A follow-up study shows that recovered patients with re-positive PCR test in Wuhan may not be infectious

Ensuring accuracy in the development and application of nucleic acid amplification tests (NAATs) for infectious disease

Diagnostic tests were heralded as crucial during the Coronavirus disease (COVID-19) pandemic with most of the key methods using bioanalytical approaches that detected larger molecules (RNA, protein antigens or antibodies) rather than conventional clinical biochemical techniques. Nucleic Acid Amplification Tests (NAATs), like the Polymerase Chain Reaction (PCR), and other molecular methods, like sequencing (that often work in combination with NAATs), were essential to the diagnosis and management during COVID-19. This was exemplified both early in the pandemic but also later on, following the emergence of new genetic SARS-CoV-2 variants. The 100 day mission to respond to future pandemic threats highlights the need for effective diagnostics, therapeutics and vaccines. Of the three, diagnostics represents the first opportunity to manage infectious diseases while also being the most poorly supported in terms of the infrastructure needed to demonstrate effectiveness. Where performance targets exist, they are not well served by consensus on how to demonstrate they are being met; this includes analytical factors such as limit of detection (LOD) false positive results as well as how to approach clinical evaluation. The selection of gold standards or use of epidemiological factors such as predictive value, reference ranges or clinical thresholds are seldom correctly considered. The attention placed on molecular diagnostic tests during COVID-19 illustrates important considerations and assumptions on the use of these methods for infectious disease diagnosis and beyond. In this manuscript, we discuss state-of-the-art approaches to diagnostic evaluation and explore how they may be better tailored to diagnostic techniques like NAATs to maximise the impact of these highly versatile bioanalytical tools, both generally and during future outbreaks.

Epidemiological contemplation for a currently pragmatic COVID-19 health passport: a perspective

The coronavirus disease 2019 (COVID-19) has caused a global pandemic that has wreaked havoc on the lives of millions of people around the world. Confinement measures aim to reduce the epidemic's spread and minimize the burden of morbidity and mortality. In response to the challenges caused by the pandemic, digital health passports have been developed exponentially. We highlight the latent epidemiological barriers to health passports to achieve standardized digital care platforms. This review paper not only highlights the epidemiological barriers but also articulates the possible infrastructure required to make the International Standard for a multi-factor authenticated and validated health passport.

Validating saliva as a biological sample for cost-effective, rapid and routine screening for SARS-CoV-2

PURPOSE

Compared to nasopharyngeal/oropharyngeal swabs (N/OPS-VTM), non-invasive saliva samples have enormous potential for scalability and routine population screening of SARS-CoV-2. In this study, we investigate the efficacy of saliva samples relative to N/OPS-VTM for use as a direct source for RT-PCR based SARS-CoV-2 detection.

METHODS

We collected paired nasopharyngeal/oropharyngeal swabs and saliva samples from suspected positive SARS-CoV-2 patients and tested using RT-PCR. We used generalized linear models to investigate factors that explain result agreement. Further, we used simulations to evaluate the effectiveness of saliva-based screening in restricting the spread of infection in a large campus such as an educational institution.

RESULTS

We observed a 75.4% agreement between saliva and N/OPS-VTM, that increased drastically to 83% in samples stored for less than three days. Such samples processed within two days of collection showed 74.5% test sensitivity. Our simulations suggest that a test with 75% sensitivity, but high daily capacity can be very effective in limiting the size of infection clusters in a workspace. Guided by these results, we successfully implemented a saliva-based screening in the Bangalore Life Sciences Cluster (BLiSC) campus.

CONCLUSION

These results suggest that saliva may be a viable alternate source for SARS-CoV-2 surveillance if samples are processed immediately. Although saliva shows slightly lower sensitivity levels when compared to N/OPS-VTM, saliva collection is logistically advantageous. We strongly recommend the implementation of saliva-based screening strategies for large workplaces and in schools, as well as for population-level screening and routine surveillance as we learn to live with the SARS-CoV-2 virus.

Characteristics of patients with SARS-COV-2 PCR re-positivity after recovering from COVID-19

The purpose of this study was to analyse the clinical characteristics of patients with severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) PCR re-positivity after recovering from coronavirus disease 2019 (COVID-19). Patients (n = 1391) from Guangzhou, China, who had recovered from COVID-19 were recruited between 7 September 2021 and 11 March 2022. Data on epidemiology, symptoms, laboratory test results and treatment were analysed. In this study, 42.7% of recovered patients had re-positive result. Most re-positive patients were asymptomatic, did not have severe comorbidities, and were not contagious. The re-positivity rate was 39%, 46%, 11% and 25% in patients who had received inactivated, mRNA, adenovirus vector and recombinant subunit vaccines, respectively. Seven independent risk factors for testing re-positive were identified, and a predictive model was constructed using these variables. The predictors of re-positivity were COVID-19 vaccination status, previous SARs-CoV-12 infection prior to the most recent episode, renal function, SARS-CoV-2 IgG and IgM antibody levels and white blood cell count. The predictive model could benefit the control of the spread of COVID-19.

