Factors associated with prolonged viral shedding and impact of lopinavir/ritonavir treatment in hospitalised non-critically ill patients with SARS-CoV-2 infection

SARS-CoV-2 test sensitivity and duration of positivity in the UK during the 2023/2024 Winter: A prospective cohort study based on self-reported data

Estimating epidemiological parameters is essential for informing an effective public health response during waves of infectious disease transmission. However, many parameters are challenging to estimate from real-world data and rely on human challenge studies or mass community testing. During Winter 2023/2024, a community cohort study of SARS-CoV-2 was conducted across households in England and Scotland. From this survey, questionnaire data and follow-up testing protocols provided valuable data on the duration of positivity and test sensitivity for lateral flow device (LFD) tests. Here, Bayesian statistical modelling methods are developed and applied to estimate the underlying parameters. The duration of LFD positivity is found to increase with increasing age, with a mean of 9.1 days (95% CrI: 8.4 days, 9.9 days) in the 18 to 34 years age group compared to 10.8 days (95% CrI: 10.3 days, 11.3 days) in the 75 years and over age group. Sex is found to have no impact on the duration of positivity. LFD test sensitivity at the time of symptom onset is very high, with an estimated sensitivity of 95% (95% CrI: 92%, 98%) across all age groups. As a function of time since symptom onset, LFD test sensitivity decays fastest in the youngest age group, reaching a minimum sensitivity of 0.26 (95% CrI: 0.16, 0.37) compared to 0.53 (95% CrI: 0.46, 0.6). Such patterns are expected since younger individuals experience less severe symptoms of COVID-19 and are likely to clear the virus faster. Females are found to have a slightly faster rate at which sensitivity decreases, but the same minimum sensitivity as Males. Combining the duration of positivity and test sensitivity distributions, we estimate the probability of returning a positive LFD test. Close to the symptom onset date, this probability is approximately 95%. However, this rapidly drops off, dropping below 5% after 13.8 days (95% CrI: 11.0 days, 17.3 days) for the youngest age group (3 to 17 years) and 17.8 days (95% CrI: 16.6 days, 19.2 days) for the 75 years and over age group. Although the probability of returning a positive LFD test rapidly drops off, it remains very high close to the time of symptom onset, which is when individuals are expected to be the most infectious.

Impact of Prolonged SARS-CoV-2 Viral Shedding on COVID-19 Disease Outcome and Viral Dynamics

This article aimed to review the current literature on the impact of continuous shedding of the COVID-19 virus in infected patients in relation to disease outcome variables and viral dynamics. Electronic databases PubMed, Google Scholar, and MedlinePlus were searched using relevant keywords, restricting the selection to thirty-two peer-reviewed articles and four gray literatures from the WHO websites. Findings from this study showed that several variables such as sex, age, immune status, treatments, and vaccines were found to affect the outcomes associated with the COVID-19 virus shedding. These findings highlight the need for further research using longitudinal whole-genome sequencing of the virus and its variants to increase the understanding.

Impact of Tuberculosis on Disease Severity and Viral Shedding Duration in COVID-19 Patients

Accumulating evidence show a potential association between tuberculosis and COVID-19 disease severity. To further clarify the impact of tuberculosis on COVID-19 disease severity and viral shedding duration, a retrospective study was conducted on 223 COVID-19 patients, including 34 with tuberculosis and 189 without tuberculosis. Clinical information and viral load shedding time were collected. A higher percentage of severe/critical COVID-19 diagnosis and deaths was observed in patients with tuberculosis than in those without tuberculosis (8.8% vs. 3.2%, p = 0.142; 2.9% vs. 1.1%, p = 0.393), and COVID-19 patients with tuberculosis had longer viral shedding than those without tuberculosis (median: 15.0 days vs. 11.0 days; p = 0.0001). Having tuberculosis (HR = 2.21, 95% CI 1.37-3.00; p = 0.000), being of elderly age (HR = 1.02, 95% CI 1.01-1.03; p = 0.001) and being diagnosed with severe or critical COVID-19 (HR = 5.63, 95% CI 2.10-15.05; p = 0.001) were independent factors associated with prolonged virus time of SARS-CoV-2. COVID-19 patients with tuberculosis receiving anti-tuberculosis therapy time (ATT) for <2 months had a significantly longer virus shedding duration than those receiving ATT for ≥ 4 months (17.5 vs. 11.5 days, p = 0.012). Our results demonstrated that COVID-19 patients with tuberculosis tend to have more severe disease and a worse prognosis, and tuberculosis prolonged viral shedding, highlighting special attention and/or care required for COVID-19 patients with tuberculosis receiving ATT for <2 months.

Therapeutic Management with Repurposing Approaches: A Mystery During COVID-19 Outbreak

The ubiquitous pandemic that emerged due to COVID-19 affected the whole planet. People all over the globe became vulnerable to the unpredictable emergence of coronavirus. The sudden emergence of respiratory disease in coronavirus infected several patients. This affected human life drastically, from mild symptoms to severe illness, leading to mortality. COVID-19 is an exceptionally communicable disease caused by SARS-CoV-2. According to a genomic study, the viral spike RBD interactions with the host ACE2 protein from several coronavirus strains and the interaction between RBD and ACE2 highlighted the potential change in affinity from the virus causing the COVID-19 outbreak to a progenitor type of SARS-CoV-2. SARS-CoV-2, which could be the principal reservoir, is phylogenetically related to the SARS-like bat virus. Other research works reported that intermediary hosts for the transmission of viruses to humans could include cats, bats, snakes, pigs, ferrets, orangutans, and monkeys. Even with the arrival of vaccines and individuals getting vaccinated and treated with FDAapproved repurposed drugs like Remdesivir, the first and foremost steps aimed towards the possible control and minimization of community transmission of the virus include social distancing, self-realization, and self-health care. In this review paper, we discussed and summarized various approaches and methodologies adopted and proposed by researchers all over the globe to help with the management of this zoonotic outbreak by following repurposed approaches.

Risk Factors Associated with Prolonged Nasopharyngeal Carriage of SARS-CoV-2 and Length of Stay among Patients Admitted to a COVID-19 Referral Center in Manila, Philippines

Objective

Prolonged nasopharyngeal carriage of SARS-CoV-2 has been linked to prolonged hospital stay and delayed radiologic recovery. To determine if clinical risk factors are associated with prolonged nasopharyngeal carriage or longer hospital stay, we performed a descriptive analysis of 169 moderate to severe COVID-19 patients admitted at the Philippine General Hospital from March to June 2020.

Methods

Length of nasopharyngeal RT-PCR positivity and clinical demographic data were extracted from existing patient records. Chi-square test, Mann-Whitney U test, and regression analysis were performed to describe the association of clinical risk factors with prolonged nasopharyngeal carriage and length of hospital stay.

Results

The median duration of carriage was 19 days (IQR 12.0-30.0 days). No comorbidities or inflammatory markers had a statistically significant association with prolonged nasopharyngeal carriage defined as >24 days of nasopharyngeal RT-PCR positivity. Characteristics associated with a statistically significant longer hospital stay included chronic kidney disease stages 3-5, severe disease, and use of empiric antibiotics on admission. Prolonged carriage >24 days, hsCRP, and D-dimer at admission, also had a statistically significant but weak correlation with length of stay.

Conclusion

Among patients with moderate disease, comorbidities and inflammatory markers were not associated with prolonged COVID-19 nasopharyngeal carriage. Prolonged nasopharyngeal carriage >24 days was associated with longer hospital stay, while D-dimer and hsCRP levels at admission, also had statistically significant but small effects on increasing the hospital length of stay.

Estimation of shedding time in laboratory-confirmed COVID-19 cases in South Africa: a population-based record linkage study, March-December 2020

Introduction

in South Africa, COVID-19 cases are notifiable and hospitalized cases are reported on a dedicated platform. It is crucial to estimate the duration of SARS-CoV-2 shedding to inform public health interventions. We aimed to estimate viral shedding time among laboratory-confirmed COVID-19 cases in South Africa.

