Clearance and persistence of SARS-CoV-2 RNA in patients with COVID-19

Precision nutrition to reset virus-induced human metabolic reprogramming and dysregulation (HMRD) in long-COVID

SARS-CoV-2, the etiological agent of COVID-19, is devoid of any metabolic capacity; therefore, it is critical for the viral pathogen to hijack host cellular metabolic machinery for its replication and propagation. This single-stranded RNA virus with a 29.9 kb genome encodes 14 open reading frames (ORFs) and initiates a plethora of virus-host protein-protein interactions in the human body. These extensive viral protein interactions with host-specific cellular targets could trigger severe human metabolic reprogramming/dysregulation (HMRD), a rewiring of sugar-, amino acid-, lipid-, and nucleotide-metabolism(s), as well as altered or impaired bioenergetics, immune dysfunction, and redox imbalance in the body. In the infectious process, the viral pathogen hijacks two major human receptors, angiotensin-converting enzyme (ACE)-2 and/or neuropilin (NRP)-1, for initial adhesion to cell surface; then utilizes two major host proteases, TMPRSS2 and/or furin, to gain cellular entry; and finally employs an endosomal enzyme, cathepsin L (CTSL) for fusogenic release of its viral genome. The virus-induced HMRD results in 5 possible infectious outcomes: asymptomatic, mild, moderate, severe to fatal episodes; while the symptomatic acute COVID-19 condition could manifest into 3 clinical phases: (i) hypoxia and hypoxemia (Warburg effect), (ii) hyperferritinemia ('cytokine storm'), and (iii) thrombocytosis (coagulopathy). The mean incubation period for COVID-19 onset was estimated to be 5.1 days, and most cases develop symptoms after 14 days. The mean viral clearance times were 24, 30, and 39 days for acute, severe, and ICU-admitted COVID-19 patients, respectively. However, about 25-70% of virus-free COVID-19 survivors continue to sustain virus-induced HMRD and exhibit a wide range of symptoms that are persistent, exacerbated, or new 'onset' clinical incidents, collectively termed as post-acute sequelae of COVID-19 (PASC) or long COVID. PASC patients experience several debilitating clinical condition(s) with >200 different and overlapping symptoms that may last for weeks to months. Chronic PASC is a cumulative outcome of at least 10 different HMRD-related pathophysiological mechanisms involving both virus-derived virulence factors and a multitude of innate host responses. Based on HMRD and virus-free clinical impairments of different human organs/systems, PASC patients can be categorized into 4 different clusters or sub-phenotypes: sub-phenotype-1 (33.8%) with cardiac and renal manifestations; sub-phenotype-2 (32.8%) with respiratory, sleep and anxiety disorders; sub-phenotype-3 (23.4%) with skeleto-muscular and nervous disorders; and sub-phenotype-4 (10.1%) with digestive and pulmonary dysfunctions. This narrative review elucidates the effects of viral hijack on host cellular machinery during SARS-CoV-2 infection, ensuing detrimental effect(s) of virus-induced HMRD on human metabolism, consequential symptomatic clinical implications, and damage to multiple organ systems; as well as chronic pathophysiological sequelae in virus-free PASC patients. We have also provided a few evidence-based, human randomized controlled trial (RCT)-tested, precision nutrients to reset HMRD for health recovery of PASC patients.

Spontaneous, persistent, T cell-dependent IFN-γ release in patients who progress to Long Covid

After acute infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a proportion of patients experience persistent symptoms beyond 12 weeks, termed Long Covid. Understanding the mechanisms that cause this debilitating disease and identifying biomarkers for diagnostic, therapeutic, and monitoring purposes are urgently required. We detected persistently high levels of interferon-γ (IFN-γ) from peripheral blood mononuclear cells of patients with Long Covid using highly sensitive FluoroSpot assays. This IFN-γ release was seen in the absence of ex vivo peptide stimulation and remains persistently elevated in patients with Long Covid, unlike the resolution seen in patients recovering from acute SARS-CoV-2 infection. The IFN-γ release was CD8+ T cell-mediated and dependent on antigen presentation by CD14+ cells. Longitudinal follow-up of our study cohort showed that symptom improvement and resolution correlated with a decrease in IFN-γ production to baseline levels. Our study highlights a potential mechanism underlying Long Covid, enabling the search for biomarkers and therapeutics in patients with Long Covid.

Amantadine for COVID-19 treatment (ACT) study: a randomized, double-blinded, placebo-controlled clinical trial

OBJECTIVES

The COVID-19 pandemic has revealed a severe need for effective antiviral treatment. The objectives of this study were to assess if pre-emptive treatment with amantadine for COVID-19 in non-hospitalized persons ≥40 years or adults with comorbidities was able to prevent disease progression and hospitalization. Primary outcomes were clinical status on day 14.

METHODS

Between 9 June 2021 and 27 January 2022, this randomized, double-blinded, placebo-controlled, single-centre clinical trial included 242 subjects with a follow-up period of 90 days. Subjects were randomly assigned 1:1 to either amantadine 100 mg or placebo twice daily for 5 days. The inclusion criteria were confirmed SARS-CoV-2 infection and at least one of (a) age ≥40 years, age ≥18 years and (b) at least one comorbidity, or (c) body mass index ≥30. The study protocol was published at www.

CLINICALTRIALS

gov (unique protocol #02032021) and at www.clinicaltrialregister.eu (EudraCT-number 2021-001177-22).

RESULTS

With 121 participants in each arm, we found no difference in the primary endpoint with 82 participants in the amantadine arm, and 92 participants in the placebo arm with no limitations to activities, respectively, and 25 and 37 with limitations to activities in the amantadine arm and the placebo arm, respectively. No participants in either group were admitted to hospital or died. The OR of having state severity increased by 1 in the amantadine group versus placebo was 1.8 (CI 1.0-3.3, [p 0.051]). On day 7, one participant was hospitalized in each group; throughout the study, this increased to five and three participants for amantadine versus placebo treatment (p 0.72). Similarly, on day 7, there was no difference in the status of oropharyngeal swabs. Most participants (108 in each group) were SARS-CoV-2 RNA positive (p 0.84).

CONCLUSION

We found no effect of amantadine on disease progression of SARS-CoV-2 infection.

Incidence rate and predictors of COVID-19 in the two largest cities of Burkina Faso - prospective cohort study in 2021 (ANRS-COV13)

BACKGROUND

Early data on COVID-19 (based primarily on PCR testing) indicated a low burden in Sub-Saharan Africa. To better understand this, this study aimed to estimate the incidence rate and identify predictors of SARS-CoV-2 seroconversion in the two largest cities of Burkina Faso. This study is part of the EmulCOVID-19 project (ANRS-COV13).

METHODS

Our study utilized the WHO Unity protocol for cohort sero-epidemiological studies of COVID-19 in general population. We conducted random sampling stratified by age group and sex. Individuals aged 10 years and older in the cities of Ouagadougou and Bobo-Dioulasso, Burkina Faso were included and surveyed at 4 time points, each 21 days apart, from March 3 to May 15, 2021. WANTAI SARS-CoV-2 Ab ELISA serological tests were used to detect total antibodies (IgM, IgG) in serum. Predictors were investigated using Cox proportional hazards regression.

RESULTS

We analyzed the data from 1399 participants (1051 in Ouagadougou, 348 in Bobo-Dioulasso) who were SARS-CoV-2 seronegative at baseline and had at least one follow-up visit. The incidence rate of SARS-CoV-2 seroconversion was 14.3 cases [95%CI 13.3-15.4] per 100 person-weeks. The incidence rate was almost three times higher in Ouagadougou than in Bobo-Dioulasso (Incidence rate ratio: IRR = 2.7 [2.2-3.2], p < 0.001). The highest incidence rate was reported among women aged 19-59 years in Ouagadougou (22.8 cases [19.6-26.4] per 100 person-weeks) and the lowest among participants aged 60 years and over in Bobo-Dioulasso, 6.3 cases [4.6-8.6] per 100 person-weeks. Multivariable analysis showed that participants aged 19 years and older were almost twice as likely to seroconvert during the study period compared with those aged 10 to 18 years (Hazard ratio: HR = 1.7 [1.3-2.3], p < 0.001). Those aged 10-18 years exhibited more asymptomatic forms than those aged 19 years and older, among those who achieved seroconversion (72.9% vs. 40.4%, p < 0.001).

CONCLUSION

The spread of COVID-19 is more rapid in adults and in large cities. Strategies to control this pandemic in Burkina Faso, must take this into account. Adults living in large cities should be the priority targets for vaccination efforts against COVID-19.