Repurposing povidone-iodine to reduce the risk of SARS-CoV-2 infection and transmission: a narrative review

BACKGROUND

Accumulating data suggest antiviral effects of povidone-iodine against the Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. This narrative review aims to examine the antiviral mechanisms of povidone-iodine, efficacy of povidone-iodine against the SARS-CoV-2 virus, and safety of povidone-iodine to human epithelial cells and thyroid function.

METHODS

We searched the electronic databases PubMed, Embase, Cochrane Library, ClinicalTrials.gov and World Health Organization's International Clinical Trials Registry Platform for articles containing the keywords "povidone-iodine", "SARS-CoV-2" and "COVID-19" from database inception till 3 June 2021.

RESULTS

Despite in vitro data supporting the anti-SARS-CoV-2 effects of povidone-iodine, findings from clinical studies revealed differences in treatment response depending on study settings (healthy vs. hospitalized individuals), treatment target (nasal vs. oral vs. pharynx), method of administration (oral rinse vs. gargle vs. throat spray) and choice of samples used to measure study endpoints (nasopharyngeal vs. saliva). One large-scale clinical trial demonstrated reduction in the incidence of SARS-CoV-2 infection among participants who administered povidone-iodine 3 times daily during an active outbreak. Povidone-iodine is also used to disinfect the oro-pharyngeal space prior to dental or otolaryngology procedures. Although existing data suggest minimal impact of povidone-iodine on thyroid function, high-quality safety data are presently lacking.

CONCLUSIONS

Povidone-iodine application to the oropharyngeal space could complement existing non-pharmacological interventions to reduce SARS-CoV-2 infection especially in high exposure settings.Key messagesAccumulating data suggest antiviral effects of povidone-iodine against the SARS-CoV-2 virus.Findings from clinical studies reveal differences in treatment response depending on study settings, treatment target, method of administration and choice of samples used to measure study endpoints. One large-scale clinical trial observed reduction in the incidence of SARS-CoV-2 infection among participants who administered povidone-iodine 3 times daily during an active outbreak.Povidone-iodine application to the oropharyngeal space could complement existing non-pharmacological interventions to reduce SARS-CoV-2 infection especially in high exposure settings.

The Capacity of Artificial Intelligence in COVID-19 Response: A Review in Context of COVID-19 Screening and Diagnosis

Artificial intelligence (AI) has been shown to solve several issues affecting COVID-19 diagnosis. This systematic review research explores the impact of AI in early COVID-19 screening, detection, and diagnosis. A comprehensive survey of AI in the COVID-19 literature, mainly in the context of screening and diagnosis, was observed by applying the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines. Data sources for the years 2020, 2021, and 2022 were retrieved from google scholar, web of science, Scopus, and PubMed, with target keywords relating to AI in COVID-19 screening and diagnosis. After a comprehensive review of these studies, the results found that AI contributed immensely to improving COVID-19 screening and diagnosis. Some proposed AI models were shown to have comparable (sometimes even better) clinical decision outcomes, compared to experienced radiologists in the screening/diagnosing of COVID-19. Additionally, AI has the capacity to reduce physician work burdens and fatigue and reduce the problems of several false positives, associated with the RT-PCR test (with lower sensitivity of 60-70%) and medical imaging analysis. Even though AI was found to be timesaving and cost-effective, with less clinical errors, it works optimally under the supervision of a physician or other specialists.

Clinical characteristics and risks of the convalescent COVID-19 patients with re-detectable positive RNA test: a 430 patients with Omicron infected cross-sectional survey in Tianjin, China

Background

The outbreak of severe acute respiratory syndrome coronavirus (SARS-CoV-2) Omicron variant occurred in Tianjin, China, at the beginning of 2022. In the present study, we identified risk factors that may affect positive (RP) RNA re-testing in recovered patients infected with Omicron variants during recovery in hospital.

Methods

We retrospectively analyzed the medical records of 425 patients with Omicron variant infection admitted to our medical center from January 21, 2022 to February 24, 2022, based on the recurrence of RT-PCR positive results for SARS-CoV-2 after cure and discharge. Patients were divided into re-tested positive (RP) and non-re-detectable positive patients (NRP) groups, and clinical data from both groups were analyzed to investigate the characteristics and risk factors of RP patients.

Results

Univariate analysis showed significant differences in age, vaccination rate and dose, partial signs and symptoms, most co-existing disorders, and levels of CRP and IL-6 between the RP and NRP groups (all P < 0.05), while multifactorial logistic regression analysis showed that vaccination status and levels of IL-6 were independent risk factors for RP patients.

