Viral cultures, cycle threshold values and viral load estimation for assessing SARS-CoV-2 infectiousness in haematopoietic stem cell and solid organ transplant patients: a systematic review

Anterior nasal swabs compared to nasopharyngeal swabs for detection of respiratory viruses in children

Respiratory viral testing often uses invasive nasopharyngeal (NP) swabs, which can be painful and require trained personnel. Anterior nasal swabs (NS) are less invasive and can be self-collected. The sensitivity of NS compared to NP specimens for detecting multiple respiratory viruses in children are not well described. Hospitalized children in Kansas City, MO, from January 2023 to February 2024, who had NP specimens obtained for standard of care multiplex respiratory viral testing in the previous 72 h, were enrolled. NS specimens were collected and tested alongside salvaged NP specimens for adenovirus, seasonal coronaviruses, human metapneumovirus, respiratory syncytial virus, influenza, rhinovirus/enterovirus, SARS-CoV-2, and parainfluenza viruses using multiplex molecular testing. Concordance, sensitivity, and specificity of NS compared to NP specimens were assessed. A total of 147 paired NP/NS specimens were analyzed. Overall, 114 (77.6 %) NP/NS pairs were concordant, including 86 (58.5 %) virus-positive and 28 (19.1 %) virus-negative pairs. NS sensitivity was 84.3 % compared to NP, increasing to 95.7 % when collected within 24 h of NP specimens. Sensitivity for seasonal coronavirus was poor (36.4 %), but was over 75 % for other viruses, and 100 % for adenovirus, influenza, parainfluenza, RSV, and SARS-CoV-2 within 24 h of NP specimens. Virus cycle threshold counts were similar among paired specimens. NS specimens showed good concordance with NP specimens and high sensitivity for most viruses, except seasonal coronavirus. NS testing may enable respiratory virus monitoring outside medical settings.

Validation of the United States isolation termination criteria using virus culture results of the omicron variant in Japan

Cycle threshold (Ct) values obtained from real-time reverse-transcription polymerase chain reaction (RT-PCR) tests are commonly used to determine COVID-19 isolation discharge from hospitals. However, not all patients with low Ct values are infectious, and studies evaluating infectivity through virus cultures in Japan remain limited. This study assessed patients with Ct values <30 at 10 days after symptom onset and compared the clinical characteristics of seven patients with positive virus culture results and 11 patients with negative virus culture results to validate the Centers for Disease Control and Prevention (CDC) isolation criteria in Japan. Among non-immunosuppressed patients with mild-to-moderate COVID-19, 80 % were virus culture-negative 10 days after symptom onset, even when the Ct values were <30. In contrast, only 33 % of patients with severe-to-critical symptoms tested negative on virus culture. All immunosuppressed patients with severe-to-critical symptoms consistently tested positive in virus cultures. Notably, three patients with hematological disorders remained virus culture-positive 20 days after symptom onset. These findings generally align with the CDC criteria. For non-immunosuppressed patients with mild-to-moderate COVID-19, isolation release after 10 days is supported without the need for additional RT-PCR testing. However, for non-immunosuppressed patients with severe-to-critical symptoms and immunocompromised patients, particularly those with hematological disorders, isolation may be safely discontinued when Ct values exceed 30 after 10 days. This study provides valuable insights into identifying individuals suitable for isolation release based on SARS-CoV-2 testing in Japan.

ORCHESTRA Delphi consensus: diagnostic and therapeutic management of SARS-CoV-2 infection in haematological patients

OBJECTIVES

COVID-19 poses a significant risk to individuals with haematological malignancies (HM), as they are particularly vulnerable to severe disease progression and hospitalization due to their compromised immune systems. Many clinical decisions regarding the management of COVID-19 in these patients are yet to be fully addressed by existing guidelines, leading to variability in care.

METHODS

A 28-item Delphi survey was developed to gather expert opinions on key areas of COVID-19 management in patients with HM, including risk stratification for severe COVID-19, diagnostic processes, and treatment decisions.

RESULTS

Twenty-one experts with backgrounds in haematology and infectious diseases were enrolled. Of the 28 questions posed to the experts, consensus was reached on 15 statements.