Methods

we analyzed COVID-19 PCR results from 5 March to 31 December 2020. We included cases with at least 2 consecutive positive PCR tests and a subsequent negative test. We performed multiple linear regression to determine the association between shedding time and predictor variables (age, sex, admission status and province). We included 2752 cases that met the inclusion criteria.

Results

about 39.9% (1099/2752) of participants were inpatients and 60.1% (1653/2752) were outpatients. The median shedding time was 17 days (range: 1-128). There was no difference in shedding time between males and females and between hospitalized patients and outpatients. Individuals aged 0-4 years had the lowest shedding time (median: 14 days, range: 1-72). After adjusting for age, sex and province, shedding time was shorter for hospitalized patients compared to outpatients (co-efficient: -0.14, CI: -0.24 - -0.03, P-value: 0.014). Six provinces (KwaZulu-Natal, Gauteng, Limpopo, North West, Mpumalanga, and Western Cape) had a significant association with shedding time.

Conclusion

the duration of viral shedding within our population varies from 1-128 days. Although prolonged shedding might not necessarily indicate infectiousness, individual patient monitoring and management are needed for patients with prolonged shedding. Further studies are required to explore the association between comorbidities and SARS-CoV-2 shedding time.

Age-dependent immune responses in COVID-19-mediated liver injury: focus on cytokines

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is potentially pathogenic and causes severe symptoms; in addition to respiratory syndromes, patients might experience other severe conditions such as digestive complications and liver complications injury. The abnormality in the liver is manifested by hepatobiliary dysfunction and enzymatic elevation, which is associated with morbidity and mortality. The direct cytopathic effect, immune dysfunction, cytokine storm, and adverse effects of therapeutic regimens have a crucial role in the severity of liver injury. According to aging and immune system alterations, cytokine patterns may also change in the elderly. Moreover, hyperproduction of cytokines in the inflammatory response to SARS-CoV-2 can lead to multi-organ dysfunction. The mortality rate in elderly patients, particularly those with other comorbidities, is also higher than in adults. Although the pathogenic effect of SARS-CoV-2 on the liver has been widely studied, the impact of age and immune-mediated responses at different ages remain unclear. This review discusses the association between immune system responses in coronavirus disease 2019 (COVID-19) patients of different ages and liver injury, focusing on cytokine alterations.

Therapeutic Interventions for COVID-19

SARS-CoV-2, a novel coronavirus, is currently represented a major public health concern. The high transmission rate of this virus increases the mortality rate worldwide. To date, significant efforts and restricted regulations were performed around the world to control this crisis effectively, but unfortunately, there is no specific and successful therapy for COVID-19. Many approaches have been repurposed for SARS-CoV-2 treatment such as antivirals and anti-inflammatories. Furthermore, antibody therapies are one of the main and important approaches of SARS-CoV-2 infection treatment. In recent trials, various immunotherapeutic interventions such as convalescent plasma therapy and monoclonal antibodies, as well as immunomodulatory agents are being proposed. However, the development of a vaccine that provides durable protective immunity will be the most effective therapy for controlling possible epidemics of this virus. The current review summarized all the proposed therapeutic approaches together with information on their safety and efficacy in treating COVID-19, as well as the vaccine candidates. The provided comprehensive information regarding the applied therapeutic strategies against COVID-19 might help the scientific community in any progress toward the treatment of COVID-19 infection.

Paxlovid (Nirmatrelvir/Ritonavir): A new approach to Covid-19 therapy?

Despite the need for novel, effective therapeutics for the COVID-19 pandemic, no curative regimen is yet available, therefore patients are forced to rely on supportive and nonspecific therapies. Some SARS-CoV-2 proteins, like the 3 C-like protease (3CLpro) or the major protease (Mpro), have been identified as promising targets for antiviral drugs. The Mpro has major a role in protein processing as well as pathogenesis of the virus, and could be a useful therapeutic target. The antiviral drug nirmatrelvir can keep SARS-CoV-2 from replicating through inhibiting Mpro. Nirmatrelvir was combined with another HIV protease inhibitor, ritonavir, to create Paxlovid (Nirmatrelvir/Ritonavir). The metabolizing enzyme cytochrome P450 3 A is inhibited by ritonavir to lengthen the half-life of nirmatrelvir, so rintonavir acts as a pharmacological enhancer. Nirmatrelvir exhibits potent antiviral activity against current coronavirus variants, despite significant alterations in the SARS-CoV-2 viral genome. Nevertheless, there are still several unanswered questions. This review summarizes the current literature on nirmatrelvir and ritonavir efficacy in treating SARS-CoV-2 infection, and also their safety and possible side effects.

COVID-19 in Elderly Patients Receiving Haemodialysis: A Current Review

There is an increased incidence of elderly adults diagnosed with kidney failure as our global aging population continues to expand. Hence, the number of elderly adults indicated for kidney replacement therapy is also increasing simultaneously. Haemodialysis initiation is more commonly observed in comparison to kidney transplantation and peritoneal dialysis for the elderly. The onset of the coronavirus 2019 (COVID-19) pandemic brought new paradigms and insights for the care of this patient population. Elderly patients receiving haemodialysis have been identified as high-risk groups for poor COVID-19 outcomes. Age, immunosenescence, impaired response to COVID-19 vaccination, increased exposure to sources of COVID-19 infection and thrombotic risks during dialysis are key factors which demonstrated significant associations with COVID-19 incidence, severity and mortality for this patient group. Recent findings suggest that preventative measures such as regular screening and, if needed, isolation in COVID-19-positive cases, alongside the fulfillment of COVID-19 vaccination programs is an integral strategy to reduce the number of COVID-19 cases and consequential complications from COVID-19, particularly for high-risk groups such as elderly haemodialysis patients. The COVID-19 pandemic brought about the rapid development and repurposing of a number of medications to treat patients in the viral and inflammatory stages of their disease. However, elderly haemodialysis patients were grossly unrepresented in many of these trials. We review the evidence for contemporary treatments for COVID-19 in this population to provide clinicians with an up-to-date guide. We hope our article increases awareness on the associations and impact of COVID-19 for the elderly haemodialysis population, and encourage research efforts to address knowledge gaps in this topical area.

Evaluation of In Vitro and In Vivo Antiviral Activities of Vitamin D for SARS-CoV-2 and Variants

The COVID-19 pandemic has brought about unprecedented medical and healthcare challenges worldwide. With the continual emergence and spread of new COVID-19 variants, four drug compound libraries were interrogated for their antiviral activities against SARS-CoV-2. Here, we show that the drug screen has resulted in 121 promising anti-SARS-CoV-2 compounds, of which seven were further shortlisted for hit validation: citicoline, pravastatin sodium, tenofovir alafenamide, imatinib mesylate, calcitriol, dexlansoprazole, and prochlorperazine dimaleate. In particular, the active form of vitamin D, calcitriol, exhibits strong potency against SARS-CoV-2 on cell-based assays and is shown to work by modulating the vitamin D receptor pathway to increase antimicrobial peptide cathelicidin expression. However, the weight, survival rate, physiological conditions, histological scoring, and virus titre between SARS-CoV-2 infected K18-hACE2 mice pre-treated or post-treated with calcitriol were negligible, indicating that the differential effects of calcitriol may be due to differences in vitamin D metabolism in mice and warrants future investigation using other animal models.

Risk of mortality in COVID-19 patients: a meta- and network analysis

Understanding the most relevant hematological/biochemical characteristics, pre-existing health conditions and complications in survivors and non-survivor will aid in predicting COVID-19 patient mortality, as well as intensive care unit (ICU) referral and death. A literature review was conducted for COVID-19 mortality in PubMed, Scopus, and various preprint servers (bioRxiv, medRxiv and SSRN), with 97 observational studies and preprints, consisting of survivor and non-survivor sub-populations. This meta/network analysis comprised 19,014 COVID-19 patients, consisting of 14,359 survivors and 4655 non-survivors. Meta and network analyses were performed using META-MAR V2.7.0 and PAST software. The study revealed that non-survivors of COVID-19 had elevated levels of gamma-glutamyl transferase and creatinine, as well as a higher number of neutrophils. Non-survivors had fewer lymphocytes and platelets, as well as lower hemoglobin and albumin concentrations. Age, hypertension, and cerebrovascular disease were shown to be the most influential risk factors among non-survivors. The most common complication among non-survivors was heart failure, followed by septic shock and respiratory failure. Platelet counts, creatinine, aspartate aminotransferase, albumin, and blood urea nitrogen levels were all linked to ICU admission. Hemoglobin levels preferred non-ICU patients. Lower levels of hemoglobin, lymphocytes, and albumin were associated with increased mortality in ICU patients. This meta-analysis showed that inexpensive and fast biochemical and hematological tests, as well as pre-existing conditions and complications, can be used to estimate the risk of mortality in COVID-19 patients.