Impaired health-related quality of life in long-COVID syndrome after mild to moderate COVID-19

A growing number of patients with SARS-CoV-2 infections experience long-lasting symptoms. Even patients who suffered from a mild acute infection show a variety of persisting and debilitating neurocognitive, respiratory, or cardiac symptoms (Long-Covid syndrome), consequently leading to limitations in everyday life. Because data on health-related quality of life (HRQoL) is scarce, we aimed to characterize the impact of Long-Covid symptoms after a mild or moderate acute infection on HRQoL. In this observational study, outpatients seeking counseling in the interdisciplinary Post-Covid consultation of the University Hospital Zurich with symptoms persisting for more than 4 weeks were included. Patients who received an alternative diagnosis or suffered from a severe acute Covid-19 infection were excluded. St. George's Respiratory Questionnaire (SGRQ), Euroquol-5D-5L (EQ-5D-5L), and the Short form 36 (SF-36) were distributed to assess HRQoL. 112 patients were included, 86 (76.8%) were female, median (IQR) age was 43 (32.0, 52.5) years with 126 (91, 180) days of symptoms. Patients suffered frequently from fatigue (81%), concentration difficulties (60%), and dyspnea (60%). Patients mostly stated impairment in performing usual activities and having pain/discomfort or anxiety out of the EQ-5D-5L. EQ index value and SGRQ activity score component were significantly lower in females. SF-36 scores showed remarkably lower scores in the physical health domain compared to the Swiss general population before and during the COVID-19 pandemic. Long-Covid syndrome has a substantial impact on HRQoL. Long-term surveillance of patients must provide clarity on the duration of impairments in physical and mental health.Trial registration: The study is registered on www.ClinicalTrials.gov , NCT04793269.

Post-COVID-More than chronic fatigue?

After the first COVID-19 survivors were medically treated in Germany from spring 2020 onwards, various courses of the disease emerged that, in addition to the acute infection, led to prolonged symptoms (long COVID), but also to a symptomatic course beyond 12 weeks, which is referred to as "post-COVID syndrome" (PCS). Currently, the incidence of PCS is estimated to be approximately 15% of all symptomatically infected patients, although over- or underestimations may occur due to the soft definition and lack of control groups. The etiology of PCS is currently unknown. The following pathogenetic processes are discussed in particular: an endothelial dysfunction with microcirculatory disturbances and subsequent organ damage, a residual virus or virus particles, and/or an excessive autoimmune process. Due to the large number of organs that may be affected, PCS presents as a very complex clinical picture with up to 200 described symptoms. An evidence-based causal therapy for PCS has not yet been established. The guideline-based inpatient rehabilitation measures adapted to the individual patient resources have proven to be an effective therapy and should therefore be involved in the therapeutic concept at an early stage. Post-COVID syndrome is a multicomplex disease that can have a considerable impact on the quality of life, but also on the professional performance of the affected patients. Thus, it is clearly more than just a chronic fatigue syndrome. In the interest of our patients, treating physicians should take this disease seriously, clarify the differential diagnoses, and provide sensitive therapeutic care.

Synergy of Small Antiviral Molecules on a Black-Phosphorus Nanocarrier: Machine Learning and Quantum Chemical Simulation Insights

Favipiravir (FP) and Ebselen (EB) belong to a broad range of antiviral drugs that have shown active potential as medications against many viruses. Employing molecular dynamics simulations and machine learning (ML) combined with van der Waals density functional theory, we have uncovered the binding characteristics of these two antiviral drugs on a phosphorene nanocarrier. Herein, by using four different machine learning models (i.e., Bagged Trees, Gaussian Process Regression (GPR), Support Vector Regression (SVR), and Regression Trees (RT)), the Hamiltonian and the interaction energy of antiviral molecules in a phosphorene monolayer are trained in an appropriate way. However, training efficient and accurate models for approximating the density functional theory (DFT) is the final step in using ML to aid in the design of new drugs. To improve the prediction accuracy, the Bayesian optimization approach has been employed to optimize the GPR, SVR, RT, and BT models. Results revealed that the GPR model obtained superior prediction performance with an R2 of 0.9649, indicating that it can explain 96.49% of the data's variability. Then, by means of DFT calculations, we examine the interaction characteristics and thermodynamic properties in a vacuum and a continuum solvent interface. These results illustrate that the hybrid drug is an enabled, functionalized 2D complex with vigorous thermostability. The change in Gibbs free energy at different surface charges and temperatures implies that the FP and EB molecules are allowed to adsorb from the gas phase onto the 2D monolayer at different pH conditions and high temperatures. The results reveal a valuable antiviral drug therapy loaded by 2D biomaterials that may possibly open a new way of auto-treating different diseases, such as SARS-CoV, in primary terms.

Persistence of SARS-CoV-2 Antigens in the Nasal Mucosa of Eight Patients with Inflammatory Rhinopathy for over 80 Days following Mild COVID-19 Diagnosis

The nasal mucosa is the main gateway for entry, replication and elimination of the SARS-CoV-2 virus, the pathogen that causes severe acute respiratory syndrome (COVID-19). The presence of the virus in the epithelium causes damage to the nasal mucosa and compromises mucociliary clearance. The aim of this study was to investigate the presence of SARS-CoV-2 viral antigens in the nasal mucociliary mucosa of patients with a history of mild COVID-19 and persistent inflammatory rhinopathy. We evaluated eight adults without previous nasal diseases and with a history of COVID-19 and persistent olfactory dysfunction for more than 80 days after diagnosis of SARS-CoV-2 infection. Samples of the nasal mucosa were collected via brushing of the middle nasal concha. The detection of viral antigens was performed using immunofluorescence through confocal microscopy. Viral antigens were detected in the nasal mucosa of all patients. Persistent anosmia was observed in four patients. Our findings suggest that persistent SARS-CoV-2 antigens in the nasal mucosa of mild COVID-19 patients may lead to inflammatory rhinopathy and prolonged or relapsing anosmia. This study sheds light on the potential mechanisms underlying persistent symptoms of COVID-19 and highlights the importance of monitoring patients with persistent anosmia and nasal-related symptoms.

Application of ultrasensitive assay for SARS-CoV-2 antigen in nasopharynx in the management of COVID-19 patients with comorbidities during the peak of 2022 Shanghai epidemics in a tertiary hospital

OBJECTIVES

Various comorbidities associated with COVID-19 add up in severity of the disease and obviously prolonged the time for viral clearance. This study investigated a novel ultrasensitive MAGLUMI^® SARS-CoV-2 Ag chemiluminescent immunoassay assay (MAG-CLIA) for diagnosis and monitoring the infectivity of COVID-19 patients with comorbid conditions during the pandemic of 2022 Shanghai.

METHODS

Analytical performances of the MAG-CLIA were evaluated, including precision, limit of quantitation, linearity and specificity. Nasopharyngeal specimens from 232 hospitalized patients who were SARS-CoV-2 RT-qPCR positive and from 477 healthy donors were included. The longitudinal studies were performed by monitoring antigen concentrations alongside with RT-qPCR results in 14 COVID-19 comorbid participants for up to 22 days. The critical antigen concentration in determining virus infectivity was evaluated at the reference cycle threshold (Ct) of 35.

RESULTS

COVID-19 patients were well-identified using an optimal threshold of 0.64 ng/L antigen concentration, with sensitivity and specificity of 95.7% (95% CI: 92.2-97.9%) and 98.3% (95% CI: 96.7-99.3%), respectively, while the Wondfo LFT exhibited those of 34.9% (95% CI: 28.8-41.4%) and 100% (95% CI: 99.23-100%), respectively. The sensitivity of MAG-CLIA remained 91.46% (95% CI: 83.14-95.8%) for the samples with Ct values between 35 and 40. Close dynamic consistence was observed between MAG-CLIA and viral load time series in the longitudinal studies. The critical value of 8.82 ng/L antigen showed adequate sensitivity and specificity in evaluating the infectivity of hospitalized convalescent patients with comorbidities.

CONCLUSIONS

The MAG-CLIA SARS-CoV-2 Ag detection is an effective and alternative approach for rapid diagnosis and enables us to evaluate the infectivity of hospitalized convalescent patients with comorbidities.

Computational Studies of Auto-Active van der Waals Interaction Molecules on Ultra-Thin Black-Phosphorus Film

Using the van der Waals density functional theory, we studied the binding peculiarities of favipiravir (FP) and ebselen (EB) molecules on a monolayer of black phosphorene (BP). We systematically examined the interaction characteristics and thermodynamic properties in a vacuum and a continuum, solvent interface for active drug therapy. These results illustrate that the hybrid molecules are enabled functionalized two-dimensional (2D) complex systems with a vigorous thermostability. We demonstrate in this study that these molecules remain flat on the monolayer BP system and phosphorus atoms are intact. It is inferred that the hybrid FP+EB molecules show larger adsorption energy due to the van der Waals forces and planar electrostatic interactions. The changes in Gibbs free energy at different surface charge fluctuations and temperatures imply that the FP and EB are allowed to adsorb from the gas phase onto the 2D film at high temperatures. Thereby, the results unveiled beneficial inhibitor molecules on two dimensional BP nanocarriers, potentially introducing a modern strategy to enhance the development of advanced materials, biotechnology, and nanomedicine.

A large series of molecular and serological specimens to evaluate mother-to-child SARS-CoV-2 transmission: a prospective study from the Italian Obstetric Surveillance System

OBJECTIVES

To assay the presence of the SARS-CoV-2 genome in vaginal, rectal, and placental swabs among pregnant women and in newborn nasopharyngeal swabs and to investigate the immunological response and maternal antibody transfer through the umbilical cord blood and milk of unvaccinated mothers.

METHODS

Vaginal, rectal, and placental specimens, maternal and neonatal serum, and milk were collected from a wide cohort of pregnant Italian women with confirmed SARS-CoV-2 infection admitted to the hospital between February 25, 2020 and June 30, 2021. Samples were tested in selected reference laboratories according to a shared interlaboratory protocol.