DISCUSSION

These Delphi consensus statements offer valuable suggestions with direct implications for clinical practice, addressing critical areas such as risk identification, appropriate diagnostic approaches, and tailored treatment strategies for patients with HM with COVID-19. The findings provide actionable insights that may help fill gaps in current scientific literature, enhancing patient care and decision-making in this high-risk population.

Clinical performance of two commercially available rapid antigen tests for influenza, RSV, and SARS-CoV-2 diagnostics

Rapid antigen tests (RATs) might provide rapid, low-cost, and easy-to-perform choice to nucleic-acid amplification methods (NAAT) in point-of-care (POC) diagnostics of respiratory infections. The clinical performance of two commercial combo-RATs for influenza A and B, respiratory syncytial virus (RSV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) POC diagnostics, was assessed. RAT and real-time-PCR (RT-PCR) analysis were performed on 620 patients admitted to the emergency department due to respiratory symptoms. The sensitivity and specificity of the RATs compared with RT-PCR results were studied. The sensitivity of the RATs with respect to symptom duration was also estimated. The tested RAT1 showed sensitivities of 98.68%, 73,53%, and 44.44% for SARS-CoV-2, influenza A, and RSV, respectively, when the cycle threshold (Ct) values were <25 and 95.45%, 68.42%, 40.0% with Ct values <30. In RAT2 analysis, respective sensitivities for influenza A and RSV in samples with Ct <25 were 85% and 100% and in samples with Ct <30 respective sensitivities dropped to 69.23% and 66.67%. Positive SARS-CoV-2 cases during the RAT2 testing period and influenza B cases during both the RAT1 and RAT2 testing periods were scarce, so they were omitted from the statistical analysis. The specificity of both tested RATs was high and varied between 99.48% and 100%. The clinical use of RATs should be carefully considered due to the possibility of insufficient sensitivity. Because the specificity of the tests is high, the use of such tests might provide added value, for example, in emergency units, particularly when the prevalence of these infections is high. However, an option to confirm negative RAT by NAAT should be available.

IMPORTANCE

Rapid diagnostics of respiratory viruses is essential for clinical management, infection control, and epidemiological surveillance. Our results showed that due to the high specificity and still inadequate sensitivity, rapid antigen tests (RATs) might be useful for influenza, respiratory syncytial virus, and severe acute respiratory syndrome coronavirus 2 point-of-care diagnostics when correctly used. The results provide useful information for laboratory and infectious disease control professionals to support decision-making when implementation of the RATs in clinical use is planned.

Bridging basic science and applied diagnostics: Comprehensive viral diagnostics enabled by graphene-based electronic biosensor technology advancements

This study presents a graphene field-effect transistor (gFET) biosensor with dual detection capabilities for SARS-CoV-2: one RNA detection assay to confirm viral positivity and the other for nucleocapsid (N-)protein detection as a proxy for infectiousness of the patient. This technology can be rapidly adapted to emerging infectious diseases, making an essential tool to contain future pandemics. To detect viral RNA, the highly conserved E-gene of the virus was targeted, allowing for the determination of SARS-CoV-2 presence or absence using nasopharyngeal swab samples. For N-protein detection, specific antibodies were used. Tested on 213 clinical nasopharyngeal samples, the gFET biosensor showed good correlation with RT-PCR cycle threshold values, proving its high sensitivity in detecting SARS-CoV-2 RNA. Specificity was confirmed using 21 pre-pandemic samples positive for other respiratory viruses. The gFET biosensor had a limit of detection (LOD) for N-protein of 0.9 pM, establishing a foundation for the development of a sensitive tool for monitoring active viral infection. Results of gFET based N-protein detection corresponded to the results of virus culture in all 16 available clinical samples and thus it also proved its capability to serve as a proxy for infectivity. Overall, these findings support the potential of the gFET biosensor as a point-of-care device for rapid diagnosis of SARS-CoV-2 infection and indirect assessment of infectiousness in patients, providing additional information for clinical and public health decision-making.