HIV and COVID-19 Disease

Despite effective antiretroviral therapy (ART), HIV infected individuals throughout the world remain at significant risk of respiratory infections and non-communicable disease. Severe disease from SARS-CoV-2 is associated with a hyperinflammatory phenotype which manifests in the lungs as pneumonia and in some cases can lead to acute respiratory failure. Progression to severe COVID-19 is associated with comorbid disease such as obesity, diabetes mellitus and cardiovascular disease, however data concerning the associated risks of HIV coinfection are still conflicting, with large population studies demonstrating poorer outcomes, whilst smaller, case-controlled studies showing better outcomes. Furthermore, underlying immunopathological processes within the lungs and elsewhere, including interactions with other opportunistic infections (OI), remain largely undefined. Nonetheless, new and repurposed anti-viral therapies and vaccines which have been developed are safe to use in this population, and anti-inflammatory agents are recommended with the caveat that the coexistence of opportunistic infections is considered and excluded. Finally, HIV infected patients remain reliant on good ART adherence practices to maintain HIV viral suppression, and some of these practices were disrupted during the COVID-19 pandemic, putting these patients at further risk for acute and long-term adverse outcomes.

A Practical Approach in Refining Binary Outcome for Treatment Effect of COVID-19 According to Geographical Diversity

The recent COVID-19 pandemic has drawn attention to health and economics worldwide. Initially, diseases only ravage local populations, while a pandemic could aggravate global economic burdens. Lopinavir/Ritonavir is an anti-HIV drug that was used on small scale patients during SARS, but its effectiveness for COVID-19 treatment is still unclear. Previous studies or meta-analysis have retrieved clinical data of subgroup analysis to evaluate the efficacy and safety of Lopinavir/Ritonavir for the treatment of COVID-19 in a few affected regions. However, geographical diversity and small number of studies bias correction were not achieved in such subgroup analysis of published meta-analysis. The present study demonstrates a practical approach in refining the binary outcome for COVID-19 treatment of Lopinavir/Ritonavir according to geographical location diversity and small number of studies (less than or equal to five) for subgroup analysis. After performing practical approach, the risk of adverse event with LPV/RTV for treatment of COVID-19 becomes nonsignificant compared to previous meta-analysis. Furthermore, we also notice heterogeneity of random effect of meta-analysis may be declined after proposed adjustment. In conclusion, proposed practical approach is recommend for performing a subgroup analysis to avoid concentration in a single geographical location and small number of studies bias.

Factors associated with prolonged viral shedding in older patients infected with Omicron BA.2.2

Background

This study explores the risk factors associated with viral shedding time in elderly Chinese patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) omicron.

Methods

Participants infected with SARS-CoV-2 omicron were enrolled in a retrospective study, and divided into two groups according to shedding time (≥10 days, "late clearance group" and <10 days, "early clearance group").

Results

A total of 180 patients were enrolled in the study (88 early, 92 late), with a median viral shedding time of 10 days and a mean age of 77.02 years. Prolonged SARS-CoV-2 omicron shedding was associated with old age (p = 0.007), lack of vaccination (p = 0.001), delayed admission to hospital after onset of diagnosis (p = 0.001), D-dimer (p = 0.003), and methylprednisolone treatment (p = 0.048). In multivariate analysis, vaccination (OR, 0.319, 95% CI, 0.130-0.786, p = 0.013), Paxlovid (OR, 0.259, 95% CI, 0.104-0.643, p = 0.004), and time from onset of diagnosis to admission (OR, 1.802, 95% CI, 1.391-2.355, p = 0.000) were significantly associated with viral clearance.

Conclusions

Time from onset of diagnosis to hospitalization, lack of treatment with Paxlovid, and lack of vaccination were independent risk factors in elderly Chinese patients infected with SARS-CoV-2 omicron for prolonged viral shedding.

Assessment of drugs administered in the Middle East as part of the COVID-19 management protocols

The pandemic spread of coronavirus (COVID-19) has been reported first at the end of 2019. It continues disturbing various human aspects with multiple pandemic waves showing more fatal novel variants. Now Egypt faces the sixth wave of the pandemic with controlled governmental measures. COVID-19 is an infectious respiratory disease-causing mild to moderate illness that can be progressed into life-threatening complications based on patients- and variant type-related factors. The symptoms vary from dry cough, fever to difficulty in breathing that required urgent hospitalization. Most countries have authorized their national protocols for managing manifested symptoms and thus lowering the rate of patients' hospitalization and boosting the healthcare systems. These protocols are still in use even with the development and approval of several vaccines. These protocols were instructed to aid home isolation, bed rest, dietary supplements, and additionally the administration of antipyretic, steroids, and antiviral drugs. The current review aimed to highlight the administered protocols in the Middle East, namely in Egypt and the Kingdom of Saudi Arabia demonstrating how these protocols have shown potential effectiveness in treating patients and saving many soles.

Vaccination, symptomatic infection and negative conversion of viral RNA by body mass index, diabetes, and age: An observational study

BACKGROUND

The associations of doses of vaccine received with symptomatic infection with SARS-CoV-2 and negative conversion rate of viral RNA by BMI, diabetes, and age are unclear.

METHODS

Included were adult cases of SARS-CoV-2 infection hospitalized at a makeshift hospital in Shanghai (N = 38,592). Each case received a real-time reverse transcriptase-polymerase chain reaction (RT-PCR) test every day until discharge. Symptomatic cases had ≥1 pre-specified symptoms. Negative conversion time (NCT) was the duration between the specimen collection date associated with the first positive RT-PCR test and the first test date of the two consecutive negative tests at least 24 h apart. BMI-, diabetes- and age-stratified multivariable logistic and Poisson regressions were applied.

FINDINGS

Coexistence of overweight/obesity and diabetes was associated with a higher risk of symptomatic infection and a longer NCT compared with coexistence of normal weight and without diabetes, but this association was primarily attributed to underlying comorbidities. Compared with absence of vaccination, booster vaccination, but not full vaccination, was consistently associated with a 42 %-56 % lower odds of symptomatic infection and ∼1.6-1.8 days of shorter NCT across different strata separately for weight and diabetes. Age-stratified analyses found that the effectiveness of booster vaccination did not attenuate with age, except for preventing symptomatic infection among adults with diabetes.

INTERPRETATION

BMI and diabetes co-determined their associations with symptomatic infection and NCT. Booster vaccination but not full vaccination was associated a lower risk of symptomatic infection, a shorter NCT or both regardless of BMI, diabetes status and age.

Enhanced inflammation and suppressed adaptive immunity in COVID-19 with prolonged RNA shedding

Little is known regarding why a subset of COVID-19 patients exhibited prolonged positivity of SARS-CoV-2 infection. Here, we found that patients with long viral RNA course (LC) exhibited prolonged high-level IgG antibodies and higher regulatory T (Treg) cell counts compared to those with short viral RNA course (SC) in terms of viral load. Longitudinal proteomics and metabolomics analyses of the patient sera uncovered that prolonged viral RNA shedding was associated with inhibition of the liver X receptor/retinoid X receptor (LXR/RXR) pathway, substantial suppression of diverse metabolites, activation of the complement system, suppressed cell migration, and enhanced viral replication. Furthermore, a ten-molecule learning model was established which could potentially predict viral RNA shedding period. In summary, this study uncovered enhanced inflammation and suppressed adaptive immunity in COVID-19 patients with prolonged viral RNA shedding, and proposed a multi-omic classifier for viral RNA shedding prediction.