Conclusion

Our results suggested that clinicians should assess the probability of "re-positive" nucleic acid tests after discharge, taking the following indicators into account: pre-admission underlying diseases, unvaccinated status, and high levels of CRP and IL-6. Post-discharge isolation and follow-up should also be strengthened.

Ultrafast one-minute electronic detection of SARS-CoV-2 infection by 3CLpro enzymatic activity in untreated saliva samples

Since its onset in December 2019, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, has caused over 6.5 million deaths worldwide as of October 2022. Attempts to curb viral transmission rely heavily on reliable testing to detect infections since a large number of transmissions are carried through asymptomatic individuals. Many available detection methods fall short in terms of reliability or point-of-care applicability. Here, we report an electrochemical approach targeting a viral proteolytic enzyme, 3CLpro, as a marker of active infection. We detect proteolytic activity directly from untreated saliva within one minute of sample incubation using a reduction-oxidation pH indicator. Importantly, clinical tests of saliva samples from 50 subjects show accurate detection of SARS-CoV-2, with high sensitivity and specificity, validated by PCR testing. These, coupled with our platform's ultrafast detection, simplicity, low cost and point-of-care compatibility, make it a promising method for the real-world SARS-CoV-2 mass-screening.

Biofilms possibly harbor occult SARS-CoV-2 may explain lung cavity, re-positive and long-term positive results

During the COVID-19 pandemic, there have been an increasing number of COVID-19 patients with cavitary or cystic lung lesions, re-positive or long-term positive nucleic acid tests, but the mechanism is still unclear. Lung cavities may appear at long time interval from initial onset of coronavirus infection, generally during the absorption phase of the disease. The main histopathological characteristic is diffuse alveolar damage and may have more severe symptoms after initial recovery from COVID-19 and an increased mortality rate. There are many possible etiologies of pulmonary cavities in COVID-19 patients and we hypothesize that occult SARS-CoV-2, in the form of biofilm, is harbored in the airway lacuna with other pathogenic microorganisms, which may be the cause of pulmonary cavities and repeated and long-term positive nucleic acid tests.

The Illness Experience of Long COVID Patients: A Qualitative Study Based on the Online Q&A Community Zhihu

Long COVID is a public health problem that cannot be ignored, and it is critical to understand the long COVID patients' living situations and support this group through their illness narratives. This study is based on grounded theory, and coded the self-produced texts of long COVID patients on the largest online Q&A community in China, Zhihu APP, in an attempt to explore the illness experiences of long COVID patients in China and to understand how they adapt to their illness and reconstruct their lives. The results show that patients face not only the threat of pain from the illness itself, but also social stigma and discrimination. Patients turn their illness experiences into motivation to move forward and reconstruct self and life by 'pushing forward the biographical flows again', 'impression management' and 'self-compassion'. These findings can help policy-makers and medical institutions to provide timely and appropriate policy support and psychological assistance to patients with long COVID, to create a supportive and inclusive social environment, and to reduce discrimination and stigma against them.

The prevalence of adaptive immunity to COVID-19 and reinfection after recovery - a comprehensive systematic review and meta-analysis

This study aims to estimate the prevalence and longevity of detectable SARS-CoV-2 antibodies and T and B memory cells after recovery. In addition, the prevalence of COVID-19 reinfection and the preventive efficacy of previous infection with SARS-CoV-2 were investigated. A synthesis of existing research was conducted. The Cochrane Library, the China Academic Journals Full Text Database, PubMed, and Scopus, and preprint servers were searched for studies conducted between 1 January 2020 to 1 April 2021. Included studies were assessed for methodological quality and pooled estimates of relevant outcomes were obtained in a meta-analysis using a bias adjusted synthesis method. Proportions were synthesized with the Freeman-Tukey double arcsine transformation and binary outcomes using the odds ratio (OR). Heterogeneity was assessed using the I² and Cochran's Q statistics and publication bias was assessed using Doi plots. Fifty-four studies from 18 countries, with around 12,000,000 individuals, followed up to 8 months after recovery, were included. At 6-8 months after recovery, the prevalence of SARS-CoV-2 specific immunological memory remained high; IgG - 90.4% (95%CI 72.2-99.9, I² = 89.0%), CD4+ - 91.7% (95%CI 78.2-97.1y), and memory B cells 80.6% (95%CI 65.0-90.2) and the pooled prevalence of reinfection was 0.2% (95%CI 0.0-0.7, I² = 98.8). Individuals previously infected with SARS-CoV-2 had an 81% reduction in odds of a reinfection (OR 0.19, 95% CI 0.1-0.3, I² = 90.5%). Around 90% of recovered individuals had evidence of immunological memory to SARS-CoV-2, at 6-8 months after recovery and had a low risk of reinfection.RegistrationPROSPERO: CRD42020201234.