RESULTS

Among 1086 enrolled women, the SARS-CoV-2 positive rate detected in all specimens ranged from 0.7% to 8.4%. Respectively, 45.2% of maternal sera collected during pregnancy and 39.7% of those collected at birth tested positive for immunoglobulin G, whereas 50.5% tested positive among neonates. Nasopharyngeal swabs were positive in 0.8% of the newborns, and immunoglobulin G was detected in 3.0% of the milk samples. The highest immunological response was recorded within 30 days during pregnancy and within 60 days of birth and in the neonatal population.

CONCLUSION

Vertical transmission should be considered a rare event; although, a good maternal immunological response and antibodies transfer throughout the umbilical cord blood was detected.

Diagnostic accuracy of the Panbio COVID-19 antigen rapid test device for SARS-CoV-2 detection in Kenya, 2021: A field evaluation

BACKGROUND

Accurate and timely diagnosis is essential in limiting the spread of SARS-CoV-2 infection. The reference standard, rRT-PCR, requires specialized laboratories, costly reagents, and a long turnaround time. Antigen RDTs provide a feasible alternative to rRT-PCR since they are quick, relatively inexpensive, and do not require a laboratory. The WHO requires that Ag RDTs have a sensitivity ≥80% and specificity ≥97%.

METHODS

This evaluation was conducted at 11 health facilities in Kenya between March and July 2021. We enrolled persons of any age with respiratory symptoms and asymptomatic contacts of confirmed COVID-19 cases. We collected demographic and clinical information and two nasopharyngeal specimens from each participant for Ag RDT testing and rRT-PCR. We calculated the diagnostic performance of the Panbio™ Ag RDT against the US Centers for Disease Control and Prevention's (CDC) rRT-PCR test.

RESULTS

We evaluated the Ag RDT in 2,245 individuals where 551 (24.5%, 95% CI: 22.8-26.3%) tested positive by rRT-PCR. Overall sensitivity of the Ag RDT was 46.6% (95% CI: 42.4-50.9%), specificity 98.5% (95% CI: 97.8-99.0%), PPV 90.8% (95% CI: 86.8-93.9%) and NPV 85.0% (95% CI: 83.4-86.6%). Among symptomatic individuals, sensitivity was 60.6% (95% CI: 54.3-66.7%) and specificity was 98.1% (95% CI: 96.7-99.0%). Among asymptomatic individuals, sensitivity was 34.7% (95% CI 29.3-40.4%) and specificity was 98.7% (95% CI: 97.8-99.3%). In persons with onset of symptoms <5 days (594/876, 67.8%), sensitivity was 67.1% (95% CI: 59.2-74.3%), and 53.3% (95% CI: 40.0-66.3%) among those with onset of symptoms >7 days (157/876, 17.9%). The highest sensitivity was 87.0% (95% CI: 80.9-91.8%) in symptomatic individuals with cycle threshold (Ct) values ≤30.

CONCLUSION

The overall sensitivity and NPV of the Panbio™ Ag RDT were much lower than expected. The specificity of the Ag RDT was high and satisfactory; therefore, a positive result may not require confirmation by rRT-PCR. The kit may be useful as a rapid screening tool only for symptomatic patients in high-risk settings with limited access to rRT-PCR. A negative result should be interpreted based on clinical and epidemiological information and may require retesting by rRT-PCR.

Safety and efficacy of four drug regimens versus standard-of-care for the treatment of symptomatic outpatients with COVID-19: A randomised, open-label, multi-arm, phase 2 clinical trial

Background

This exploratory study investigated four repurposed anti-infective drug regimens in outpatients with COVID-19.

Methods

This phase 2, single centre, randomised, open-label, clinical trial was conducted in South Africa between 3rd September 2020 and 23rd August 2021. Symptomatic outpatients aged 18–65 years, with RT-PCR confirmed SARS-CoV-2 infection were computer randomised (1:1:1:1:1) to standard-of-care (SOC) with paracetamol, or SOC plus artesunate-amodiaquine (ASAQ), pyronaridine-artesunate (PA), favipiravir plus nitazoxanide (FPV + NTZ), or sofosbuvir-daclatasvir (SOF-DCV). The primary endpoint was the incidence of viral clearance, i.e., the proportion of patients with a negative SARS-CoV-2 RT-PCR on day 7, compared to SOC using a log-binomial model in the modified intention-to-treat (mITT) population.

Findings

The mITT population included 186 patients: mean age (SD) 34.9 (10.3) years, body weight 78.2 (17.1) kg. Day 7 SARS-CoV-2 clearance rates (n/N; risk ratio [95% CI]) were: SOC 34.2% (13/38), ASAQ 38.5% (15/39; 0.80 [0.44, 1.47]), PA 30.3% (10/33; 0.69 [0.37, 1.29]), FPV + NTZ 27.0% (10/37; 0.60 [0.31, 1.18]) and SOF-DCV 23.5% (8/34; 0.47 [0.22, 1.00]). Three lower respiratory tract infections occurred (PA 6.1% [2/33]; SOF-DCV 2.9% [1/34]); two required hospitalisation (PA, SOF-DCV). There were no deaths. Adverse events occurred in 55.3% (105/190) of patients, including one serious adverse event (pancytopenia; FPV + NTZ).

Interpretation

There was no statistical difference in viral clearance for any regimen compared to SOC. All treatments were well tolerated.

Funding

10.13039/501100004167Medicines for Malaria Venture, with funding from the UK Foreign, Commonwealth and Development Office, within the Covid-19 Therapeutics Accelerator in partnership with 10.13039/100004440Wellcome, the 10.13039/100000865Bill and Melinda Gates Foundation, and Mastercard.

[German S1 Guideline Long-/Post-COVID]

The German Society of Pneumology initiated 2021 the AWMF S1 guideline Long COVID/Post-COVID. In a broad interdisciplinary approach, this S1 guideline was designed based on the current state of knowledge.The clinical recommendations describe current Long COVID/Post-COVID symptoms, diagnostic approaches, and therapies.In addition to the general and consensus introduction, a subject-specific approach was taken to summarize the current state of knowledge.The guideline has an explicit practical claim and will be developed and adapted by the author team based on the current increase in knowledge.

Genomic Evidence Suggests Viral Persistence of SARS-CoV-2 for 386 Days in Health Worker: A Case Report from Santiago of Chile

The COVID-19 pandemic continues to affect several countries. One of the best ways to control its spread is the timely identification of infected patients for isolation and quarantine. While an episode of infection lasts an average of 8-10 days from the onset of symptoms, there is literature describing long-lasting viral persistence events. Here, we report a case of persistence of SARS-CoV-2 for 386 days in a health worker from Santiago de Chile. Our study could be one of the longest reported viral persistence events. RNA sequencing analyses indicated that the first positive diagnosis (8 June 2020) corresponded to a SARS-CoV-2 variant belonging to Clade Nextstrain 20A. Three hundred eighty-six days later (23 September 2021), the second positive result reached the same viral variant (Clade 20A) but without presence or circulation in Chile since May 2021. Both sequencing coverages showed an identity of 99.21%, with some mutations related to the severity of the disease (ORF1b:P314L) and more infectivity (S:D614G). This work reinforces the idea of implementing an RT-qPCR or rapid antigen test once the quarantine is fulfilled to ensure viral absence, identify potential persistence, and, consequently, minimize the risk of local outbreaks of SARS-CoV-2 infection.

Is SARS-CoV-2 viral load a predictor of mortality in COVID-19 acute respiratory distress syndrome patients?

Objective

Viral load varies during infection and is higher during the initial stages of disease. Given the importance of the intensive care unit (ICU) in the late stages of COVID-19 infection, analyzing cycle threshold values to detect viral load upon ICU admission can be a clinically valuable tool for identifying patients with the highest mortality risk.

Methods

This was a retrospectively designed study. Patients older than 18 years who tested positive for SARS-CoV-2 PCR and had a PaO2/FiO2 ratio <200 were included in the study. The patient population was divided into two groups: survivors and non-survivors.

Results

Two hundred patients were included in the study. In non-survivors, age, relevant ICU admission scores, and procalcitonin levels were significantly higher whereas PaO2/FiO2 ratios and cycle threshold levels were significantly lower than in survivors.

Conclusion

Viral load at ICU admission has significant prognostic value. In combination with age, comorbidities, and severity scores, viral load may assist clinicians in identifying individuals who need more intensive monitoring. Increased awareness may improve outcomes by allowing the more effective monitoring and treatment of patients. More prospective studies are needed to determine how a high viral load worsens disease and how to avoid irreversible results.

Clinical predictors and RT-PCR profile of prolonged viral shedding in patients with SARS-CoV-2 Omicron variant in Shanghai: A retrospective observational study

Objective

To evaluate determinants of prolonged viral RNA shedding in hospitalized patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant infection.

Materials and methods

Hospitalized patients tested SARS-CoV-2 positive by nasopharyngeal real-time reverse transcriptase-polymerase chain reaction (RT-PCR) were included in the single-center, retrospective study. Patients were divided into 2 groups according to the timing of viral clearance (≤ 8 days, "early clearance" and ≥15 days, "late clearance").