Update March 2022: management of hospitalised adults with coronavirus disease-19 (COVID-19): a European Respiratory Society living guideline

Since the identification of SARS-CoV-2 at the end of 2019, the coronavirus disease 2019 (COVID-19) pandemic has affected more than 410 million people worldwide and killed almost 6 million [1, 2]. The predecessors of COVID-19, i.e. the SARS (severe acute respiratory syndrome) and MERS (Middle East respiratory syndrome) outbreaks, had been relatively self-limiting, preventing clinicians and researchers from establishing evidence-based specific therapeutic strategies [3]. Conversely, COVID-19 rapidly proved to be extremely fast spreading, which led stakeholders to encourage, guide, build or fund multidirectional therapeutic research strategies based on both repurposing and development of new agents [4–8]. In parallel, considerable efforts were directed at describing the disease and understanding the underlying mechanisms [9–13]. As a result, there has been a huge generation of evidence, as highlighted by the impressive number of COVID-19 publications (more than 200 000 since the end of 2019). As a consequence, it proved rapidly impossible for any clinician, researcher or decision-maker to gather and analyse all the corresponding literature to derive appropriate guidance [14]. The first step of such a process is to select the relevant high-quality research that can be used to answer the question(s) of interest [15]. Even if limiting the search to clinical trials, systematic reviews and meta-analyses, almost 4000 papers appear in the PubMed database, as of mid-February 2022. In June and July 2020, the European Respiratory Society (ERS) and the American Thoracic Society (ATS) released early guidance on several aspects of COVID-19 management (i.e. rehabilitation, palliative care and acute management); at that time, direct specific evidence was sparse or absent [16–18]. Simultaneously, the ERS launched a living guideline on the management of COVID-19. The format was that of a “short” guideline, as per ERS standards [19, 20], in that the purpose was to release the first iteration within 12 months. However, the number of PICO (Population, Intervention, Comparator, Outcomes) questions to be addressed (n=12) already exceeded markedly what the ERS considers as being feasible during such a short timeframe (i.e. n=1–2), which was a direct consequence of the high number of unanswered issues in the field of acute COVID-19 management, all corresponding to outstanding clinical needs. The first version of these guidelines was published in March 2021 and addressed the following potential therapeutic options: corticosteroids, interleukin (IL)-6 receptor antagonists, hydroxychloroquine, azithromycin and both combined, colchicine, lopinavir-ritonavir, remdesivir, interferon-β, anticoagulation and non-invasive ventilatory support [6, 21]. An update of the mortality meta-analyses for corticosteroids, hydroxychloroquine, azithromycin, remdesivir, anti-IL-6 monoclonal antibodies, colchicine, lopinavir/ritonavir and interferon-β was published in December 2021 [22].

The ERS COVID-19 guidelines make recommendations for corticosteroids, anti-IL-6 monoclonal antibodies, baricitinib, anticoagulation and non-invasive respiratory support for hospitalised patients with COVID-19 https://bit.ly/3QgHH7U

Duration of SARS-CoV-2 RNA positivity from various specimens and clinical characteristics in patients with COVID-19: a systematic review and meta-analysis

BACKGROUND

The duration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA positivity will be important to prevent the spread of coronavirus disease 2019 (COVID-19). A systematic review and meta-analysis were conducted following PRISMA to determine the duration from several parts of the body and clinical characteristics affecting it.

MAIN TEXT

PubMed, Web of Science, Scopus, and CENTRAL were searched for original studies reporting the duration from COVID-19 onset to the disappearance of viral RNA. Of the 1682 studies identified, 100 met the selection criteria and 13,431 patients were included in this study. The duration of SARS-CoV-2 RNA positivity was 18.29 [95% confidence interval: 17.00-19.89] days in the upper respiratory tract samples, 23.79 [20.43-27.16] days in the sputum, 14.60 [12.16-17.05] days in the blood, and 22.38 [18.40-26.35] days in the stool. Sensitivity analysis revealed that the duration was positively correlated with age, comorbidities, severity, and usage of glucocorticoid. Subgroup analysis indicated that the presence or absence of complications had the greatest impact on the difference in DSRP.

CONCLUSIONS

The duration of SARS-CoV-2 RNA positivity was 18.29 days in the upper respiratory tract samples. The duration in the sputum and the stool was longer, while that in the blood was shorter. The duration in the upper respiratory tract samples was longer in older, with any comorbidities, severer, and treated with glucocorticoid. These results provide the basic data for the duration of SARS-CoV-2 RNA positivity, and in the future, the effect of vaccination against SARS-CoV-2 and the SARS-CoV-2 variants on the duration of RNA positivity should be assessed.

Development of Evidence-Based COVID-19 Management Guidelines for Local Context: The Methodological Challenges

Background

The coronavirus disease 2019 (COVID-19) pandemic has presented as a therapeutic challenge for clinicians worldwide due to its rapid spread along with evolving evidence and understanding of the disease. Internationally, recommendations to guide the management of COVID-19 have been created and updated continuously by the WHO and CDC, which have been locally adapted by different countries. Similarly, Pakistan's National Command Operation Center (NCOC), in its national COVID-19 management strategy, generated guidelines for national implementation. Keeping the guidelines updated has proved challenging globally and locally. Here, we present a summary of the process to assess the evidence, including a time-restricted systematic review based on NCOC Clinical Management Guidelines for COVID-19 Infections v4 published on 11^th December 2020 version, correlating it with current recommendations and with input one of the guidelines authors, particularly noting the methodological challenges.

Methods

We conducted a systematic review synthesizing global research on treatment options for COVID-19 hospitalized patients, limiting it to pharmacological interventions for hospitalized COVID-19 patients included in Pakistan's NCOC's national guidelines v4 published on 11^th December 2020. Each treatment recommendation's strength and quality of evidence was assessed based on the grading of recommendations assessment, development, and evaluation (GRADE) methodology. These were then compared to the most current living WHO COVID-19 pharmacological treatment guidelines v7.1. One of the authors of the NCOC guidelines reviewed and commented on the findings as well.

Results

We note that the data from our systematic review strongly supports corticosteroids use in treating severe and critically ill COVID-19 hospitalized patients correlating with WHO v7.1 guidelines 24 September 2021. However, evidence from our review and WHO v7.1 for the use of tocilizumab had some conflicting evidence, with data from our review until December 2020 supporting only a weak recommendation for its use, compared to the strong recommendation by the WHO for the use of tocilizumab in patients with severe or critical COVID-19 infection. Regarding the use of antibiotics and ivermectin use in treating COVID-19 hospitalized patients, data from our review and WHO v 7.1 recommend against their use.

Conclusion

Research data about the efficacy and safety of pharmacological interventions to treat hospitalized patients with COVID-19 are rapidly evolving, and based on it, the evidence for or against recommendations changes accordingly. Our study illustrates the challenges of keeping up with the evidence; the recommendations were based on studies up till December 2021, and we have compared our recommendations with the WHO v7.1, which showed some significant changes in the use of pharmacological treatment options.

Antiviral Used among Non-Severe COVID-19 Cases in Relation to Time till Viral Clearance: A Retrospective Cohort Study

(1) Background: The WHO identified COVID-19 as a fast-growing epidemic worldwide. A few antivirals have shown promising effectiveness in treating COVID-19. This study aimed to assess the correlation between antiviral drugs and the time until viral clearance of SARS-CoV-2. (2) Methods: This was a retrospective cohort study that included 1731 non-severe COVID-19 patients treated in NMC Royal Hospital, UAE. (3) Results: A total of 1446 patients received symptomatic treatment only (mean age of 35.6 ± 9.0 years). The analyzed antiviral treatment protocols were azithromycin, hydroxychloroquine, lopinavir/ritonavir, and favipiravir. The produced Kaplan–Meier plots showed no significant differences in the time until viral clearance among the compared protocols, which showed overlapping confidence intervals, which were determined by performing the log-rank and adjusted pairwise log-rank tests (p = 0.2, log-rank = 9.3). The age and gender of patients did not significantly affect the rate of viral clearance regardless of the antiviral therapy administered, even when compared to patients who received symptomatic treatment only, with the exception of hydroxychloroquine (HCQ), azithromycin, and favipiravir, which increased the odds of a faster rate of viral clearance by 46% after adjustments. (4) Conclusions: No significant differences were observed regarding the time until viral clearance among non-severe COVID-19 patients following the prescription of different antiviral drugs.

