Extensive environmental contamination and prolonged severe acute respiratory coronavirus-2 (SARS CoV-2) viability in immunosuppressed recent heart transplant recipients with clinical and virologic benefit with remdesivir

Rajakumar, Irina; Isaac, Debra; Fine, Nowell M.; Clarke, Brian; Ward, Linda; Malott, Rebecca J.; Gill, Kara; Berenger, Byron M.; Lin, Yi-Chan; Evans, David H.; Conly, John

doi:10.1017/ice.2021.89

Cited by 15 publications

(28 citation statements)

References 10 publications

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“…The singular exceptions to this general rule were seen in patients characterized by some type of immunodeficiency. Two of these were solid organ transplant patients, with a persistent viremia that eventually responded well to Remdesivir treatment combined with a reduction in their immunosuppressive regimens (Rajakumar et al 2021). We also collected specimens from a patient with follicular lymphoma who had infectious virus from saliva and NP swabs which were plaque positive (1.5×10 2 PFU/mL) 5 months from the date of original symptom onset ( Figure 3A ) with C t values in the 27-28 range ( Figure 3B ).…”

Section: Resultsmentioning

confidence: 99%

Detection and Quantification of Infectious Severe Acute Respiratory Coronavirus-2 in Diverse Clinical and Environmental Samples from Infected Patients: Evidence to Support Respiratory Droplet, and Direct and Indirect Contact as Significant Modes of Transmission

Lin

Malott

Ward

et al. 2021

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Few studies have assessed for infectious SARS-CoV-2 in multiple types of clinical and environmental samples. In almost 500 samples from 75 hospitalized and community cases, we detected infectious virus with quantitative burdens varying from 5.0 plaque-forming units/mL (PFU/mL) up to 1.0×106 PFU/mL in clinical specimens and up to 1.3×106 PFU/mL on fomites including facial tissues, nasal prongs, call bells/cell phones, dentures, and sputum deposits with confirmation by plaque morphology, PCR, immunohistochemistry, and sequencing. Expectorated sputum samples had the highest percentage of positive samples and virus titers (71%, 2.9×102 to 5.2×105 PFU/mL), followed by saliva (58%, 10 to 4.6×104 PFU/mL), and cough samples without sputum (19%, 5 to 1.9×103 PFU/mL). We also detected infectious SARS-CoV-2 from patients’ hands (28%, 60 to 2.3×102 PFU/mL) but no infectious virus was found in continuous speech samples despite finding high levels of infectious virus in the associated nasopharynx, throat, or saliva specimens. We demonstrated infectious virus stability in clinical samples, including those dried for prolonged periods of time. Infectious virus correlated with time since symptom onset with no detection after 7-8 days in immunocompetent hosts and with N-gene based Ct values ≤ 25 significantly predictive of yielding plaques in culture. One PFU was associated with ∼105 copies of N gene RNA across a diversity of samples and times from symptom onset. Clinical salivary isolates caused illness in a hamster model with a minimum infectious dose of ≤14 PFU/mL. Our findings of high quantitative burdens of infectious virus, stability even with drying, and a very low minimal infectious dose suggest multiple modes of transmission are exploited by SARS-CoV-2, including direct contact, large respiratory droplet, and fomite transmission and in the context of a high binding avidity to human cellular receptors, offer an explanation of the high contagiousness of this virus.Research in ContextEvidence before this studyWe searched the literature for articles that reported on the presence of infectious SARS-CoV-2 in patients’ samples from clinical and environmental sources. We found several key primary studies and systematic reviews providing valuable background on the carriage of infectious virus and the correlation with cycle threshold (Ct) and/or RNA copies/mL on PCR testing. Clinical correlations with respect to underlying clinical conditions and details on the onset of illness were not commonly reported with respect to the timing of obtaining specimens for culture. Few studies carefully assessed the presence of infectious virus in cough samples, sputum, nasal secretions, hands, and common high touch surfaces. A few published works were found on factors which may be associated with shedding of infectious virus.Added value of this studyWe assessed the presence of infectious virus shedding in almost 500 specimens from 75 patients with COVID-19 in both the hospital and community setting. High titers of infectious virus were detected in multiple clinical and environmental samples. The longest duration of recovery of infectious virus in a fomite sample was from a dried facial tissue found at a patient’s bedside table, used at least 9 hours earlier. Cough specimens revealed infectious virus in 28% of specimens with infectious virus titers as high as 5.2×105 PFU/mL. Hand samples contained infectious virus with titers ranging from 55 to 2.3×102 PFU/mL. Infectious viral loads correlated with N-gene based Ct values and showed that Ct values ≤ 25 were predictive of yielding plaques in culture. These experiments also showed that infectious virus is most often recovered during a 7 to 8-day period following illness onset in immunocompetent persons, and during that time the ratio of RNA/PFU in these clinical specimens varies relatively little, with a ratio ∼160,000:1. Infectious virus may be recovered for weeks to several months in immunosuppressed persons. We also showed that virus recovered from saliva specimens, representing a commonly encountered fomite sample, caused infection in the Syrian hamster model, hence demonstrating the infectiousness of the virus sourced from this type of specimen. A challenge dose as low as 14 PFU/mL yielded infection in this model.Implications of all the available evidenceWe have shown that SARS-CoV-2 is relatively easy to culture when obtained early in the course of illness and there are high levels of cultivatable SARS-CoV-2 in multiple types of clinical specimens and common fomites, including high-touch surfaces and demonstrated their infectiousness in a mammalian host. Our results demonstrate the presence of high quantitative burdens of SARS-CoV-2 in sputum, saliva, and droplets from coughing, which would lend support to large respiratory droplet transmission, hands which would support direct contact transmission, and fomites which would promote indirect contact transmission. We were unable to detect any infectious virus in continuous speech samples which suggests that brief conversations, without coughing or sneezing, pose little risk of transmitting SARS-CoV-2. Our findings provide an explanation for the high contagiousness of this virus and support current public health measures and infection prevention and control guidelines including physical distancing, hand hygiene, masking, and cleaning and disinfection.