Results

4,084 patients were included in the study (1,023 late clearance, 3,061 early clearance), with median age of 50 years and a higher proportion (61.4%) of male. Univariate analyses showed that comorbidities (including hypertension, diabetes, and coronary heart disease), receiving vaccine, the number of vaccinations, cycle threshold (Ct) open reading frame 1ab (ORF 1ab), and nucleocapsid protein (N) gene values on admission were associated with late viral clearance. In the multivariable analysis, the number of vaccinations (P = 0.010) and Ct ORF 1ab gene (P < 0.001) values on admission were significantly associated with late viral clearance. Generalized Estimating Equations (GEE) analysis showed that the Ct value of ORF 1ab gene and N gene remained unchanged within 3 days, and showed progressively higher values with increasing days during late viral RNA clearance.

Conclusion

The number of vaccinations and Ct values of ORF 1ab gene were independently associated with a prolonged SARS-CoV-2 RNA shedding.

Rapid antigen test for SARS-CoV-2: results of validation and use in real life

Aim: To verify a SARS-CoV-2 rapid antigen test (RAT) compared with PCR. Materials & methods: Validation of RAT included 2295 subjects. Next matching of RAT with the PCR was checked in 13,852 subjects referred to PCR after being positive in RAT. Results: Sensitivity and specificity of RAT were 77.38 and 99.10%, respectively. A 74.60% of RAT positive results were confirmed with PCR. Conclusion: The test met WHO susceptibility criteria in a group of symptomatic subjects. In terms of specificity, it met requirements in all subjects. The concordance of RAT with PCR in real life was in line with our verification data.

Association between chemosensory dysfunctions and inflammatory biomarkers in patients with SARS-CoV-2 infection: a systematic review and meta-analysis

BACKGROUND

There is evidence that chemosensory dysfunctions, including smell and taste disorders, are common findings in patients with SARS-CoV-2 infection. However, the underlying biological mechanisms and the role of inflammatory markers are still poorly understood.

AIM

To investigate the inflammatory biomarkers levels in patients with COVID-19 presenting chemosensory dysfunctions.

METHODS

This review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline. A systematic literature search was performed from January 1, 2020, to May 12, 2022. Observational studies that provided data on hematological, biochemical, infection-related indices and cellular immunity, and coagulation function in patients with COVID-19 experiencing smell and/or taste disorders were considered eligible. Effect sizes were reported as standardized mean difference (SMD) with 95% confidence intervals (CI). A negative effect size indicated that the inflammatory biomarker levels were lower among patients with chemosensory dysfunctions.

RESULTS

Eleven studies were included. Patients with chemosensory disturbances had lower levels of leukocytes (SMD - 0.18, 95% CI - 0.35 to - 0.01, p = 0.04), lactate dehydrogenase (SMD - 0.45, 95% CI - 0.82 to - 0.09, p = 0.01), IL-6 (SMD - 0.25, 95% CI - 0.44 to - 0.06, p < 0.01), and C-reactive protein (SMD - 0.33, 95% CI - 0.58 to - 0.08, p < 0.01) than patients without chemosensory disturbances.

CONCLUSION

Patients with SARS-CoV-2 infection who have olfactory and gustatory disorders have a lower inflammatory response than patients who do not have chemosensory alterations. The presence of these symptoms may indicate a more favorable clinical course for COVID-19.

Comparing swab- and different symptoms-based strategies to ascertain COVID-19 recovery in healthcare workers: a cost-effectiveness analysis

Objective

Given the human and economic cost of the COVID-19 pandemic, protecting healthcare workers (HCW) and ensuring continuity of care is critical. The aim of this study is to evaluate the cost-effectiveness of different strategies to ascertain COVID-19 recovery in HCWs.

Methods

Data were collected from the hospital health surveillance program on HCWs at the University Hospital of Verona between 29/02/2020 and 14/04/2021. The diagnosis of SARS-CoV-2 infection and the assessment of the recovery were made through RT-PCR on oro-nasopharyngeal swab-sample. Recovery time and probability were estimated through Kaplan–Meier estimate. For each recovery assessment strategy costs (laboratory diagnostics and human resources), expressed in local currency (euro—€), and working days saved (WDS—effectiveness) were estimated. A decision-tree was created where each knot was a time point scheduled by the different recovery assessment strategies. A Monte Carlo simulation method was used, and probabilistic sensitivity analysis assessed the effect of input uncertainty.

Results

In the study period 916 (9.9%) HCWs tested positive. Recovery time through symptom-based strategy (21 days 0.95 CI 16–24) was significantly lower compared to swab-based one (25 days 0.95 CI 23–28, p < 0.001). The swab-based strategy was dominated by all symptoms-based ones. Symptoms-based with a swab on days 14 and 17 had an ICER of 2 €/WDS and 27 €/WDS compared to the one scheduled on days 10 and 17 and with only one swab on the 17th day.

Conclusions

Scheduling swabs on days 14 and 17 in a symptom-based strategy was the most cost-effective, saving 7.5 more working days than the standard one with swabs on days 10 and 17.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12962-022-00385-w.

Predictors of chronic COVID-19 symptoms in a community-based cohort of adults

Background

COVID-19 can cause some individuals to experience chronic symptoms. Rates and predictors of chronic COVID-19 symptoms are not fully elucidated.

Objective

To examine occurrence and patterns of post-acute sequelae of SARS-CoV2 infection (PASC) symptomatology and their relationship with demographics, acute COVID-19 symptoms and anti-SARS-CoV-2 IgG antibody responses.

Methods

A multi-stage observational study was performed of adults (≥18 years) from 5 US states. Participants completed two rounds of electronic surveys (May-July 2020; April-May 2021) and underwent testing to anti-SARS-CoV-2 nucleocapsid protein IgG antibody testing. Latent Class Analysis was used to identify clusters of chronic COVID-19 symptoms.

Results

Overall, 390 adults (median [25%ile, 75%ile] age: 42 [31, 54] years) with positive SARS-CoV-2 antibodies completed the follow-up survey; 92 (24.7%) had ≥1 chronic COVID-19 symptom, with 11-month median duration of persistent symptoms (range: 1–12 months). The most common chronic COVID-19 symptoms were fatigue (11.3%), change in smell (9.5%) or taste (5.6%), muscle or joint aches (5.4%) and weakness (4.6%). There were significantly higher proportions of ≥1 persistent COVID-19 symptom (31.5% vs. 18.6%; Chi-square, P = 0.004), and particularly fatigue (15.8% vs. 7.3%, P = 0.008) and headaches (5.4% vs. 1.0%, P = 0.011) in females compared to males. Chronic COVID-19 symptoms were also increased in individuals with ≥6 acute COVID-19 symptoms, Latent class analysis revealed 4 classes of symptoms. Latent class-1 (change of smell and taste) was associated with lower anti-SARS-CoV-2 antibody levels; class-2 and 3 (multiple chronic symptoms) were associated with higher anti-SARS-CoV-2 antibody levels and more severe acute COVID-19 infection.

Limitations

Ambulatory cohort with less severe acute disease.

Conclusion

Individuals with SARS-CoV-2 infection commonly experience chronic symptoms, most commonly fatigue, changes in smell or taste and muscle/joint aches. Female sex, severity of acute COVID-19 infection, and higher anti-SARS-CoV-2 IgG levels were associated with the highest risk of having chronic COVID-19 symptoms.

Onset and window of SARS-CoV-2 infectiousness and temporal correlation with symptom onset: a prospective, longitudinal, community cohort study

Background

Knowledge of the window of SARS-CoV-2 infectiousness is crucial in developing policies to curb transmission. Mathematical modelling based on scarce empirical evidence and key assumptions has driven isolation and testing policy, but real-world data are needed. We aimed to characterise infectiousness across the full course of infection in a real-world community setting.

Methods

The Assessment of Transmission and Contagiousness of COVID-19 in Contacts (ATACCC) study was a UK prospective, longitudinal, community cohort of contacts of newly diagnosed, PCR-confirmed SARS-CoV-2 index cases. Household and non-household exposed contacts aged 5 years or older were eligible for recruitment if they could provide informed consent and agree to self-swabbing of the upper respiratory tract. The primary objective was to define the window of SARS-CoV-2 infectiousness and its temporal correlation with symptom onset. We quantified viral RNA load by RT-PCR and infectious viral shedding by enumerating cultivable virus daily across the course of infection. Participants completed a daily diary to track the emergence of symptoms. Outcomes were assessed with empirical data and a phenomenological Bayesian hierarchical model.

Findings

Between Sept 13, 2020, and March 31, 2021, we enrolled 393 contacts from 327 households (the SARS-CoV-2 pre-alpha and alpha variant waves); and between May 24, 2021, and Oct 28, 2021, we enrolled 345 contacts from 215 households (the delta variant wave). 173 of these 738 contacts were PCR positive for more than one timepoint, 57 of which were at the start of infection and comprised the final study population. The onset and end of infectious viral shedding were captured in 42 cases and the median duration of infectiousness was 5 (IQR 3–7) days. Although 24 (63%) of 38 cases had PCR-detectable virus before symptom onset, only seven (20%) of 35 shed infectious virus presymptomatically. Symptom onset was a median of 3 days before both peak viral RNA and peak infectious viral load (viral RNA IQR 3–5 days, n=38; plaque-forming units IQR 3–6 days, n=35). Notably, 22 (65%) of 34 cases and eight (24%) of 34 cases continued to shed infectious virus 5 days and 7 days post-symptom onset, respectively (survival probabilities 67% and 35%). Correlation of lateral flow device (LFD) results with infectious viral shedding was poor during the viral growth phase (sensitivity 67% [95% CI 59–75]), but high during the decline phase (92% [86–96]). Infectious virus kinetic modelling suggested that the initial rate of viral replication determines the course of infection and infectiousness.