RT- PCR testing of upper respiratory tract samples for diagnosis of SARS-CoV-2: Between justification and overestimation, a multi-center international study

Background

It has been found that patients recovered from COVID 19 may still test Reverse Transcriptase- Polymerase Chain Reaction (RT- PCR) positive without being infectious; the reasons are unclear. The occurrence of false-negative results of RT- PCR interferes with a proper diagnosis. The objectives of that work were to determine factors associated with persistently detectable SARS-CoV-2 RNA among recovered hospitalized patients and to determine the incidence of false-negative RT-PCR results and associated factors.

Methods

Relevant data were collected from 482 COVID 19 patients hospitalized in six referral centers from four countries.

Results

The median duration of RT- PCR conversion to negative was 20 days. Out of 482 studied patients, 8.7% tested positive after more than four weeks and were considered prolonged convertors. Binary logistic regression analysis revealed headache as an independent risk factor for short conversion time while fever, hypertension, chronic obstructive pulmonary disease, lymphopenia, elevated erythrocyte sedimentation rate, and the number of lobes affected, and bilateralism were found to be independent risk factors for prolonged positivity. Eighteen patients had initial negative results then turned positive after 24–48 h. Associated factors and outcomes were identified.

Conclusion

Identifying patients with a high likelihood of COVID-19 despite a negative RT-PCR is critical for effective clinical care. However, patient isolation resumption depending on positive RT-PCR despite clinical and radiological recovery is an overrating that greatly burdens the health sector.

Just breathe: a review of sex and gender in chronic lung disease

Chronic lung diseases are the third leading cause of death worldwide and are increasing in prevalence over time. Although much of our traditional understanding of health and disease is derived from study of the male of the species - be it animal or human - there is increasing evidence that sex and gender contribute to differences in disease risk, prevalence, presentation, severity, treatment approach, response and outcomes. Chronic obstructive pulmonary disease, asthma and bronchiectasis represent the most prevalent and studied chronic lung diseases and have key sex- and gender-based differences which are critical to consider and incorporate into clinical and research approaches. Mechanistic differences present opportunities for therapeutic development whereas behavioural and clinical differences on the part of patients and providers present opportunities for greater education and understanding at multiple levels. In this review, we seek to summarise the sex- and gender-based differences in key chronic lung diseases and outline the clinical and research implications for stakeholders.

Prolonged fecal shedding of SARS-CoV-2 in a young immunocompetent COVID-19 patient: a case report and literature overview

Clinicians are facing several challenges in tackling coronavirus disease 2019 (COVID‐19); one issue is prolonged detection of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) RNA. Here, we describe a case of SARS‐CoV‐2 infection in a young immunocompetent patient with a virological course lasting for 71 days. Following antiviral treatment, but no additional glucocorticoid or interferon therapy, the patient recovered from COVID‐19 pneumonia (moderate). Detection of viral RNA via throat swabs showed negative results. However, the viral RNA reappeared and persisted in stool samples for an additional 27 days, while the patient remained asymptomatic and exhibited no abnormal signs. This case indicates that SARS‐CoV‐2 can result in a prolonged fecal RNA shedding, even in an immunocompetent patient with zero exposure to immunosuppressive therapies.

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.

Gastrointestinal and hepatic side effects of potential treatment for COVID-19 and vaccination in patients with chronic liver diseases

The outbreak of coronavirus disease 2019 (COVID-19) is a global pandemic. Many clinical trials have been performed to investigate potential treatments or vaccines for this disease to reduce the high morbidity and mortality. The drugs of higher interest include umifenovir, bromhexine, remdesivir, lopinavir/ritonavir, steroid, tocilizumab, interferon alpha or beta, ribavirin, fivapiravir, nitazoxanide, ivermectin, molnupiravir, hydroxychloroquine/chloroquine alone or in combination with azithromycin, and baricitinib. Gastrointestinal (GI) symptoms and liver dysfunction are frequently seen in patients with COVID-19, which can make it difficult to differentiate disease manifestations from treatment adverse effects. GI symptoms of COVID-19 include anorexia, dyspepsia, nausea, vomiting, diarrhea and abdominal pain. Liver injury can be a result of systemic inflammation or cytokine storm, or due to the adverse drug effects in patients who have been receiving different treatments. Regular monitoring of liver function should be performed. COVID-19 vaccines have been rapidly developed with different technologies including mRNA, viral vectors, inactivated viruses, recombinant DNA, protein subunits and live attenuated viruses. Patients with chronic liver disease or inflammatory bowel disease and liver transplant recipients are encouraged to receive vaccination as the benefits outweigh the risks. Vaccination against COVID-19 is also recommended to family members and healthcare professionals caring for these patients to reduce exposure to the severe acute respiratory syndrome coronavirus 2 virus.

Recent Advancements on COVID-19: A Comprehensive Review

Over the last few decades, there have been several global outbreaks of severe respiratory infections. The causes of these outbreaks were coronaviruses that had infected birds, mammals and humans. The outbreaks predominantly caused respiratory tract and gastrointestinal tract symptoms and other mild to very severe clinical signs. The current coronavirus disease-2019 (COVID-19) outbreak, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a rapidly spreading illness affecting millions of people worldwide. Among the countries most affected by the disease are the United States of America (USA), India, Brazil, and Russia, with France recording the highest infection, morbidity, and mortality rates. Since early January 2021, thousands of articles have been published on COVID-19. Most of these articles were consistent with the reports on the mode of transmission, spread, duration, and severity of the sickness. Thus, this review comprehensively discusses the most critical aspects of COVID-19, including etiology, epidemiology, pathogenesis, clinical signs, transmission, pathological changes, diagnosis, treatment, prevention and control, and vaccination.

Efficacy of lopinavir-ritonavir combination therapy for the treatment of hospitalized COVID-19 patients: a meta-analysis

Aim: To evaluate the efficacy and safety of lopinavir-ritonavir (LPV/r) therapy in treating hospitalized COVID-19 patients. Materials & methods: Data from randomized and observational studies were included in meta-analyses. Primary outcomes were length of stay, time for SARS-CoV-2 test conversion, mortality, incidence of mechanical ventilation, time to body temperature normalization and incidence of adverse events. Results: Twenty-four studies (n = 10,718) were included. LPV/r demonstrated no significant benefit over the control groups in all efficacy outcomes. The use of LPV/r was associated with a significant increase in the odds of adverse events. Conclusion: Given the lack of efficacy and increased incidence of adverse events, the clinical use of LPV/r in hospitalized COVID-19 patients is not recommended.

Repurposed pharmacological agents for the potential treatment of COVID-19: a literature review

Background

The COVID-19 pandemic has affected the world extraordinarily. This disease has a potential to cause a significantly severe course of disease leading to respiratory complications, multiple organ failure and possibly death. In the fight against this pandemic-causing disease, medical professionals around the world are searching for pharmacological agents that could treat and prevent disease progression and mortality. To speed the search of promising treatment options, already existing pharmacological agents are repurposed for the potential treatment of COVID-19 and tested in clinical trials. The aim of this literature review is to investigate the efficacy and safety of repurposed pharmacological agents for the treatment of COVID-19 at different pathophysiologic stages of the disease. For this literature review, online-databases PubMed and Google Scholar were utilised. Keywords “COVID-19”, “SARS-CoV-2”, “pathogenesis”, “drug targets”, “pharmacological treatment”, “cytokine storm”, “coagulopathy” and individual drug names were used. Scientific articles, including reviews, clinical trials, and observational cohorts, were collected and analysed. Furthermore, these articles were examined for references to find more clinical trials testing for the potential treatment of COVID-19. In total, 97 references were used to conduct this research paper.