Epidemiology and pathogen characteristics of infections following solid organ transplantation

Solid organ transplantation (SOT) recipients have a heightened risk for infection due to prolonged immunosuppressive drug use following transplant procedures. The occurrence of post-transplant infections is influenced not only by the transplanted organ type but also by varied factors. The kidney is the most common organ in SOT, followed by the liver, heart, and lung. This review aims to provide a comprehensive overview of the current epidemiological characteristics of infections after kidney, liver, heart, and lung transplantation, focusing on bacterial, fungal, and viral infections. The incidence and infection types demonstrated significant variability across different SOTs. Furthermore, this review attempts to elucidate the clinical characteristics of infections across patients following different SOTs and contribute to the development of individualized prevention strategies according to infection incidence, ultimately enhancing the quality of life of transplant recipients.

Oro-faecal transmission of SARS-CoV-2: A systematic review of studies employing viral culture from gastrointestinal and other potential oro-faecal sources and evidence for transmission to humans

The extent to which the oro-faecal route contributes to the transmission of SARS-CoV-2 is not established.We systematically reviewed the evidence on the presence of infectious SARS-CoV-2 in faeces and other gastrointestinal sources by examining studies that used viral culture to investigate the presence of replication-competent virus in these samples. We conducted searches in the WHO COVID-19 Database, LitCovid, medRxiv, and Google Scholar for SARS-CoV-2 using keywords and associated synonyms, with a search date up to 28 November 2023.We included 13 studies involving 229 COVID-19 subjects - providing 308 faecal or rectal swab SARS-CoV2 reverse transcription-polymerase chain reaction (RT-PCR)-positive samples tested with viral culture. The methods used for viral culture across the studies were heterogeneous. Three studies (two cohorts and one case series) reported observing replication-competent SARS-CoV-2 confirmed by quantitative RT-PCR (qPCR) and whole-genome sequencing, and qPCR including appropriate cycle threshold changes. Overall, six (1.9%) of 308 faecal samples subjected to cell culture showed replication-competent virus. One study found replication-competent samples from one immunocompromised patient. No studies were identified demonstrating direct evidence of oro-faecal transmission to humans.Our review found a relatively low frequency of replication-competent SARS-CoV-2 in faecal and other gastrointestinal sources. Although it is biologically plausible, more research is needed using standardized cell culture methods, control groups, adequate follow-up, and robust epidemiologic methods, including whether secondary infections occurred, to determine the role of the oro-faecal route in the transmission of SARS-CoV-2.

Comprehensive Review of COVID-19: Epidemiology, Pathogenesis, Advancement in Diagnostic and Detection Techniques, and Post-Pandemic Treatment Strategies

At present, COVID-19 remains a public health concern due to the ongoing evolution of SARS-CoV-2 and its prevalence in particular countries. This paper provides an updated overview of the epidemiology and pathogenesis of COVID-19, with a focus on the emergence of SARS-CoV-2 variants and the phenomenon known as 'long COVID'. Meanwhile, diagnostic and detection advances will be mentioned. Though many inventions have been made to combat the COVID-19 pandemic, some outstanding ones include multiplex RT-PCR, which can be used for accurate diagnosis of SARS-CoV-2 infection. ELISA-based antigen tests also appear to be potential diagnostic tools to be available in the future. This paper also discusses current treatments, vaccination strategies, as well as emerging cell-based therapies for SARS-CoV-2 infection. The ongoing evolution of SARS-CoV-2 underscores the necessity for us to continuously update scientific understanding and treatments for it.

Early combination therapy of COVID-19 in high-risk patients

PURPOSE

Prolonged shedding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been observed in immunocompromised hosts. Early monotherapy with direct-acting antivirals or monoclonal antibodies, as recommended by the international guidelines, does not prevent this with certainty. Dual therapies may therefore have a synergistic effect.

METHODS

This retrospective, multicentre study compared treatment strategies for corona virus disease-19 (COVID-19) with combinations of nirmatrelvir/ritonavir, remdesivir, molnupiravir, and/ or mABs during the Omicron surge. Co-primary endpoints were prolonged viral shedding (≥ 106 copies/ml at day 21 after treatment initiation) and days with SARS-CoV-2 viral load ≥ 106 copies/ml. Therapeutic strategies and risk groups were compared using odds ratios and Fisher's tests or Kaplan-Meier analysis and long-rank tests. Multivariable regression analysis was performed.