Interpretation

Less than a quarter of COVID-19 cases shed infectious virus before symptom onset; under a crude 5-day self-isolation period from symptom onset, two-thirds of cases released into the community would still be infectious, but with reduced infectious viral shedding. Our findings support a role for LFDs to safely accelerate deisolation but not for early diagnosis, unless used daily. These high-resolution, community-based data provide evidence to inform infection control guidance.

Funding

National Institute for Health and Care Research.

Interstitial Pulmonary Fibrosis and Extensive Dendriform Ossification with Persistent Viral Load: A Rare Presentation of Post-COVID-19 Condition in Need of Lung Transplantation

The incidence, presentation, and predisposing factors of post-acute sequelae of COVID-19 (PASC) are currently poorly understood. Lung explants may provide a rare insight into terminal SARS-CoV-2-associated lung damage and its pathophysiology. A 62-year-old man presented with progressively worsening respiratory symptoms after recovering from mild COVID-19 3 months earlier. No underlying pulmonary comorbidities were reported. A chest CT revealed bilateral extensive ground-glass and reticular opacities, suspicious of pulmonary fibrosis. Despite initial high-dose glucocorticoid therapy, the interstitial lung disease progressed, and after exhausting all viable therapeutic options, bilateral lung transplantation was successfully conducted. Histological analysis revealed extensive end-stage interstitial fibrosis with diffuse dendriform ossification and bronchiolar and transitional cell metaplasia. Signs of interstitial remodeling such as an increased interstitial collagen deposition, a pathological accumulation of CD163+/CD206+ M2-polarized macrophages with an increased expression of phosphorylated ERK, and an increased density of CD105+ newly formed capillaries were observed. qRT-PCR and immunohistochemistry for SARS-CoV-2 N-protein in the endothelium of medium-sized vessels confirmed a persistence of SARS-CoV-2. Our findings highlight a highly unusual presentation of SARS-CoV-2-associated lung fibrosis, implying that incomplete viral clearance in the vascular compartment may play a vital pathophysiological role in the development of PASC.

Long COVID and long chain fatty acids (LCFAs): Psychoneuroimmunity implication of omega-3 LCFAs in delayed consequences of COVID-19

The global spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the lasting pandemic of coronavirus disease 2019 (COVID-19) and the post-acute phase sequelae of heterogeneous negative impacts in multiple systems known as the "long COVID." The mechanisms of neuropsychiatric complications of long COVID are multifactorial, including long-term tissue damages from direct CNS viral involvement, unresolved systemic inflammation and oxidative stress, maladaptation of the renin-angiotensin-aldosterone system and coagulation system, dysregulated immunity, the dysfunction of neurotransmitters and hypothalamus-pituitaryadrenal (HPA) axis, and the psychosocial stress imposed by societal changes in response to this pandemic. The strength of safety, well-acceptance, and accumulating scientific evidence has now afforded nutritional medicine a place in the mainstream of neuropsychiatric intervention and prophylaxis. Long chain omega-3 polyunsaturated fatty acids (omega-3 or n-3 PUFAs) might have favorable effects on immunity, inflammation, oxidative stress and psychoneuroimmunity at different stages of SARS-CoV-2 infection. Omega-3 PUFAs, particularly EPA, have shown effects in treating mood and neurocognitive disorders by reducing pro-inflammatory cytokines, altering the HPA axis, and modulating neurotransmission via lipid rafts. In addition, omega-3 PUFAs and their metabolites, including specialized pro-resolvin mediators, accelerate the process of cleansing chronic inflammation and restoring tissue homeostasis, and therefore offer a promising strategy for Long COVID. In this article, we explore in a systematic review the putative molecular mechanisms by which omega-3 PUFAs and their metabolites counteract the negative effects of long COVID on the brain, behavior, and immunity.

Incidence and outcome of SARS-CoV-2 infection in a pediatric kidney transplant recipient cohort from a single center in Northern Italy

BACKGROUND

Concern about SARS-CoV-2 infection has increased over the possible effects on immunocompromised patients. Among them, recipients of solid organ transplantation deserve special attention. Data from the adult population suggest they may be at high risk for developing severe COVID-19, but little data are available for pediatric solid organ transplantation recipients.

METHODS

From March 2020 to April 2021, KT recipients aged <21 years, routinely managed at our center, who underwent RT-PCR testing with nasopharyngeal swabs to detect SARS-CoV-2 infection, were studied. Tests were performed according to clinical and/or epidemiological criteria.

RESULTS

One hundred one transplanted patients were managed at our center during the observation period. Among this population, 57 patients were tested for SARS-CoV-2 infection with a RT-PCR test and were subsequently enrolled. A total of 111 swabs were performed. Twelve out of the 57 patients tested (21.1%) had a positive RT-PCR test result. Among the positive patients, eight were symptomatic (66.7%). Median duration of symptoms and RT-PCR positivity was two days (IQR 1-2.25) and 17 days (IQR 11-27.25), respectively. No patients required specific treatment or IS therapy reduction; no one was admitted to hospital.

CONCLUSIONS

Our data show that pediatric renal transplant recipients are at low risk of clinically relevant COVID-19, as is the healthy age-related population. On the contrary, our results differed substantially from those seen in adult SOT recipient populations that have a high incidence and an even earlier and higher mortality rate.

Factors Associated with Prolonged RT-PCR SARS-CoV-2 Positive Testing in Patients with Mild and Moderate Forms of COVID-19: A Retrospective Study

Background and objectives: This article aims to evaluate the number of days necessary for patients with mild and moderate forms of COVID-19 to reach undetectable levels of SARS-CoV-2 RNA in the upper respiratory tract specimens. As a secondary objective, we sought to establish a correlation between different conditions associated with longer viral load as this could result in a longer period of contagion and infectivity. Materials and Methods: It is a retrospective study. A total of 70 patients with confirmed mild and moderate forms of COVID-19 were enrolled in our study. Results: Number of days with traceable viral load was 25.93 (±6.02) days in patients with mild COVID-19 and 26.97 (±8.30) in moderate form (p = 0.72). Age, male gender, and obesity, along with several chronic conditions (cardiac, liver, renal, and neurological disease), were associated with prolonged positive RT-PCR test from the nasal swab (therefore prolonged viral load). These are in general, risk factors for severe forms of COVID-19. Conclusions: There are several conditions associated with prolonged positive RT-PCR in mild and moderate forms of COVID-19. As to why and what is the significance of it remains to be studied.

Estimate and determinants of SARS-CoV-2 RNA clearance time among non-severe COVID-19 patients

Objectives:

To estimate SARS-CoV-2 RNA clearance time among non-severe COVID-19 patients and explore factors associated with delayed negative conversion.

Methods:

A retrospective cohort study was conducted at the COVID-19 unit of a tertiary care center in the Western region of Saudi Arabia. Reverse transcriptase-polymerase chain reaction (RT-PCR) confirmed COVID-19 patients diagnosed between April 1 and June 30, 2020, were considered. The primary outcome was the time (days) from disease onset to first negative RT-PCR, which was analyzed using Kaplan–Meier and Cox regression survival methods. Demographic data, clinical history, baseline clinical, radiological and laboratory findings and management, and outcome data were collected and analyzed as factors associated with the viral RNA clearance time.

Results:

One hundred and forty-four patients were included. The mean (standard deviation [SD]) age was 36.93 (14.41) years, 50.7% were females, and 45.1% were healthcare workers. COVID19 was asymptomatic, mild and moderate in 11.1%, 71.5% and 17.4% of the participants, respectively. Fever (59.4%) and cough (58.0%) were the dominant onset symptoms. The mean viral RNA clearance time was 22.9 days (SD = 8.6; 95% confidence interval [CI] = 21.5–24.3 days). Extended clearance time was associated with older age (mean = 24.0 vs. 22.0 days; log-rank = 0.037), married status (23.2 vs. 22.6 days; log-rank = 0.021), working in health sector (24.2 vs. 21.8 days; log-rank = 0.006), and having a chronic disease (24.8 vs. 21.9 days; log-rank = 0.028), compared to their counterparts, respectively. In the adjusted model, the job sector was the only factor that was independently associated with clearance time. Non-healthcare sector showed hazard ratio 1.8 (95% CI = 1.3–2.7; log-rank = 0.002) with reference to healthcare sector.

Conclusion:

SARS-CoV-2 RNA clearance time is likely to be longer in non-severe COVID-19 patients, representing an additional risk for the virus dissemination among the community and calling for higher caution among the population.

Biology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the humoral immunoresponse: a systematic review of evidence to support global policy-level actions and research

BACKGROUND

Both population-level epidemiological data and individual-level biological data are needed to control the coronavirus disease 2019 (COVID-19) pandemic. Population-level data are widely available and efforts to combat COVID-19 have generated proliferate data on the biology and immunoresponse to the causative pathogen, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, there remains a paucity of systemized data on this subject.

OBJECTIVE

In this review, we attempt to extract systemized data on the biology and immuno-response to SARS-CoV-2 from the most up-to-date peer-reviewed studies. We will focus on the biology of the virus and immunological variations that are key for determining long-term immunity, transmission potential, and prognosis.