Results

The most beneficial pharmacological agent for the treatment of COVID-19 are corticosteroids, especially dexamethasone, for the treatment of mechanically ventilated COVID-19 patients. Other promising agents are remdesivir for the treatment of patients with COVID-19 pneumonia requiring minimal supplemental oxygen therapy, and IL-6 receptor antagonist monoclonal antibodies in severe COVID-19. Lopinavir/ritonavir, as well as chloroquine or hydroxychloroquine with or without azithromycin demonstrate the least efficacy in the treatment of COVID-19. The clinical benefits of the treatment of a COVID-19-specific coagulopathy with increased dosing of anticoagulation need further research and confirmation of randomised controlled trials.

Conclusion

The search for pharmacological treatment of COVID-19 has elicited great controversy. Whereas drugs like chloroquine, hydroxychloroquine, and lopinavir/ritonavir have not shown proven benefit, the agents remdesivir and dexamethasone are recommended for clinical use for the treatment of COVID-19. Further randomised trials for other pharmacological treatment strategies are awaited.

COVID-19 Advanced Care

The coronavirus disease 2019 (COVID-19) pandemic, related to the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a worldwide sudden and substantial burden in public health due to an enormous increase in hospitalizations for pneumonia with the multiorgan disease. Treatment for individuals with COVID-19 includes best practices for supportive management of acute hypoxic respiratory failure. Emerging data indicate that dexamethasone therapy reduces 28-day mortality in patients requiring supplemental oxygen compared with usual care, and ongoing trials are testing the efficacy of antiviral therapies, immune modulators and anticoagulants in the prevention of disease progression and complications, while monoclonal antibodies and hyperimmune globulin may provide additional preventive strategies. Consensus suggestions can standardize care, thereby improving outcomes and facilitating future research. This review discusses current evidence regarding the pharmacotherapy of COVID-19.

Recurrent SARS-CoV-2 RNA positivity and prolonged viral shedding in a patient with COVID-19: a case report

Background

The ongoing coronavirus disease 2019 (COVID-19) global pandemic caused by the SARS-CoV-2 virus remains a major threat to public health. At present, it is recommended that patients with known or suspected COVID-19 undergo quarantine or medical observation for 14 days. However, recurrent SARS-CoV-2 RNA positivity and prolonged viral shedding have been documented in convalescent COVID-19 patients, complicating efforts to control viral spread and ensure patient recovery.

Case presentation

We report the case of a patient who experienced two recurrent episodes of SARS-CoV-2 RNA and IgM positivity and viral shedding over 60 days during hospitalization.

Conclusions

This case report demonstrates that relapses of SARS-CoV-2 RNA and IgM positivity may occur even after COVID-19 symptoms have resolved, possibly as a consequence of prolonged viral shedding rather than re-infection.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-06776-3.

Association between glucocorticoids treatment and viral clearance delay in patients with COVID-19: a systematic review and meta-analysis

BACKGROUND

Evidence of glucocorticoids on viral clearance delay of COVID-19 patients is not clear.

METHODS

In this systematic review and meta-analysis, we searched for studies on Medline, Embase, EBSCO, ScienceDirect, Web of Science, Cochrane Library, and ClinicalTrials.gov from 2019 to April 20, 2021. We mainly pooled the risk ratios (RRs) and mean difference (MD) for viral clearance delay and did subgroup analyses by the severity of illness and doses of glucocorticoids.

RESULTS

38 studies with a total of 9572 patients were identified. Glucocorticoids treatment was associated with delayed viral clearance in COVID-19 patients (adjusted RR 1.52, 95% CI 1.29 to 1.80, I2 = 52%), based on moderate-quality evidence. In subgroup analyses, risk of viral clearance delay was significant both for COVID-19 patients being mild or moderate ill (adjusted RR 1.86, 95% CI 1.35 to 2.57, I2 = 48%), and for patients of being severe or critical ill (adjusted RR 1.59, 95% CI 1.23 to 2.07, I2 = 0%); however, this risk significantly increased for patients taking high doses (unadjusted RR 1.85, 95% CI 1.08 to 3.18; MD 7.19, 95% CI 2.78 to 11.61) or medium doses (adjusted RR 1.86, 95% CI 0.96 to 3.62, I2 = 45%; MD 3.98, 95% CI 3.07 to 4.88, I2 = 4%), rather those taking low doses (adjusted RR 1.38, 95% CI 0.94 to 2.02, I2 = 59%; MD 1.46, 95% CI -0.79 to 3.70, I2 = 82%).

CONCLUSIONS

Glucocorticoids treatment delayed viral clearance in COVID-19 patients of taking high doses or medium doses, rather in those of taking low doses of glucocorticoids.

Elaboration of a Radiomics Strategy for the Prediction of the Re-positive Cases in the Discharged Patients With COVID-19

Objective: A considerable part of COVID-19 patients were found to be re-positive in the SARS-CoV-2 RT-PCR test after discharge. Early prediction of re-positive COVID-19 cases is of critical importance in determining the isolation period and developing clinical protocols. Materials and Methods: Ninety-one patients discharged from Wanzhou Three Gorges Central Hospital, Chongqing, China, from February 10, 2020 to March 3, 2020 were administered nasopharyngeal swab SARS-CoV-2 tests within 12-14 days, and 50 eligible patients (32 male and 18 female) with completed data were enrolled. Average age was 48 ± 11.5 years. All patients underwent non-enhanced chest CT on admission. A total of 568 radiomics features were extracted from the CT images, and 17 clinical factors were collected based on the medical record. Student's t-test and support vector machine-based recursive feature elimination (SVM-RFE) method were used to determine an optimal subset of features for the discriminative model development. Results: After Student's t-test, 62 radiomics features showed significant inter-group differences (p < 0.05) between the re-positive and negative cases, and none of the clinical features showed significant differences. These significant features were further selected by SVM-RFE algorithm, and a more compact feature subset containing only two radiomics features was finally determined, achieving the best predictive performance with the accuracy and area under the curve of 72.6% and 0.773 for the identification of the re-positive case. Conclusion: The proposed radiomics method has preliminarily shown potential in identifying the re-positive cases among the recovered COVID-19 patients after discharge. More strategies are to be integrated into the current pipeline to improve its precision, and a larger database with multi-clinical enrollment is required to extensively verify its performance.

Median duration and factors that influence the duration of symptom resolution in COVID-19 patients in Ethiopia: A follow-up study involving symptomatic cases

Background

Understanding the clinical features of COVID-19 and duration for resolution of symptoms is crucial for isolation of patients and tailoring public health messaging, interventions and policy. Therefore, this study aims to assess the median duration of COVID-19 signs and symptoms' resolution and explore its predictors among symptomatic COVID-19 patients in Ethiopia.

Methods

A hospital-based prospective cohort study involving 124 COVID-19 cases was conducted at Eka Kotebe General Hospital, COVID-19 Isolation and Treatment Center. The study participants were all symptomatic COVID-19 adult patients admitted to the hospital from 18 March to 20 August 2020. Physicians at the centre recorded the data using a log sheet. Cox proportional-hazards regression model was conducted. Statistical significance was defined at P < 0.05.

Results

A total of 124 symptomatic COVID-19 patients with a mean age of 42 years (±17) were involved in the study. The median duration of symptom resolution of COVID-19 was seven days with a minimum of two and a maximum of sixty-eight days. Sex and body mass index (BMI) were statistically significant predictors of the symptom resolution. The hazard of having delayed sign or symptom resolution in males was 55% higher than in females (P = 0.039; CI: 0.22-0.96) and the hazard of delayed sign or symptom resolution in those with BMI ≥ 25 kg/m2 was 35% higher than in those with BMI < 25 kg/m2 (P = 0.041; CI: 0.44-0.98]).

Conclusions

The median duration of COVID-19 symptom resolution was seven days. Being male and/or having a BMI ≥ 25 kg/m2 were predictors of a delayed sign or symptom resolution time. Therefore, it is important to consider proportion of males and those with BMI ≥ 25 kg/m2 when preparing isolation and treatment centres. Males and individuals with BMI ≥ 25 kg/m2 shall also be given priority when shielding from the COVID-19.

