Persistence of live virus in critically ill patients infected with SARS-COV-2: a prospective observational study

Background Research on the duration of infectivity of ICU patients with COVID-19 has been sparse. Tests based on Reverse Transcriptase polymerase chain reaction (RT-PCR) detect both live virus and non-infectious viral RNA. We aimed to determine the duration of infectiousness based on viral culture of nasopharyngeal samples of patients with COVID-19. Methods Prospective observational study in adult intensive care units with a diagnosis of COVID-19 Pneumonia. Patients had repeated nasopharyngeal sampling performed after day 10 of ICU admission. Culture positive rate (based on viral culture on Vero cells in a level 4 lab) and Cycle threshold from RT-PCR were measured. Results Nine patients of the 108 samples (8.3%, 95% CI 3.9–15.2%) grew live virus at a median of 13 days (interquartile range 11–19) after their initial positive test. 74.1% of patients were RT-PCR positive but culture negative, and the remaining (17.6%) were RT-PCR and culture negative. Cycle threshold showed excellent ability to predict the presence of live virus, with a Ct < 25 with an AUC of 0.90 (95% CI 0.83–0.97, p < 0.001). The specificity of a Ct > 25 to predict negative viral culture was 100% (95% CI 70–100%). Conclusion 8.3% of our ICU patients with COVID-19 grew live virus at a median of 13 days post-initial positive RT-PCR test. Severity of illness, use of mechanical ventilation, and time between tests did not predict the presence of live virus. Cycle threshold of > 25 had the best ability to determine the lack of live virus in these patents.

Longitudinal serologic and viral testing post-SARS-CoV-2 infection and post-receipt of mRNA COVID-19 vaccine in a nursing home cohort—Georgia, October 2020–April 2021

Importance: There are limited data describing SARS-CoV-2-specific immune responses and their durability following infection and vaccination in nursing home residents. Objective: To evaluate the quantitative titers and durability of binding antibodies detected after SARS-CoV-2 infection and subsequent COVID-19 vaccination. Design: A prospective longitudinal evaluation included nine visits over 150 days; visits included questionnaire administration, blood collection for serology, and paired anterior nasal specimen collection for testing by BinaxNOW™ COVID-19 Ag Card (BinaxNOW), reverse transcription polymerase chain reaction (RT-PCR), and viral culture. Setting: A nursing home during and after a SARS-CoV-2 outbreak. Participants: 11 consenting SARS-CoV-2-positive nursing home residents. Main Outcomes and Measures: SARS-CoV-2 testing (BinaxNOW™, RT-PCR, viral culture); quantitative titers of binding SARS-CoV-2 antibodies post-infection and post-vaccination (beginning after the first dose of the primary series). Results: Of 10 participants with post-infection serology results, 9 (90%) had detectable Pan-Ig, IgG, and IgA antibodies and 8 (80%) had detectable IgM antibodies. At first antibody detection post-infection, two-thirds (6/9, 67%) of participants were RT-PCR-positive but none were culture positive. Ten participants received vaccination; all had detectable Pan-Ig, IgG, and IgA antibodies through their final observation ≤90 days post-first dose. Post-vaccination geometric means of IgG titers were 10-200-fold higher than post-infection. Conclusions and Relevance: Nursing home residents in this cohort mounted robust immune responses to SARS-CoV-2 post-infection and post-vaccination. The augmented antibody responses post-vaccination are potential indicators of enhanced protection that vaccination may confer on previously infected nursing home residents.

Viral cultures, PCR Cycle threshold values and viral load estimation for COVID-19 infectious potential assessment in transplant patients: systematic review - Protocol Version 29 December 2021

This is the protocol for a systematic review focussing on people receiving solid organ or hematopoietic stem cell transplants. Our research questions are as follows: What is the relationship between serial PCR Ct value or other measures of viral burden, and the likelihood and duration of the presence of infectious virus from viral culture, among transplant recipients with SARS-CoV-2 infection? What is the influence of age, sex, underlying pathologies, degree of immunosuppression, vaccination status, COVID-19 symptoms and COVID-19 disease course on viral burden and the likelihood of presence of infectious SARS-CoV-2? We will include single studies reporting serial Cts from sequential rt-PCR testing or other measures of viral burden such as RNA gene copies of respiratory samples (from nasopharyngeal specimens) along with viral culture data on the same samples, from patients about to receive a transplant or who are post transplant with SARS-CoV-2 infection.