DATA SOURCES AND METHODS

Peer-reviewed articles were sourced from the PubMed database and by snowballing search of selected publications. Search terms included: "Novel Coronavirus" OR "COVID-19" OR "SARS-CoV-2" OR "2019-nCoV" AND "Immunity" OR "Immune Response" OR "Antibody Response" OR "Immunologic Response". Studies published from December 31, 2019 to December 31, 2020 were included. To ensure validity, papers in pre-print were excluded.

RESULTS

Of 2 889 identified papers, 36 were included. Evidence from these studies suggests early seroconversion in patients infected with SARS-CoV-2. Antibody titers appear to markedly increase two weeks after infection, followed by a plateau. A more robust immune response is seen in patients with severe COVID-19 as opposed to mild or asymptomatic presentations. This trend persists with regard to the length of antibody maintenance. However, overall immunity appears to wane within two to three months post-infection.

CONCLUSION

Findings of this study indicate that immune responses to SARS-CoV-2 follow the general pattern of viral infection. Immunity generated through natural infection appears to be short, suggesting a need for long-term efforts to control the pandemic. Antibody testing will be essential to gauge the epidemic and inform decision-making on effective strategies for treatment and prevention. Further research is needed to illustrate immunoglobulin-specific roles and neutralizing antibody activity.

The Persistence Time of SARS-CoV-2 RNA in hospitalized COVID-19 Patients: A prospective Study

BACKGROUND

In the late December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), the causative agent of coronavirus disease 2019 (COVID-19), spreads to almost all countries worldwide. The outbreak of this virus has also been confirmed since 19 February 2020 in Iran.

OBJECTIVE

The aim of this study was to investigate the time of viral RNA clearance in swab and serum samples of COVID-19 patients who received different medications. We also evaluated different factors that may be affected viral RNA persistence in patients infected by SARS-CoV-2.

METHODS

In March 2020, twenty-one hospitalized COVID-19 patients were participated in this prospective study. All patients received antiviral agents in their routine care. Throat swabs and blood samples were obtained from all patients in different intervals including day 3 or 5, day 7, day 10 and finally 14 days after the first positive real time RT-PCR (rRT-PCT) test Results: The median time from the SO to first negative rRT-PCR results for throat swabs and serum samples of COVID-19 patients were 18 and 14 days, respectively. These times were more significant in patients with lymphopenia, oxygen saturation ≤ 90% and comorbidity.

CONCLUSION

This preliminary study highlights that SASR-CoV-2 RNA was not detectable in the upper respiratory tract longer than three weeks. In addition, SARS-CoV may persist for a long period of time in the respiratory than the serum samples. This study support the idea that in the settings of limited resources the patients should cease to be tested earlier than three weeks for discharge management.

Antiviral Immunity in SARS-CoV-2 Infection: From Protective to Deleterious Responses

After two previous episodes, in 2002 and 2012, when two highly pathogenic coronaviruses (SARS, MERS) with a zoonotic origin emerged in humans and caused fatal respiratory illness, we are today experiencing the COVID-19 pandemic produced by SARS-CoV-2. The main question of the year 2021 is if naturally- or artificially-acquired active immunity will be effective against the evolving SARS-CoV-2 variants. This review starts with the presentation of the two compartments of antiviral immunity-humoral and cellular, innate and adaptive-underlining how the involved cellular and molecular actors are intrinsically connected in the development of the immune response in SARS-CoV-2 infection. Then, the SARS-CoV-2 immunopathology, as well as the derived diagnosis and therapeutic approaches, will be discussed.

[Guideline S1: Long COVID: Diagnostics and treatment strategies]

This guideline comprises the state of science at the time of the editorial deadline. In view of the high turnover of knowledge the guideline is designed as a living guideline. The main objective was to provide a tool for the use in primary care, being considered well suited as a first point of entry and for the provision of care. The guideline gives recommendations on the differential diagnosis of symptoms following SARS-CoV‑2 infection, on their therapeutic options, as well as for guidance and care of the patients concerned. It also offers advice concerning return to daily life and rehabilitation. Long COVID being a very variable condition, we chose an interdisciplinary approach.

Detection and predictors of anti-SARS-CoV-2 antibody levels in COVID-19 patients at 8 months after symptom onset

Aim: To determine SARS-CoV-2 specific IgM and IgG levels of patients with COVID-19 at 8 months after symptom onset and to explore the predictors of antibody levels. Materials & methods: The magnetic chemiluminescence method was used to measure the antibody levels. Clinical data were collected and analyzed retrospectively. Results: A total of 54 patients were enrolled in this study, of whom 59.3% were IgM positive and 96.4% were IgG positive. The multiple linear regression analysis revealed that the duration of RNA shedding, C-reactive protein level and disease severity were independent predictors of IgG levels. Conclusion: COVID-19 patients retained long-term viral-specific protective immunity. Disease severity, C-reactive protein level and duration of RNA shedding were related to antibody levels 8 months after symptom onset.

This study aimed to detect the levels of antibodies made by the body in response to COVID-19, 8 months after infection. We reviewed the characteristics of 54 patients with a history COVID-19 to find factors that may influence antibody levels. The results showed that 8 months after infection, almost all the patients had sufficient antibody levels to protect them from another episode of COVID-19 and that antibody levels were especially well maintained in those with a history of severe COVID-19.

Persistent Positivity of Reverse Transcriptase-Polymerase Chain Reaction Test among Patients with COVID-19 in Rural Teaching Hospital: A Descriptive Cross-sectional Study

INTRODUCTION

The persistence positivity detected for severe acute respiratory syndrome coronavirus 2 ribonucleic acid by real-time reverse transcriptase-polymerase chain reaction test in asymptomatic coronavirus disease 2019 positive patients has attracted a lot of attention. There is limited data on the duration of viral shedding. We aimed to determine the proportion of coronavirus disease patients with persistent positivity of real-time reverse transcriptase-polymerase chain reaction test in a teaching hospital of Nepal.

METHODS

A descriptive cross-sectional study was conducted using medical records from May to September 2020 in a teaching hospital of Nepal. The study was approved by the Institutional Review Committee of Karnali Academy of Health Sciences (Reference no 077/078/03). Convenient sampling method was used. Data was analysed by Statistical Package for the Social Sciences. Point estimate at 90% Confidence Interval was calculated along with frequency and proportion for binary data.

RESULTS

Of the total 95 cases, 9 (9.5%) cases (4.6-14.4 at 90% Confidence Interval), were repeat positive after achieving the first negative. The mean day required of achieving the last negative for the repeat positive group was 62.11±3.95, range (60-70 days). The mean time duration for the virus shedding was found to be 20.43±12.19 days (range 7-60 days) after the first positive test result.

CONCLUSIONS

This study concludes that there might be a persistent positivity of the polymerase chain reaction test among patients with COVID-19. The majority of the patients were test positive for 8-14 days, and some were positive till 60-70 days.

SARS-CoV-2 identification in an acute appendicitis case: Acute abdomen as manifestation of Multisystem Inflammatory Syndrome in a child with COVID-19

Coronavirus disease 2019 (COVID-19) pandemic is a global health emergency. The clinical course of COVID-19 in children is mild in most of the cases, but multisystem inflammatory syndrome in children (MIS-C) is recognized as a potential life-threatening complication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Acute abdomen as a presentation of COVID-19 is rare, and its correlation to COVID-19 features and prognosis remains undetermined. Herein, we describe a case of appendicitis in a child with confirmed diagnosis of COVID-19 and subsequent SARS-CoV-2 identification in appendix tissue.

Coronavirus persistence in human respiratory tract and cell culture: An overview

Emerging human coronaviruses, including the recently identified SARS-CoV-2, are relevant respiratory pathogens due to their potential to cause epidemics with high case fatality rates, although endemic coronaviruses are also important for immunocompromised patients. Long-term coronavirus infections had been described mainly in experimental models, but it is currently evident that SARS-CoV-2 genomic-RNA can persist for many weeks in the respiratory tract of some individuals clinically recovered from coronavirus infectious disease-19 (COVID-19), despite a lack of isolation of infectious virus. It is still not clear whether persistence of such viral RNA may be pathogenic for the host and related to long-term sequelae.

In this review, we summarize evidence of SARS-CoV-2 RNA persistence in respiratory samples besides results obtained from cell culture and histopathology describing long-term coronavirus infection. We also comment on potential mechanisms of coronavirus persistence and relevance for pathogenesis.

Long COVID or post-COVID-19 syndrome: putative pathophysiology, risk factors, and treatments

Long COVID or post-COVID-19 syndrome first gained widespread recognition among social support groups and later in scientific and medical communities. This illness is poorly understood as it affects COVID-19 survivors at all levels of disease severity, even younger adults, children, and those not hospitalized. While the precise definition of long COVID may be lacking, the most common symptoms reported in many studies are fatigue and dyspnoea that last for months after acute COVID-19. Other persistent symptoms may include cognitive and mental impairments, chest and joint pains, palpitations, myalgia, smell and taste dysfunctions, cough, headache, and gastrointestinal and cardiac issues. Presently, there is limited literature discussing the possible pathophysiology, risk factors, and treatments in long COVID, which the current review aims to address. In brief, long COVID may be driven by long-term tissue damage (e.g. lung, brain, and heart) and pathological inflammation (e.g. from viral persistence, immune dysregulation, and autoimmunity). The associated risk factors may include female sex, more than five early symptoms, early dyspnoea, prior psychiatric disorders, and specific biomarkers (e.g. D-dimer, CRP, and lymphocyte count), although more research is required to substantiate such risk factors. While preliminary evidence suggests that personalized rehabilitation training may help certain long COVID cases, therapeutic drugs repurposed from other similar conditions, such as myalgic encephalomyelitis or chronic fatigue syndrome, postural orthostatic tachycardia syndrome, and mast cell activation syndrome, also hold potential. In sum, this review hopes to provide the current understanding of what is known about long COVID.

