Virus World

Carl Johnson, Cornelius Vanderbilt Professor of Biological Sciences and expert in biological clocks, identifies temporal component to COVID-19 viral shedding. 

THE IDEA

Throughout the COVID-19 pandemic, health care practitioners have relied on COVID-19 testing to tell them what safety precautions to follow with each patient. Carl Johnson, Cornelius Vanderbilt Professor of Biological Sciences, wondered how the virus might act differently depending on the time of day and the body’s circadian rhythms. Johnson collaborated with Candace McNaughton, former adjunct assistant professor of emergency medicine, and Thomas Lasko, associate professor of biomedical informatics at Vanderbilt University Medical Center, to determine if the percentage of people testing positive for COVID-19 varies based on time of day. They found that people were up to two times as likely to have an accurate positive test result if they tested in the middle of the day compared to at night. The data support the hypothesis that COVID-19 acts differently in the body based on our natural circadian rhythm, which has also been implied by studies of other viral and bacterial infections. COVID-19 virus shedding—when infected cells release infectious virus particles into the blood and mucus—appears to be more active in the middle of the day due to modulation of the immune system by our biological clock.

WHY IT MATTERS

“Taking a COVID-19 test at the optimal time of day improves test sensitivity and will help us to be accurate in diagnosing people who may be infected but asymptomatic,” Johnson said. Their results indicate that viral load is lower after 8 p.m. If people choose to get tested at that time, there could be a higher chance of a false-negative result. False negatives can be harmful to the community and for the patient, who might not seek additional care due to their negative test result. A difference in COVID-19 viral shedding throughout the day is important information that may inform how we test for and treat the virus. As Johnson and his co-authors report, the peak shedding in the afternoon, when patients are more likely to interact with others or seek medical care, could play a role in increasing the spread of the virus in hospitals and the wider community.

WHAT’S NEXT

Further research is needed to confirm the diurnal—meaning active during the day—nature of SARS-CoV-2, the virus that causes COVID-19. Experimentally testing patients who are infected with COVID-19 to see if individuals shed the virus differently throughout the day would have important public health implications, Johnson said. Johnson and his co-authors hope this early research can be used to optimize COVID-19 testing and improve test accuracy. The researchers believe temporal considerations may be leveraged to maximize the effectiveness of intervention strategies and even vaccine strategies.

Original Research Published in Journal of Biological Rhythms  (Oct. 26, 2021):

https://doi.org/10.1177/07487304211051841

Serological SARS-CoV-2 assays are needed to support clinical diagnosis and epidemiological investigations. Recently, assays for the large-volume detection of total antibodies (Ab) and immunoglobulin (Ig) G and M against SARS-CoV-2 antigens have been developed, but there are limited data on the diagnostic accuracy of these assays. This study was organized as a Danish national collaboration and included fifteen commercial and one in-house anti-SARS-CoV-2 assays in sixteen laboratories. Sensitivity was evaluated using 150 serum samples from individuals diagnosed with asymptomatic, mild or moderate nonhospitalized (n=129) or hospitalized (n=31) COVID-19, confirmed by nucleic acid amplification tests, collected 13-73 days from symptom onset. Specificity and cross-reactivity were evaluated in samples collected prior to the SARS-CoV-2 epidemic from > 586 blood donors and patients with autoimmune diseases or CMV or EBV infections. Predefined specificity criteria of ≥99% were met by all total-Ab and IgG assays except one (Diasorin/LiaisonXL-IgG 97.2%).

The sensitivities in descending order were: Wantai/ELISA total-Ab (96.7%), CUH/NOVO in-house ELISA total-Ab (96.0%), Ortho/Vitros total-Ab (95.3%), YHLO/iFlash-IgG (94.0%), Ortho/Vitros-IgG (93.3%), Siemens/Atellica total-Ab (93.2%), Roche-Elecsys total-Ab (92.7%), Abbott-Architect-IgG (90.0%), Abbott/Alinity-IgG (median 88.0%), Diasorin/LiaisonXL-IgG (84.6%), Siemens/Vista total-Ab (81.0%), Euroimmun/ELISA-IgG (78.0%), and Snibe/Maglumi-IgG (median 78.0%). The IgM results were variable, but one assay (Wantai/ELISA-IgM) had both high sensitivity (82.7%) and specificity (99%). The rate of seropositivity increased with time from symptom onset and symptom severity.

In conclusion, predefined sensitivity and specificity acceptance criteria of 90%/99%, respectively, for diagnostic use were met in five of six total-Ab and three of seven IgG assays.