Monoclonal antibody treatment drives rapid culture conversion in SARS-CoV-2 infection

Monoclonal antibodies (mAbs) are the treatment of choice for high-risk ambulatory persons with mild to moderate COVID-19. We studied viral culture dynamics post-treatment in a subset of participants receiving the mAb bamlanivimab in the ACTIV-2 trial. Viral load by qPCR and viral culture were performed from anterior nasal swabs collected on study days 0 (day of treatment), 1, 2, 3, and 7. Treatment with mAb resulted in rapid clearance of culturable virus in participants without treatment-emergent resistance. One day after treatment, 0 of 28 (0%) participants receiving mAb and 16 of 39 (41%) receiving placebo still had culturable virus (p <0.0001); nasal viral loads were only modestly lower in the mAb-treated group at days 2 and 3. Recrudescence of culturable virus was detected in three participants with emerging mAb resistance and viral load rebound. The rapid reduction in shedding of viable SARS-CoV-2 after mAb treatment highlights the potential role of mAbs in preventing disease transmission.

DETECTION OF SARS-COV-2 FROM SURFACE OF PATIENTS’ LEFTOVER FOOD PACKAGES AT A COVID-19 QUARANTINE CENTRE

In healthcare facilities, food waste and its packaging are mostly managed as non-infectious general waste. However, waste from SARS-CoV-2 positive patients, are treated as medical waste as they may be contaminated by the virus. We investigated the possibility of SARS-CoV-2 contamination from positive COVID-19 patients to their leftover food packages at a quarantine centre. Food packages surface was swabbed using prewetted cellular foam, placed into viral transport media and analysed using real time reverse transcription polymerase chain reaction. SARS-CoV-2 RNA was detected in two samples (4.5%) from asymptomatic patients who were at day-2 positive SARS-CoV-2 with cycle threshold (Ct) value (RdRp/E), 34.96/35.72 and 37.1/36.48 respectively. Detection of SARS-CoV-2 supports that there is contamination to the waste. These poses risk of exposure as SAR-COV-2 survive on the surfaces, thus, safe handling and disposal of food waste should be maintained. However, further study involving viral culture should be explored to determine the viability of the SARS-CoV-2 from leftover food packages

SARS-CoV-2 Antigen Tests Predict Infectivity Based on Viral Culture: Comparison of Antigen, PCR Viral Load, and Viral Culture Testing on a Large Sample Cohort

The relationship of SARS-CoV-2 antigen testing results, viral load, and viral culture detection remains to be fully defined. Presumptively, viral culture can provide a surrogate measure for infectivity of sampled individuals, and thereby inform how and where to most appropriately deploy available diagnostic testing modalities. We therefore determined the relationship of antigen testing results from three lateral flow and one microfluidics assay to viral culture performed in parallel in 181 nasopharyngeal swab samples positive for SARS-CoV-2. Sample viral loads, determined by RT-qPCR, were distributed across the range of viral load values observed in our testing population. We found that antigen tests were predictive of viral culture positivity, with the LumiraDx method showing enhanced sensitivity (90%; 95% confidence interval (95% CI) 83-94%) compared with the BD Veritor (74%, 95% CI 65-81%), CareStart (74%, 95% CI 65-81%) and Oscar Corona (74%, 95% CI 65-82%) lateral flow antigen tests. Antigen and viral culture positivity were also highly correlated with sample viral load, with areas under the receiver?operator characteristic curves (ROCs) of 0.94-0.97 and 0.92, respectively. In particular, a viral load threshold of 100,000 copies/mL was 95% sensitive (95% CI, 90-98%) and 72% specific (95% CI, 60-81%) for predicting viral culture positivity. Taken together, the detection of SARS-CoV-2 antigen identified highly infectious individuals, some of whom may harbor 10,000-fold more virus in their samples than those with any detectable infectious virus. As such, our data support use of antigen testing in defining infectivity status at the time of sampling.

Clinical and Epidemiological Characteristics of COVID-19 Patients with SARS-CoV-2 Re-Detected on PCR Test after Discharge from Isolation

There have been multiple reports of patients with coronavirus disease (COVID-19) testing positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) after discharge; however, information on the characteristics of such cases is limited. In this case report, we aimed to identify clinical and epidemiological characteristics of patients who had a repeat positive polymerase chain reaction (PCR) test for SARS-CoV-2. We analyzed data of 22 COVID-19 patients who tested positive for SARS-CoV-2 on polymerase chain reaction (PCR) testing after two consecutive negative PCR results following discharge from hospitals. The interval between the two positive tests in the episodes of COVID-19 ranged from 4 to 117 days. More than one-third of the cases were healthcare workers (HCWs) and one-third of them had comorbidities. The main symptoms were cough and fever, and we noticed that males experienced more symptoms and signs of COVID-19 than females. Individuals with repeat SARS-CoV-2 positivity tend to experience milder illness during the second episode than the first episode. To confirm the reinfection of SARS-CoV-2, the results of other tests, such as viral culture and immunological assays of immunoglobulin G (IgG) and immunoglobulin M (IgM), need to be considered. Recovered COVID-19 patients should continue social distancing, using face masks, and practicing hand hygiene, especially HCWs who are more likely to be exposed to SARS-CoV-2.