RESULTS

144 patients were included with a median duration of SARS-CoV-2 viral load ≥ 106 copies/ml of 8.0 days (IQR 6.0-15.3). Underlying haematological malignancies (HM) (p = 0.03) and treatment initiation later than five days after diagnosis (p < 0.01) were significantly associated with longer viral shedding. Prolonged viral shedding was observed in 14.6% (n = 21/144), particularly in patients with underlying HM (OR 3.5; 95% CI 1.2-9.9; p = 0.02). Clinical courses of COVID-19 were mild to moderate with only few adverse effects potentially related to combination treatment.

CONCLUSION

Early combination treatment of COVID-19 effectively prevented prolonged viral shedding in 85.6% of cases. Considering the rapid viral clearance rates and low toxicity, individualized dual therapy approaches may be beneficial in high-risk patients.

Analysis of two sequential SARS-CoV-2 outbreaks on a haematology-oncology ward and the role of infection prevention

Two SARS-CoV-2 nosocomial outbreaks occurred on the haematology ward of our hospital. Patients on the ward were at high risk for severe infection because of their immunocompromised status. Whole Genome Sequencing proved transmission of a particular SARS-CoV-2 variant in each outbreak. The first outbreak (20 patients/31 healthcare workers (HCW)) occurred in November 2020 and was caused by a variant belonging to lineage B.1.221. At that time, there were still uncertainties on mode of transmission of SARS-CoV-2, and vaccines nor therapy were available. Despite HCW wearing II-R masks in all patient contacts and FFP-2 masks during aerosol generating procedures (AGP), the outbreak continued. Therefore, extra measures were introduced. Firstly, regular PCR-screening of asymptomatic patients and HCW; positive patients were isolated and positive HCW were excluded from work as a rule and they were only allowed to resume their work if a follow-up PCR CT-value was ≥30 and were asymptomatic or having only mild symptoms. Secondly, the use of FFP-2 masks was expanded to some long-lasting, close-contact, non-AGPs. After implementing these measures, the incidence of new cases declined gradually. Thirty-seven percent of patients died due to COVID-19. The second outbreak (10 patients/2 HCW) was caused by the highly transmissible omicron BA.1 variant and occurred in February 2022, where transmission occurred on shared rooms despite the extra infection control measures. It was controlled much faster, and the clinical impact was low as the majority of patients was vaccinated; no patients died and symptoms were relatively mild in both patients and HCW.

Clinical outcomes and immunological features of COVID-19 patients receiving B-cell depletion therapy during the Omicron era

Background: The clinical outcomes and immunological features of coronavirus disease 2019 (COVID-19) patients receiving B-cell depletion therapy (BCDT), especially in Omicron variant era, have not been fully elucidated. We aimed to investigate the outcomes and immune responses of COVID-19 patients receiving BCDT during the Omicron period.Methods: We retrospectively compared clinical outcomes between COVID-19 patients treated with BCDT (the BCDT group) and those with the same underlying diseases not treated with BCDT (the non-BCDT group). For immunological analyses, we prospectively enrolled COVID-19 patients receiving BCDT and immunocompetent COVID-19 patients as controls. We measured humoral and cellular immune responses using the enzyme-linked immunosorbent assay and flow cytometry.Results: Severe to critical COVID-19 was more frequent in the BCDT group than in the non-BCDT group (41.9% vs. 28.3%, p = .030). BCDT was an independent risk factor for severe to critical COVID-19 (adjusted odds ratio [aOR] 2.21, 95% confidence interval [CI] 1.21-4.04, p = .010) as well as for COVID-19-related mortality (aOR 4.03, 95% CI 1.17-13.86, p = .027). Immunological analyses revealed that patients receiving BCDT had lower anti-S1 IgG titres and a tendency to higher proportions of activated CD4+ T-cells than the controls.Conclusions: BCDT was associated with worse COVID-19 outcomes in the Omicron period. Humoral immune response impairment and T-cell hyperactivation were the main immunological features of COVID-19 patients treated with BCDT, which may have contributed to the worse outcomes of COVID-19 in this population.