Prolonged SARS-Cov-2 shedding with rapid IgG antibody decay in a COVID-19 patient: A case report

Background

The coronavirus disease 2019 (COVID‐19) epidemic is still spreading rapidly around the world. Recent cases with prolonged severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) RNA detection have been successively reported, and the phenomenon of false‐negative real‐time polymerase chain reaction (RT‐PCR) results of SARS‐CoV‐2 RNA or “repositive” was also described in COVID‐19 patients.

Methods

We report a 69‐year‐old female patient with hypertension, suspected lung tumor, and previous history of total hysterectomy for hysteromyoma who presented with moderate COVID‐19 symptoms and was positive for SARS‐CoV‐2 RNA by RT‐PCR when she traveled from the USA to China.

Results

The patient required second and third re‐hospitalizations due to “repositive” SARS‐CoV‐2 throat swab test results during post‐charge solitary isolation and observation, and serum SARS‐CoV‐2‐IgG decayed rapidly before disappearing on illness Day 139 when the throat swab was still positive. The virus shedding lasted for at least 146 days (the last positive throat swab test result was on illness Day 146, and the first true‐negative test result was on illness Day 151) since her initial positive test.

Conclusion

Prolonged SARS‐CoV‐2 RNA viral shedding is prone to occur in an immunocompromised host, wherein changes in the host immune status can lead to repeated positive SARS‐CoV‐2 detection. Moreover, the SARS‐CoV‐2‐IgG may decrease rapidly and disappear before virus removal, indicating there may be certain limitations on the protective effect of the SARS‐CoV‐2 antibody, which deserves clinical attention.

Drug repurposing in COVID-19: A review with past, present and future

The coronavirus SARS-CoV-2 which causes the COVID-19 disease is a global public health emergency. Coronavirus are single-stranded positive-sense RNA viruses and their genome size is approximately 30 kb, which encodes some important structural proteins. The interaction between viral Spike protein and ACE2 on the host cell surface is of significant interest since it initiates the infection process. This review will focus on the effectiveness of reuse of currently used drugs against COVID-19, including clinical trials, molecular docking, and computational modelling approach.

Methods

A systematic search in Pubmed, MEDLINE, EMBASE was conducted from from January 2020 to July 2021.

Applying computational, clinical and experimental approaches, numerous drugs such as remdesivir, favipiravir, ribavirin, lopinavir, ritonavir, tocilizumab have been repurposed and have shown promising protection against SARS-CoV2 both in vitro and in clinical conditions. Although there is only one repurposed drug approved by the U.S. Food and Drug Administration (FDA) to treat coronavirus disease 2019 (COVID-19), i.e, Remdesivir. However, the FDA withdrew the authorization of the drugs Hydroxychloroquine and chloroquine,that are not effective for COVID-19 and can also cause serious heart problems. Molecular coupling would be the ideal technique to identify such therapeutic agents against COVID19.

Risk factors for prolonged virus shedding of respiratory tract and fecal in adults with severe acute respiratory syndrome coronavirus-2 infection

BACKGROUND

The dynamic alteration and comparative study of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA shedding pattern during treatment are limited. This study explores the potential risk factors influencing prolonged viral shedding in COVID-19.

METHODS

A total of 126 COVID-19 patients were enrolled in this retrospective longitudinal study. A multivariate logistic regression analysis was carried out to estimate the potential risk factors.

RESULTS

38.1% (48/126) cases presented prolonged respiratory tract viral shedding, and 30 (23.8%) cases presented prolonged rectal swab viral shedding. Obesity (OR, 3.31; 95% CI, 1.08-10.09), positive rectal swab (OR, 3.43; 95% CI, 1.53-7.7), treatment by lopinavir/ritonavir with chloroquine phosphate (OR, 2.5; 95% CI, 1.04-6.03), the interval from onset to antiviral treatment more than 7 days (OR, 2.26; 95% CI, 1.04-4.93), lower CD4+ T cell (OR, 0.92; 95% CI, 0.86-0.99) and higher NK cells (OR, 1.11; 95% CI, 1.02-1.20) were significantly associated with prolonged respiratory tract viral shedding. CD3-CD56+ NK cells (OR, 0.87; 95% CI, 0.76-0.99) were related with prolonged fecal shedding.

CONCLUSIONS

Obesity, delayed antiviral treatment, and positive SARS-CoV-2 for stool were independent risk factors for prolonged SARS-CoV-2 RNA shedding of the respiratory tract. A combination of LPV/r and abidol as the initial antiviral regimen was effective in shortening the duration of viral shedding compared with LPV/r combined with chloroquine phosphate. CD4+ T cell and NK cells were significantly associated with prolonged viral shedding, and further studies are to be warranted to determine the mechanism of immunomodulatory response in virus clearance.

Comprehensive Consensus Analysis of SARS-CoV-2 Drug Repurposing Campaigns

The current COVID-19 pandemic has elicited extensive repurposing efforts (both small and large scale) to rapidly identify COVID-19 treatments among approved drugs. Herein, we provide a literature review of large-scale SARS-CoV-2 antiviral drug repurposing efforts and highlight a marked lack of consistent potency reporting. This variability indicates the importance of standardizing best practices-including the use of relevant cell lines, viral isolates, and validated screening protocols. We further surveyed available biochemical and virtual screening studies against SARS-CoV-2 targets (Spike, ACE2, RdRp, PLpro, and Mpro) and discuss repurposing candidates exhibiting consistent activity across diverse, triaging assays and predictive models. Moreover, we examine repurposed drugs and their efficacy against COVID-19 and the outcomes of representative repurposed drugs in clinical trials. Finally, we propose a drug repurposing pipeline to encourage the implementation of standard methods to fast-track the discovery of candidates and to ensure reproducible results.

Smoking is associated with worse outcomes of COVID-19 particularly among younger adults: a systematic review and meta-analysis

BACKGROUND

Smoking impairs lung immune function and damages upper airways, increasing risks of contracting and severity of infectious diseases. This paper quantifies the association between smoking and COVID-19 disease progression.

METHODS

We searched PubMed and Embase for studies published from January 1-May 25, 2020. We included studies reporting smoking behavior of COVID-19 patients and progression of disease, including death. We used random effects meta-analysis, meta-regression and locally weighted regression and smoothing to examine relationships in the data.

RESULTS

We identified 46 peer-reviewed papers with a total of 22,939 COVID-19 patients, 5421 (23.6%) experienced disease progression and 2914 (12.7%) with a history of smoking (current and former smokers). Among those with a history of smoking, 33.5% experienced disease progression, compared with 21.9% of non-smokers. The meta-analysis confirmed an association between ever smoking and COVID-19 progression (OR 1.59, 95% CI 1.33-1.89, p = 0.001). Ever smoking was associated with increased risk of death from COVID-19 (OR 1.19, 95% CI 1.02-1.39, p = 0.003). We found no significant difference (p = 0.864) between the effects of ever smoking on COVID-19 disease progression between adjusted and unadjusted analyses, suggesting that smoking is an independent risk factor for COVID-19 disease progression. We also found the risk of having COVID-19 progression higher among younger adults (p = 0.001), with the effect most pronounced among younger adults under about 45 years old.

CONCLUSIONS

Smoking is an independent risk for having progression of COVID-19, including mortality. The effects seem to be higher among young people. Smoking prevention and cessation should remain a priority for the public, physicians, and public health professionals during the COVID-19 pandemic.

Antiviral Therapeutic Approaches for SARS-CoV-2 Infection: A Systematic Review

Due to the lack of an etiologic treatment for SARS-CoV-2 and the difficulties involved in developing new drugs, some drugs already approved for other diseases or with efficacy against SARS and MERS, have been used in patients with COVID-19. This systematic review aims to summarize evidence on the efficacy and safety of five antivirals applied to patients with COVID-19, that have proven to be effective either in vitro studies or in studies on SARS-CoV and MERS.; An intensive search of different databases (Pub Med, WoS, MEDLINE and Cochrane COVID-19 Study Register) has been carried out until the end of April 2021. This systematic review has been conducted according to the PRISMA statement. From each of the included studies, the characteristics of the intervention and comparison groups, demographic data and results were extracted independently; Remdesivir is well tolerated and helps to accelerate clinical improvement but is ineffective in reducing mortality. Favipiravir is safe and shows promising results regarding symptom resolution but does not improve viral clearance. The use of lopinavir/ritonavir has been associated with an increased risk of gastrointestinal adverse events and it has not proven to be effective. No significant differences were observed between patients treated with ribavirin or umifenovir and their respective control groups; Remdesivir and favipiravir are well tolerated and effective in accelerating clinical improvement. This systematic review does not support the use of lopinavir/ritonavir, ribavirin and umifenovir in hospitalized patients with COVID-19.