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Section: Resultsmentioning

confidence: 99%

Detection and Quantification of Infectious Severe Acute Respiratory Coronavirus-2 in Diverse Clinical and Environmental Samples from Infected Patients: Evidence to Support Respiratory Droplet, and Direct and Indirect Contact as Significant Modes of Transmission

Lin

Malott

Ward

et al. 2021

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“…Of the nine included studies (Figure 1 5 ) they reported data for 30 transplant patients (7 females and 23 males): renal (21), cardiac (5), bone marrow transplant (1), liver (2), bilateral lung (1). The 30 patients were in six countries: Saudi Arabia 6 , France 7 8 , Germany 9 10 11 , Austria 12 , Denmark 13 , and Canada 14 , and were aged between 26 and 75 years old.…”

Section: Resultsmentioning

confidence: 99%

Viral cultures, Polymerase Chain Reaction Cycle Threshold Values and Viral Load Estimation for SARS-CoV-2 Infectious Potential Assessment in Hematopoietic Stem Cell and Solid Organ Transplant Patients: A Systematic Review

Jefferson

Spencer

Roşca

et al. 2022

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Background: Organ transplant recipients are at increased vulnerability to SARS-CoV-2 due to immunosuppression and may pose a continued transmission risk especially within hospital settings. Detailed case reports including symptoms, viral load and infectiousness, defined by the presence of replication-competent viruses in culture, provide an opportunity to examine the relationship between clinical course, burden and contagiousness, and provide guidance on release from isolation. Objectives: We performed a systematic review to investigate the relationship in transplant recipients between serial SARS-CoV-2 RT-PCR cycle threshold (Ct) value or cycle of quantification value (Cq), or other measures of viral burden and the likelihood and duration of the presence of infectious virus based on viral culture including the influence of age, sex, underlying pathologies, degree of immunosuppression, and/or vaccination on this relationship. Methods: We searched LitCovid, medRxiv, Google Scholar and WHO Covid-19 databases, from 1 November 2019 until 31 December 2021. We included studies reporting relevant data for transplantees with SARS-CoV-2 infection: results from serial RT-PCR testing and viral culture data from the same respiratory samples. We assessed methodological quality using five criteria, and synthesised the data narratively and graphically. Results: We included 9 case reports and case series reporting on 30 transplantees. We observed a relationship between proxies of viral burden and likelihood of shedding replication-competent SARS-CoV-2 particles. Two individuals shed replication-competent particles over 100 days after infection onset. Lack of standardisation of testing and reporting precludes establishing a viral burden cutoff. Most transplantees stopped shedding competent particles when the RT-PCR cycle threshold was above 30, but there are differences across platforms. Conclusions Viral burden is a reasonable proxy for infectivity when considered within the context of the clinical status of each patient. Standardised study design and reporting are essential to avoid research waste and generate guidance based on an increasing evidence base.

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“…In people receiving immunosuppressive agents (henceforth “immunosuppressed”) either preceding or following a solid organ or hematopoietic stem cell transplant, infection with SARS-CoV-2 is likely to be of longer duration than in non-immunocompromised patients 2, 7 . As infectious virus carriage may be greatly prolonged in immunosuppressed transplant patients compared to immune competent people, safe removal from isolation should be based on the potential for forward transmission of infectious virus as established using viral culture methods or suitable surrogate markers.…”

Section: Introductionmentioning

confidence: 99%

Viral cultures, PCR Cycle threshold values and viral load estimation for COVID-19 infectious potential assessment in transplant patients: systematic review - Protocol Version 30 December 2021

Jefferson

Spencer

Maltoni

et al. 2022

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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.

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Extensive environmental contamination and prolonged severe acute respiratory coronavirus-2 (SARS CoV-2) viability in immunosuppressed recent heart transplant recipients with clinical and virologic benefit with remdesivir

Cited by 15 publications

References 10 publications

Detection and Quantification of Infectious Severe Acute Respiratory Coronavirus-2 in Diverse Clinical and Environmental Samples from Infected Patients: Evidence to Support Respiratory Droplet, and Direct and Indirect Contact as Significant Modes of Transmission

Detection and Quantification of Infectious Severe Acute Respiratory Coronavirus-2 in Diverse Clinical and Environmental Samples from Infected Patients: Evidence to Support Respiratory Droplet, and Direct and Indirect Contact as Significant Modes of Transmission

Viral cultures, Polymerase Chain Reaction Cycle Threshold Values and Viral Load Estimation for SARS-CoV-2 Infectious Potential Assessment in Hematopoietic Stem Cell and Solid Organ Transplant Patients: A Systematic Review

Viral cultures, PCR Cycle threshold values and viral load estimation for COVID-19 infectious potential assessment in transplant patients: systematic review - Protocol Version 30 December 2021

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