Persistence of Infectivity in Elderly Individuals Diagnosed with SARS-CoV-2 Infection 10 Days after Onset of Symptoms: A Cross-Sectional Study

We performed viral culture of nasopharyngeal specimens in individuals aged 79 and older, infected with SARS-CoV-2, 10 days after symptom onset. A positive viral culture was seen in 10/22 participants (45%), including 4/12 (33%) individuals with improving symptoms. This small study suggests that infectivity may be prolonged among older individuals.

Viral Culture in Hospitalized Congregate Care Patients With Prolonged SARS-CoV-2 Viral RNA Detection

Prolonged detection of SARS-CoV-2 viral RNA has been observed in hospitalized congregate care patients following resolution of clinical symptoms. It is unknown whether patients with persistent PCR positivity pose a risk for COVID-19 transmission. The purpose of this study was to examine the results of serial PCR testing, viral load, and viral culture in patients awaiting discharge prior to a negative PCR test. We sampled 14 patients who were admitted from skilled nursing and/or rehabilitation facilities to a large academic medical center, had clinical signs and symptoms of COVID-19, and had multiple PCR-positive tests separated by at least 14 days. PCR-positive nasopharyngeal swabs were obtained from each patient for viral load quantification and viral culture. The mean age of patients was 72.5 years (55 – 92), with a mean peak SOFA score of 5.6 (1 – 11). Patients were hospitalized for a mean of 37.0 days (25 – 60). RNA was detected by PCR for a mean of 32.9 days (19 – 47). Mean viral load for the first PCR-positive nasopharyngeal swab collected at our hospital was 5.81 genomic copies/mL (2.12 – 9.72). Viral load decreased significantly with days from clinical symptom onset (R = -0.69, 95% CI, -0.80 – -0.55). Four out of 28 samples grew active virus via culture, with no active virus isolates after 2 days of symptom onset. Our viral culture data suggests that persistent PCR positivity may not correlate with infectivity, which has important implications for COVID-19 infection control precautions among older congregate care patients.

Descriptive Evaluation of Antibody Responses to SARS-CoV-2 Infection in Plasma and Gingival Crevicular Fluid in a Nursing Home Cohort—Arkansas, June–August 2020

Objective: Characterize and compare SARS-CoV-2–specific immune responses in plasma and gingival crevicular fluid (GCF) from nursing home residents during and after natural infection Design: Prospective cohort Setting: Nursing home Participants: SARS-CoV-2–infected nursing home residents Methods: A convenience sample of 14 SARS-CoV-2–infected nursing home residents, enrolled 4–13 days after real-time reverse transcription polymerase chain reaction diagnosis, were followed for 42 days. Post diagnosis, plasma SARS-CoV-2–specific pan-Immunoglobulin (Ig), IgG, IgA, IgM, and neutralizing antibodies were measured at 5 timepoints and GCF SARS-CoV-2–specific IgG and IgA were measured at 4 timepoints. Results: All participants demonstrated immune responses to SARS-CoV-2 infection. Among 12 phlebotomized participants, plasma was positive for pan-Ig and IgG in all 12, neutralizing antibodies in 11, IgM in 10, and IgA in 9. Among 14 participants with GCF specimens, GCF was positive for IgG in 13 and IgA in 12. Immunoglobulin responses in plasma and GCF had similar kinetics; median times to peak antibody response was similar across specimen types (4 weeks for IgG; 3 weeks for IgA). Participants with pan-Ig, IgG, and IgA detected in plasma and GCF IgG remained positive through this evaluation’s end 46–55 days post-diagnosis. All participants were viral culture negative by the first detection of antibodies. Conclusions: Nursing home residents had detectable SARS-CoV-2 antibodies in plasma and GCF after infection. Kinetics of antibodies detected in GCF mirrored those from plasma. Non-invasive GCF may be useful for detecting and monitoring immunologic responses in populations unable or unwilling to be phlebotomized.