Reduction of mycophenolate mofetil dosage to limit prolonged viral shedding in solid organ transplant recipients with COVID-19: Two case reports

Solid organ transplant (SOT) recipients with coronavirus disease-2019 (COVID-19) experience prolonged viral shedding, and they are forced to stay in the hospital because of the requirement for COVID-19 isolation. Here, we present two cases (lung and renal transplant recipients), wherein the isolation period was shortened by reducing the dosage of mycophenolate mofetil (MMF). Both patients recovered well from COVID-19 pneumonia. This case study suggests that a reduction in MMF dosage may lead to a shorter hospitalization period in SOT recipients with COVID-19.

Nasopharyngeal SARS-CoV-2 viral load kinetics using digital PCR

Background

The relationship between the viral kinetics of SARS-CoV-2 and clinical outcomes remains unclear.

Methods

A convenience sample of 955 remnant nasopharyngeal swabs collected during routine care between 11/18/20 and 9/26/21 were analyzed using digital PCR and associated clinical data extracted from the medical record. 18 individuals had >1 sample within 30 days of onset of symptoms.

Results

Paired samples were an average of 6 [range: 0-13] days apart. Four individuals sampled twice on the same day had a median 0.52 log10 viral load difference between samples. Of the remaining, 12 individuals had a decrease in viral load over time, with an average decay of -0.23 log10/day.

Conclusions

Our study found a similar rate of viral decay to others, but did not find associations between viral kinetics and clinical outcomes. Larger studies would be useful to support the use of this measurement as a surrogate endpoint for therapeutic studies.

Revisiting the personal protective equipment components of transmission-based precautions for the prevention of COVID-19 and other respiratory virus infections in healthcare

The COVID-19 pandemic highlighted some potential limitations of transmission-based precautions. The distinction between transmission through large droplets vs aerosols, which have been fundamental concepts guiding infection control measures, has been questioned, leading to considerable variation in expert recommendations on transmission-based precautions for COVID-19. Furthermore, the application of elements of contact precautions, such as the use of gloves and gowns, is based on low-quality and inconclusive evidence and may have unintended consequences, such as increased incidence of healthcare-associated infections and spread of multidrug-resistant organisms. These observations indicate a need for high-quality studies to address the knowledge gaps and a need to revisit the theoretical background regarding various modes of transmission and the definitions of terms related to transmission. Further, we should examine the implications these definitions have on the following components of transmission-based precautions: (i) respiratory protection, (ii) use of gloves and gowns for the prevention of respiratory virus infections, (iii) aerosol-generating procedures and (iv) universal masking in healthcare settings as a control measure especially during seasonal epidemics. Such a review would ensure that transmission-based precautions are consistent and rationally based on available evidence, which would facilitate decision-making, guidance development and training, as well as their application in practice.

Judicious ending of isolation based on reverse transcription-polymerase chain reaction (RT-PCR) cycle threshold only for patients with coronavirus disease 2019 (COVID-19) requiring in-hospital therapy for longer than 20 days after symptom onset

BACKGROUND

For patients with coronavirus disease 2019 (COVID-19) requiring hospitalization, extending isolation is warranted. As a cautious protocol, ending isolation based on polymerase chain reaction cycle threshold (Ct) value was introduced for patients requiring therapy for >20 days after symptom onset.

METHOD

We compared a Ct-based strategy using Smart Gene® between March 2022 and January 2023 with a preceding control period (March 2021 to February 2022) when two consecutive negative reverse transcription-polymerase chain reaction tests using FilmArray® were required for ending isolation. Ct was evaluated on day 21, and ending isolation was permitted in patients with Ct ≥ 38. Although patients with Ct 35-37 were transferred to a non-COVID-19 ward, isolation was continued.

RESULTS

The duration of stay on a COVID-19 ward in the Ct group was 9.7 days shorter than that in controls. The cumulative number of tests was 3.7 in controls and 1.2 in the Ct group. There was no nosocomial transmission after ending isolation in either group. The number of days from symptom onset to testing was 20.7 ± 2.1 in Ct group, and five patients had Ct < 35, nine Ct 35-37, and 71 Ct ≥ 38. No patients were moderately or severely immunocompromised. Steroid use was an independent risk factor for prolonged low Ct (odds ratio 9.40, 95% confidence interval 2.31-38.15, p = 0.002) CONCLUSIONS: The efficacy of ending isolation based on Ct values could improve bed utilization without the risk of transmission among patients with COVID-19 requiring therapy for >20 days after symptom onset.