspect that variability in the discovered susceptibility genes may determine disease progression. To get at results, researchers had to treat each patient as an independent case to identify an average of three disease-causing mutations involved in COVID-19 susceptibility. Understanding the genetic profile of patients may allow the repurposing of existing medicines for specific therapeutic approaches as well as speed the development of new antiviral drugs. The next step is to analyze another 2,000 samples from 35 Italian hospitals involved with the GEN-COVID project. Researchers have developed a mathematical model in collaboration with the Siena Artificial Intelligence Lab to understand the genetic determinants of genetic susceptibility and say they intend to compare it with classical genome-wide association studies in the context of the COVID-19 Host Genetics Initiative. Press release.
The University of California – Los Angeles Health Sciences launched an innovative effort in April that is solving the health system's shortage of nasopharyngeal swabs. In just over a month, and after conducting rigorous clinical testing of several 3D-printed swab prototypes on patients with COVID-19, UCLA Health was granted permission from the FDA to use the most promising design from Resolution Medical LLC. Before the pandemic, UCLA Health was using about 200 nasopharyngeal swabs a day, but now needs 500-600 for COVID-19 testing alone and anticipates needing over 1,000 each day in the coming months. Press release.