Antiviral Drug Delivery System for Enhanced Bioactivity, Better Metabolism and Pharmacokinetic Characteristics

Antiviral drugs (AvDs) are the primary resource in the global battle against viruses, including the recent fight against corona virus disease 2019 (COVID-19). Most AvDs require multiple medications, and their use frequently leads to drug resistance, since they have poor oral bioavailability and low efficacy due to their low solubility/low permeability. Characterizing the in vivo metabolism and pharmacokinetic characteristics of AvDs may help to solve the problems associated with AvDs and enhance their efficacy. In this review of AvDs, we systematically investigated their structure-based metabolic reactions and related enzymes, their cellular pharmacology, and the effects of metabolism on AvD pharmacodynamics and pharmacokinetics. We further assessed how delivery systems achieve better metabolism and pharmacology of AvDs. This review suggests that suitable nanosystems may help to achieve better pharmacological activity and pharmacokinetic behavior of AvDs by altering drug metabolism through the utilization of advanced nanotechnology and appropriate administration routes. Notably, such AvDs as ribavirin, remdesivir, favipiravir, chloroquine, lopinavir and ritonavir have been confirmed to bind to the severe acute respiratory syndrome-like coronavirus (SARS-CoV-2) receptor and thus may represent anti-COVID-19 treatments. Elucidating the metabolic and pharmacokinetic characteristics of AvDs may help pharmacologists to identify new formulations with high bioavailability and efficacy and help physicians to better treat virus-related diseases, including COVID-19.

Detection and viral RNA shedding of SARS-CoV-2 in respiratory specimens relative to symptom onset among COVID-19 patients in Bavaria, Germany

We assessed severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) reverse transcriptase-polymerase chain reaction (RT-PCR) diagnostic sensitivity and cycle threshold (Ct) values relative to symptom onset in symptomatic coronavirus disease-2019 (COVID-19) patients from Bavaria, Germany, of whom a subset was repeatedly tested. Locally weighted scatterplot smoothing method was used to assess the relationship between symptom onset and Ct-values. Kaplan−Meier plots were used to visualise the empirical probability of detecting viral ribonucleic acid (RNA) over time and estimate the time until clearance of viral RNA among the repeatedly tested patients. Among 721 reported COVID-19 cases, the viral RNA was detected in specimens taken between three days before and up to 48 days after symptom onset. The mean Ct-value was 28.6 (95% confidence interval (CI) 28.2–29.0) with the lowest mean Ct-value (26.2) observed two days after symptom onset. Up to 7 days after symptom onset, the diagnostic sensitivity of the RT-PCR among repeatedly sampled patients (n = 208) remained above 90% and decreased to 50% at day 12 (95% CI 10.5–21.5). Our data provide valuable estimates to optimise the timing of sampling of individuals for SARS-CoV-2 detection. A considerable proportion of specimens sampled before symptom onset had Ct-values comparable with Ct-values after symptom onset, suggesting the probability of presymptomatic transmission.

SARS-CoV-2 Viral Shedding and Transmission Dynamics: Implications of WHO COVID-19 Discharge Guidelines

The evolving nature of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has necessitated periodic revisions of COVID-19 patient treatment and discharge guidelines. Since the identification of the first COVID-19 cases in November 2019, the World Health Organization (WHO) has played a crucial role in tackling the country-level pandemic preparedness and patient management protocols. Among others, the WHO provided a guideline on the clinical management of COVID-19 patients according to which patients can be released from isolation centers on the 10th day following clinical symptom manifestation, with a minimum of 72 additional hours following the resolution of symptoms. However, emerging direct evidence indicating the possibility of viral shedding 14 days after the onset of symptoms called for evaluation of the current WHO discharge recommendations. In this review article, we carried out comprehensive literature analysis of viral shedding with specific focus on the duration of viral shedding and infectivity in asymptomatic and symptomatic (mild, moderate, and severe forms) COVID-19 patients. Our literature search indicates that even though, there are specific instances where the current protocols may not be applicable ( such as in immune-compromised patients there is no strong evidence to contradict the current WHO discharge criteria.

Efficacy and safety of antivirals for Covid-19: A systematic review and meta-analysis

Background

Coronavirus disease 2019 (Covid-19) has led to a severe medical, social and economic crisis globally. Use of antivirals has given inconsistent results; thus systematic summaries of available evidence are required for any recommendations for treatment. We conducted a systematic review and meta-analysis on the use of antivirals for Covid-19.

Methods

The databases we searched were-Medline, Embase, Cochrane CENTRAL and Medrxiv. Title/abstract screening, full-text screening and data abstraction were carried out in duplicate by two researchers. Pooled effect sizes and 95% confidence intervals (CI) were calculated using the Mantel-Haenszel method of random effects for meta-analysis.

Results

Twenty studies were found eligible for inclusion: 6 randomized controlled trials, 9 cohort studies and 5 case series. Moderate-quality evidence suggests a likely clinical benefit from the use of remdesivir in improving the number of recoveries (RR 1.18; 95% CI 1.07-1.31; I² = 0%) and time to recovery in days (median -3.02; 95% CI -4.98 to -1.07; I² = 97%). A possibility of lower mortality is suggested by low-quality evidence with remdesivir (RR 0.74; 95% CI 0.40-1.37, I² = 58%). Moderate-quality evidence suggests no certain benefit of using lopinavir/ritonavir for Covid-19 compared to arbidol, lopinavir/ritonavir combined with arbidol or other medications used as controls.

Conclusion

Further evidence from randomized controlled trials is required for all antivirals to treat Covid-19. At present, remdesivir seems more promising than other antivirals.

Pharmacological considerations for the treatment of COVID-19 in people living with HIV (PLWH)

INTRODUCTION

When coronavirus infectious disease-2019 (COVID-19) blew up, ill-fated auguries on the collision between COVID-19 and the human immunodeficiency virus (HIV) epidemics loomed.

AREAS COVERED

Data from observational studies suggest similar incidence attacks of SARS-CoV-2 infection in people living with HIV (PLWH) and HIV-uninfected populations. The mortality rate of COVID-19 is similar in both populations too. The authors discuss the role of combination antiretroviral therapy (cART) in preventing infection or reducing COVID-19 severity. They also discuss the pharmacological interventions for COVID-19 in PLWH.

EXPERT OPINION

Management of COVID-19 in PLWH is no different from the general population. It should be based on careful supportive care, emphasizing lung-protective ventilation, and wise pharmacological interventions. The antiviral drug remdesivir and dexamethasone are the only pharmacological interventions with clinical benefit for COVID-19, whereas anticoagulation may prevent thrombotic complications. The experience with using these drugs in PLWH is limited, which prevents from rendering well-founded conclusions. Until more data on COVID-19 in PLWH become available, the best weapons within our reach are sound supportive care and sensible use of RDV and dexamethasone, bearing in mind the potential for drug-drug interactions of most corticosteroids and antiretroviral drugs.

Prolonged SARS-CoV2 Viral Shedding in an Elderly Patient

Coronavirus disease 2019 (COVID-19) has been devastating to the elderly population, especially due to a lack of clear guidelines for treatment. Corticosteroids have been the mainstay in treating the cytokine storm caused by the virus. In the past, prolonged viral shedding of Middle East Respiratory Syndrome (MERS) was noted in patients treated with high-dose corticosteroids. It is unclear whether this also holds true for severe acute respiratory syndrome coronavirus (SARS-CoV2). To our knowledge, this case report highlights the longest reported disease course of SARS-CoV2, lasting approximately 210 days.