Production and persistence of specific antibodies in COVID-19 patients with hematologic malignancies: role of rituximab

The ability of patients with hematologic malignancies (HM) to develop an effective humoral immune response after COVID-19 is unknown. A prospective study was performed to monitor the immune response to SARS-CoV-2 of patients with follicular lymphoma (FL), diffuse large B-cell lymphoma (DLBCL), chronic lymphoproliferative disorders (CLD), multiple myeloma (MM), or myelodysplastic/myeloproliferative syndromes (MDS/MPN). Antibody (Ab) levels to the SARS-CoV-2 nucleocapsid (N) and spike (S) protein were measured at +1, +3, +6 months after nasal swabs became PCR-negative. Forty-five patients (9 FL, 8 DLBCL, 8 CLD, 10 MM, 10 MDS/MPS) and 18 controls were studied. Mean anti-N and anti-S-Ab levels were similar between HM patients and controls, and shared the same behavior, with anti-N Ab levels declining at +6 months and anti-S-Ab remaining stable. Seroconversion rates were lower in HM patients than in controls. In lymphoma patients mean Ab levels and seroconversion rates were lower than in other HM patients, primarily because all nine patients who had received rituximab within 6 months before COVID-19 failed to produce anti-N and anti-S-Ab. Only one patient requiring hematological treatment after COVID-19 lost seropositivity after 6 months. No reinfections were observed. These results may inform vaccination policies and clinical management of HM patients.

[S1 Guideline Post-COVID/Long-COVID]

The German Society of Pneumology initiated the AWMFS1 guideline Post-COVID/Long-COVID. In a broad interdisciplinary approach, this S1 guideline was designed based on the current state of knowledge.The clinical recommendation describes current post-COVID/long-COVID symptoms, diagnostic approaches, and therapies.In addition to the general and consensus introduction, a subject-specific approach was taken to summarize the current state of knowledge.The guideline has an expilcit practical claim and will be continuously developed and adapted by the author team based on the current increase in knowledge.

A Recombinant Fragment of Human Surfactant Protein D Binds Spike Protein and Inhibits Infectivity and Replication of SARS-CoV-2 in Clinical Samples

Coronavirus disease (COVID-19) is an acute infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Human SP-D (surfactant protein D) is known to interact with the spike protein of SARS-CoV, but its immune surveillance against SARS-CoV-2 is not known. The current study aimed to examine the potential of a recombinant fragment of human SP-D (rfhSP-D) as an inhibitor of replication and infection of SARS-CoV-2. The interaction of rfhSP-D with the spike protein of SARS-CoV-2 and human ACE-2 (angiotensin-converting enzyme 2) receptor was predicted via docking analysis. The inhibition of interaction between the spike protein and ACE-2 by rfhSP-D was confirmed using direct and indirect ELISA. The effect of rfhSP-D on replication and infectivity of SARS-CoV-2 from clinical samples was assessed by measuring the expression of RdRp gene of the virus using quantitative PCR. In silico interaction studies indicated that three amino acid residues in the receptor-binding domain of spike protein of SARS-CoV-2 were commonly involved in interacting with rfhSP-D and ACE-2. Studies using clinical samples of SARS-CoV-2–positive cases (asymptomatic, n = 7; symptomatic, n = 8) and negative control samples (n = 15) demonstrated that treatment with 1.67 μM rfhSP-D inhibited viral replication by ∼5.5-fold and was more efficient than remdesivir (100 μM) in Vero cells. An approximately two-fold reduction in viral infectivity was also observed after treatment with 1.67 μM rfhSP-D. These results conclusively demonstrate that the rfhSP-D mediated calcium independent interaction between the receptor-binding domain of the S1 subunit of the SARS-CoV-2 spike protein and human ACE-2, its host cell receptor, and significantly reduced SARS-CoV-2 infection and replication in vitro.

Persistence of SARS-CoV-2 RNA in the nasopharyngeal, blood, urine, and stool samples of patients with COVID-19: a hospital-based longitudinal study

BACKGROUND

The persistence of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) RNA in the body fluids of patients with the novel coronavirus disease 2019 (COVID-19) may increase the potential risk of viral transmission. There is still uncertainty on whether the recommended quarantine duration is sufficient to reduce the risk of transmission. This study aimed to investigate the persistence of SARS-CoV-2 RNA in the nasopharyngeal, blood, urine, and stool samples of patients with COVID-19.

METHODS

In this hospital-based longitudinal study, 100 confirmed cases of COVID-19 were recruited between March 2020 and August 2020 in Guilan Province, north of Iran. Nasopharyngeal, blood, urine, and stool samples were obtained from each participant at the time of hospital admission, upon discharge, 1 week after discharge, and every 2 weeks until all samples were negative for SARS-CoV-2 RNA by reverse transcription-polymerase chain reaction (RT-PCR) assay. A survival analysis was also performed to identify the duration of viral persistence.

RESULTS

The median duration of viral RNA persistence in the nasopharyngeal samples was 8 days from the first positive RT-PCR result upon admission (95% CI 6.91-9.09); the maximum duration of viral shedding was 25 days from admission. Positive blood, urine, and stool RT-PCR results were detected in 24%, 7%, and 6% of the patients, respectively. The median duration of viral persistence in the blood, urine, and stool samples was 7 days (95% CI 6.07-7.93), 6 days (95% CI 4.16-8.41), and 13 days (95% CI 6.96-19.4), respectively. Also, the maximum duration of viral persistence in the blood, urine, and stool samples was 17, 11, and 42 days from admission, respectively.

CONCLUSION

According to the present results, immediately after the hospitalized patients were discharged, no evidence of viral genetic materials was found. Therefore, appropriate treatments were selected for the patients at this hospital. However, we recommend further investigations on a larger sample size in multi-center and prospective randomized controlled trials (RCTs) to evaluate the effects of different drugs on the shedding of the virus through body secretions.

Persistence of SARS-CoV-2 RNA in the nasopharyngeal, blood, urine, and stool samples of patients with COVID-19: a hospital-based longitudinal study

BACKGROUND

The persistence of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) RNA in the body fluids of patients with the novel coronavirus disease 2019 (COVID-19) may increase the potential risk of viral transmission. There is still uncertainty on whether the recommended quarantine duration is sufficient to reduce the risk of transmission. This study aimed to investigate the persistence of SARS-CoV-2 RNA in the nasopharyngeal, blood, urine, and stool samples of patients with COVID-19.

METHODS

In this hospital-based longitudinal study, 100 confirmed cases of COVID-19 were recruited between March 2020 and August 2020 in Guilan Province, north of Iran. Nasopharyngeal, blood, urine, and stool samples were obtained from each participant at the time of hospital admission, upon discharge, 1 week after discharge, and every 2 weeks until all samples were negative for SARS-CoV-2 RNA by reverse transcription-polymerase chain reaction (RT-PCR) assay. A survival analysis was also performed to identify the duration of viral persistence.

RESULTS

The median duration of viral RNA persistence in the nasopharyngeal samples was 8 days from the first positive RT-PCR result upon admission (95% CI 6.91-9.09); the maximum duration of viral shedding was 25 days from admission. Positive blood, urine, and stool RT-PCR results were detected in 24%, 7%, and 6% of the patients, respectively. The median duration of viral persistence in the blood, urine, and stool samples was 7 days (95% CI 6.07-7.93), 6 days (95% CI 4.16-8.41), and 13 days (95% CI 6.96-19.4), respectively. Also, the maximum duration of viral persistence in the blood, urine, and stool samples was 17, 11, and 42 days from admission, respectively.

CONCLUSION

According to the present results, immediately after the hospitalized patients were discharged, no evidence of viral genetic materials was found. Therefore, appropriate treatments were selected for the patients at this hospital. However, we recommend further investigations on a larger sample size in multi-center and prospective randomized controlled trials (RCTs) to evaluate the effects of different drugs on the shedding of the virus through body secretions.

Detection of SARS-CoV-2 RNA in serum is associated with increased mortality risk in hospitalized COVID-19 patients

COVID-19 has overloaded national health services worldwide. Thus, early identification of patients at risk of poor outcomes is critical. Our objective was to analyse SARS-CoV-2 RNA detection in serum as a severity biomarker in COVID-19. Retrospective observational study including 193 patients admitted for COVID-19. Detection of SARS-CoV-2 RNA in serum (viremia) was performed with samples collected at 48-72 h of admission by two techniques from Roche and Thermo Fischer Scientific (TFS). Main outcome variables were mortality and need for ICU admission during hospitalization for COVID-19. Viremia was detected in 50-60% of patients depending on technique. The correlation of Ct in serum between both techniques was good (intraclass correlation coefficient: 0.612; p < 0.001). Patients with viremia were older (p = 0.006), had poorer baseline oxygenation (PaO2/FiO2; p < 0.001), more severe lymphopenia (p < 0.001) and higher LDH (p < 0.001), IL-6 (p = 0.021), C-reactive protein (CRP; p = 0.022) and procalcitonin (p = 0.002) serum levels. We defined "relevant viremia" when detection Ct was < 34 with Roche and < 31 for TFS. These thresholds had 95% sensitivity and 35% specificity. Relevant viremia predicted death during hospitalization (OR 9.2 [3.8-22.6] for Roche, OR 10.3 [3.6-29.3] for TFS; p < 0.001). Cox regression models, adjusted by age, sex and Charlson index, identified increased LDH serum levels and relevant viremia (HR = 9.87 [4.13-23.57] for TFS viremia and HR = 7.09 [3.3-14.82] for Roche viremia) as the best markers to predict mortality. Viremia assessment at admission is the most useful biomarker for predicting mortality in COVID-19 patients. Viremia is highly reproducible with two different techniques (TFS and Roche), has a good consistency with other severity biomarkers for COVID-19 and better predictive accuracy.