Preprint of the study available at medRxiv (August 2, 2020):

https://doi.org/10.1101/2020.07.30.20165373

Rapid Antigen Tests (RAT) have become an invaluable tool for combating the COVID-19 pandemic. However, concerns have been raised regarding the ability of existing RATs to effectively detect emerging SARS-CoV-2 variants. We compared the performance of eight commercially available, emergency use authorized RATs against the Delta and Omicron SARS-CoV-2 variants using individual patient and serially diluted pooled clinical samples. The RATs exhibited lower sensitivity for Omicron samples when using PCR Cycle threshold (CT) value (a proxy for RNA concentration) as the comparator. Interestingly, however, they exhibited similar sensitivity for Omicron and Delta samples when using quantitative antigen concentration as the comparator. We further found that the Omicron samples had lower ratios of antigen to RNA, which offers a potential explanation for the apparent lower sensitivity of RATs for that variant when using CT value as a reference. Our findings underscore the complexity in assessing RAT performance against emerging variants and highlight the need for ongoing evaluation in the face of changing population immunity and virus evolution.

Preprint available in medRxiv (Feb. 10, 2023):

https://doi.org/10.1101/2023.02.09.23285583 

Saliva Specimens to Detect SARS-CoV-2 Infection In this letter, the investigators report that saliva specimens and nasopharyngeal swab specimens had similar sensitivity in the detection of COVID-19.  Rapid and accurate diagnostic tests are essential for controlling the ongoing Covid-19 pandemic. Although the current standard involves testing of nasopharyngeal swab specimens by quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR) to detect SARS-CoV-2, saliva specimens may be an alternative diagnostic sample. Rigorous evaluation is needed to determine how saliva specimens compare with nasopharyngeal swab specimens with respect to sensitivity in detection of SARS-CoV-2 during the course of infection. 

A total of 70 inpatients with Covid-19 provided written informed consent to participate in our study available with the full text of this letter at NEJM.org). After Covid-19 was confirmed with a positive nasopharyngeal swab specimen at hospital admission, we obtained additional samples from the patients during hospitalization. We tested saliva specimens collected by the patients themselves and nasopharyngeal swabs collected from the patients at the same time point by health care workers. Using primer sequences from the Centers for Disease Control and Prevention, we detected more SARS-CoV-2 RNA copies in the saliva specimens (mean log copies per milliliter, 5.58; 95% confidence interval [CI], 5.09 to 6.07) than in the nasopharyngeal swab specimens (mean log copies per milliliter, 4.93; 95% CI, 4.53 to 5.33).  In addition, a higher percentage of saliva samples than nasopharyngeal swab samples were positive up to 10 days after the Covid-19 diagnosis. At 1 to 5 days after diagnosis, 81% (95% CI, 71 to 96) of the saliva samples were positive, as compared with 71% (95% CI, 67 to 94) of the nasopharyngeal swab specimens. These findings suggest that saliva specimens and nasopharyngeal swab specimens have at least similar sensitivity in the detection of SARS-CoV-2 during the course of hospitalization...

Published in New England J. Medicine (August 28, 2020):

https://doi.org/10.1056/NEJMc2016359

Serology tests detect the presence of antibodies in the blood when the body is responding to a specific infection, like COVID-19. In other words, the tests detect the body’s immune response to the infection caused by the virus rather than detecting the virus itself. In the early days of an infection when the body’s immune response is still building, antibodies may not be detected.

This limits the test’s effectiveness for diagnosing COVID-19, and this is one reason serology tests should not be used as the sole basis to diagnose COVID-19. Serology tests could play a role in the fight against COVID-19 by helping healthcare professionals identify individuals have developed an immune response to SARS-CoV-2. In addition, these test results can aid in determining who may donate a part of their blood called convalescent plasma, which may serve as a possible treatment for those who are seriously ill from COVID-19. However, to use these test properly, it is important to understand their performance characteristics and limitations. Moreover, studies are underway to address questions that will better inform the appropriate use of these tests, such as whether the presence of antibodies conveys a level of immunity that would prevent or minimize the severity of re-infection as well as the duration for which immunity lasts.

The performance of these tests is described by their “sensitivity,” or their ability to identify those with antibodies to SARS-CoV-2 (true positive rate), and their “specificity,” or their ability to identify those without antibodies to SARS-CoV-2 (true negative rate). A test’s sensitivity can be estimated by determining whether or not it is able to detect antibodies in blood samples from patients who have been confirmed to have COVID-19 with a nucleic acid amplification test, or NAAT. In some validation studies of these tests, like the one FDA is conducting in partnership with NIH, CDC, and BARDA, the samples used, in addition to coming from patients confirmed to have COVID-19 by a NAAT, may also be confirmed to have antibodies present using other serology tests. A test’s specificity can be estimated by testing large numbers of samples collected and frozen before SARS-CoV-2 is known to have circulated to demonstrate that the test does not produce positive results in response to the presence of other causes of a respiratory infection, such as other coronaviruses....