Viral Dynamics and Real-Time RT-PCR Ct Values Correlation with Disease Severity in COVID-19

Real-time RT-PCR is considered the gold standard confirmatory test for coronavirus disease 2019 (COVID-19). However, many scientists disagree, and it is essential to understand that several factors and variables can cause a false-negative test. In this context, cycle threshold (Ct) values are being utilized to diagnose or predict SARS-CoV-2 infection. This practice has a significant clinical utility as Ct values can be correlated with the viral load. In addition, Ct values have a strong correlation with multiple haematological and biochemical markers. However, it is essential to consider that Ct values might be affected by pre-analytic, analytic, and post-analytical variables such as collection technique, specimen type, sampling time, viral kinetics, transport and storage conditions, nucleic acid extraction, viral RNA load, primer designing, real-time PCR efficiency, and Ct value determination method. Therefore, understanding the interpretation of Ct values and other influential factors could play a crucial role in interpreting viral load and disease severity. In several clinical studies consisting of small or large sample sizes, several discrepancies exist regarding a significant positive correlation between the Ct value and disease severity in COVID-19. In this context, a revised review of the literature has been conducted to fill the knowledge gaps regarding the correlations between Ct values and severity/fatality rates of patients with COVID-19. Various databases such as PubMed, Science Direct, Medline, Scopus, and Google Scholar were searched up to April 2021 by using keywords including "RT-PCR or viral load", "SARS-CoV-2 and RT-PCR", "Ct value and viral load", "Ct value or COVID-19". Research articles were extracted and selected independently by the authors and included in the present review based on their relevance to the study. The current narrative review explores the correlation of Ct values with mortality, disease progression, severity, and infectivity. We also discuss the factors that can affect these values, such as collection technique, type of swab, sampling method, etc.

Relative COVID-19 Viral Persistence and Antibody Kinetics

A total of 15 RT-PCR confirmed COVID-19 patients were admitted to our hospital during the in-itial outbreak in Taiwan. The average time of virus clearance was delayed in seven patients, 24.14 ± 4.33 days compared to 10.25 ± 0.56 days post-symptom onset (PSO) in the other eight pa-tients. There was strong antibody response in patients with viral persistence at the pharynx, with peak values of serum antibody 677.2 ± 217.8 vs. 76.70 ± 32.11 in patients with delayed versus rapid virus clearance. The patients with delayed viral clearance had excessive antibodies of compromised quality in an early stage with the delay in peak virus neutralization efficacy, 34.14 ± 7.15 versus 12.50 ± 2.35 days PSO in patients with rapid virus clearance. Weak antibody re-sponse of patients with rapid viral clearance was also effective, with substantial and comparable neutralization efficacy, 35.70 ± 8.78 versus 41.37 ± 11.49 of patients with delayed virus clearance. Human Cytokine 48-Plex Screening of the serial sera samples revealed elevated concentrations of proinflammatory cytokines and chemokines in a deceased patient with delayed virus clear-ance and severe disease. The levels were comparatively less in the other two patients who suf-fered from severe disease but eventually survived.

COVID-19-related anosmia is associated with viral persistence and inflammation in human olfactory epithelium and brain infection in hamsters

Whereas recent investigations have revealed viral, inflammatory, and vascular factors involved in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lung pathogenesis, the pathophysiology of neurological disorders in coronavirus disease 2019 (COVID-19) remains poorly understood. Olfactory and taste dysfunction are common in COVID-19, especially in mildly symptomatic patients. Here, we conducted a virologic, molecular, and cellular study of the olfactory neuroepithelium of seven patients with COVID-19 presenting with acute loss of smell. We report evidence that the olfactory neuroepithelium is a major site of SARS-CoV2 infection with multiple cell types, including olfactory sensory neurons, support cells, and immune cells, becoming infected. SARS-CoV-2 replication in the olfactory neuroepithelium was associated with local inflammation. Furthermore, we showed that SARS-CoV-2 induced acute anosmia and ageusia in golden Syrian hamsters, lasting as long as the virus remained in the olfactory epithelium and the olfactory bulb. Last, olfactory mucosa sampling from patients showing long-term persistence of COVID-19-associated anosmia revealed the presence of virus transcripts and of SARS-CoV-2-infected cells, together with protracted inflammation. SARS-CoV-2 persistence and associated inflammation in the olfactory neuroepithelium may account for prolonged or relapsing symptoms of COVID-19, such as loss of smell, which should be considered for optimal medical management of this disease.

COVID-19: Rapid antigen detection for SARS-CoV-2 by lateral flow assay: A national systematic evaluation of sensitivity and specificity for mass-testing

BACKGROUND

Lateral flow device (LFD) viral antigen immunoassays have been developed around the world as diagnostic tests for SARS-CoV-2 infection. They have been proposed to deliver an infrastructure-light, cost-economical solution giving results within half an hour.

METHODS

LFDs were initially reviewed by a Department of Health and Social Care team, part of the UK government, from which 64 were selected for further evaluation from 1st August to 15th December 2020. Standardised laboratory evaluations, and for those that met the published criteria, field testing in the Falcon-C19 research study and UK pilots were performed (UK COVID-19 testing centres, hospital, schools, armed forces).

FINDINGS

4/64 LFDs so far have desirable performance characteristics (orient Gene, Deepblue, Abbott and Innova SARS-CoV-2 Antigen Rapid Qualitative Test). All these LFDs have a viral antigen detection of >90% at 100,000 RNA copies/ml. 8951 Innova LFD tests were performed with a kit failure rate of 5.6% (502/8951, 95% CI: 5.1-6.1), false positive rate of 0.32% (22/6954, 95% CI: 0.20-0.48). Viral antigen detection/sensitivity across the sampling cohort when performed by laboratory scientists was 78.8% (156/198, 95% CI 72.4-84.3).

INTERPRETATION

Our results suggest LFDs have promising performance characteristics for mass population testing and can be used to identify infectious positive individuals. The Innova LFD shows good viral antigen detection/sensitivity with excellent specificity, although kit failure rates and the impact of training are potential issues. These results support the expanded evaluation of LFDs, and assessment of greater access to testing on COVID-19 transmission.

FUNDING

Department of Health and Social Care. University of Oxford. Public Health England Porton Down, Manchester University NHS Foundation Trust, National Institute of Health Research.

Estimating COVID-19 recovery time in a cohort of Italian healthcare workers who underwent surveillance swab testing

OBJECTIVES

The COVID-19 pandemic is putting a huge strain on the provision and continuity of care. The length of sickness absence of the healthcare workers as a result of SARS-CoV-2 infection plays a pivotal role in hospital staff management. Therefore, the aim of this study was to explore the timing of COVID-19 recovery and viral clearance, and its predictive factors, in a large sample of healthcare workers.

STUDY DESIGN

This is a retrospective cohort study.

METHODS

The analysis was conducted on data collected during the hospital health surveillance programme for healthcare staff at the University Hospital of Verona; healthcare workers were tested for SARS-CoV-2 through RT-PCR with oronasopharyngeal swab samples. The health surveillance programme targeted healthcare workers who either had close contact with SARS-CoV-2-infected patients or were tested as part of the screening-based strategy implemented according to national and regional requirements. Recovery time was estimated from the first positive swab to two consecutive negative swabs, collected 24 h apart, using survival analysis for both right-censored and interval-censored data. Cox proportional hazard was used for multivariate analysis.

RESULTS

During the health surveillance programme, 6455 healthcare workers were tested for SARS-CoV-2 and 248 (3.8%, 95% confidence interval [CI]: 3.4-4.3) reported positive results; among those who tested positive, 49% were asymptomatic, with a median age of 39.8 years, which is significantly younger than symptomatic healthcare workers (48.2 years, P < 0.001). Screening tests as part of the health surveillance programme identified 31 (12.5%) of the positive cases. Median recovery time was 24 days (95% CI: 23-26) and 21.5 days (95% CI: 15.5-30.5) in right- and interval-censoring analysis, respectively, with no association with age, sex or presence of symptoms. Overall, 63% of participants required >20 days to test negative on two consecutive swabs. Hospitalised healthcare workers (4.8%) were older and had a significantly longer recovery time compared with non-hospitalised healthcare workers in both analyses (33.5 vs 24 days, P = 0.005).

CONCLUSIONS

Recovery from COVID-19 and viral clearance may take a long time, especially in individuals who are hospitalised. To detect asymptomatic cases, screening programmes for healthcare workers is recommended.