Clinical and Gene Features of SARS-CoV-2-Positive Recurrence in Patients Recovered From COVID-19

There are still frequent reports that a number of recovered coronavirus disease 2019 (COVID-19) patients following discharge have re-detectable positive (RP) results by RT-PCR. Understanding the clinical and molecular characteristics of RP patients may have implications for curbing the COVID-19 pandemic. In this study, 318 COVID-19 convalescent patients, including 59 RP patients and 259 non-RP (NRP) patients, were enrolled. Among RP patients, women accounted for a significantly high proportion (67.8%), and the titers of IgG and IgM antibodies in this group were also significantly high. Differentially expressed genes (DEGs), including 692 upregulated and 383 downregulated genes, overlapped in two public GEO datasets containing RP and NRP blood cell samples. Enrichment analysis indicated that these DEGs were related to several key signaling pathways, such as viral infection, immune activation, and inflammatory responses. Importantly, 59 indicator genes constituting the core network exhibited high diagnostic values and were correlated with markers of different immune cells. Among these, 12 drug-related genes were associated with the RP results. Our work suggests that, in addition to clinically available features, blood cell transcriptome sequencing can be performed to obtain gene signatures for diagnosis of RP patients.

Virological and Serological Assessment of US Army Trainees Isolated for Coronavirus Disease 2019

BACKGROUND

Laboratory screening for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a key mitigation measure to avoid the spread of infection among recruits starting basic combat training in a congregate setting. Because viral nucleic acid can be detected persistently after recovery, we evaluated other laboratory markers to distinguish recruits who could proceed with training from those who were infected.

METHODS

Recruits isolated for coronavirus disease 2019 (COVID-19) were serially tested for SARS-CoV-2 subgenomic ribonucleic acid (sgRNA), and viral load (VL) by reverse-transcriptase polymerase chain reaction (RT-PCR), and for anti- SARS-CoV-2. Cluster and quadratic discriminant analyses of results were performed.

RESULTS

Among 229 recruits isolated for COVID-19, those with a RT-PCR cycle threshold >30.49 (sensitivity 95%, specificity 96%) or having sgRNA log10 RNA copies/mL <3.09 (sensitivity and specificity 96%) at entry into isolation were likely SARS-CoV-2 uninfected. Viral load >4.58 log10 RNA copies/mL or anti-SARS-CoV-2 signal-to-cutoff ratio <1.38 (VL: sensitivity and specificity 93%; anti-SARS-CoV-2: sensitivity 83%, specificity 79%) had comparatively lower sensitivity and specificity when used alone for discrimination of infected from uninfected.

CONCLUSIONS

Orthogonal laboratory assays used in combination with RT-PCR may have utility in determining SARS-CoV-2 infection status for decisions regarding isolation.

The Short- and Long-Term Clinical, Radiological and Functional Consequences of COVID-19

As with the rapid increase of the number of patients who have recovered from COVID-19 globally, there needs to be a major shift of the focus from rapid pathogen detection, treatment and prevention to the promotion of better recovery. Notwithstanding the scarcity of our understandings, recent studies have unraveled a plethora of pulmonary and systemic consequences which require medical attention. These consequences remained as of the end of follow-up which ranged from 1 month to 1 year. Here, we review the consequences of COVID-19 in terms of the residual symptoms, radiological and functional manifestations, and identify the potential risk factors that contribute to a prolonged recovery. We also summarize the benefits of clinical interventions (particularly the pulmonary rehabilitation program), and address several undetermined concerns and key future research directions.

Comprehensive Survey of Using Machine Learning in the COVID-19 Pandemic

Since December 2019, the global health population has faced the rapid spreading of coronavirus disease (COVID-19). With the incremental acceleration of the number of infected cases, the World Health Organization (WHO) has reported COVID-19 as an epidemic that puts a heavy burden on healthcare sectors in almost every country. The potential of artificial intelligence (AI) in this context is difficult to ignore. AI companies have been racing to develop innovative tools that contribute to arm the world against this pandemic and minimize the disruption that it may cause. The main objective of this study is to survey the decisive role of AI as a technology used to fight against the COVID-19 pandemic. Five significant applications of AI for COVID-19 were found, including (1) COVID-19 diagnosis using various data types (e.g., images, sound, and text); (2) estimation of the possible future spread of the disease based on the current confirmed cases; (3) association between COVID-19 infection and patient characteristics; (4) vaccine development and drug interaction; and (5) development of supporting applications. This study also introduces a comparison between current COVID-19 datasets. Based on the limitations of the current literature, this review highlights the open research challenges that could inspire the future application of AI in COVID-19.

Immunoglobulin Response and Prognostic Factors in Repeated SARS-CoV-2 Positive Patients: A Systematic Review and Meta-Analysis

With repeated positivity being an undiscovered and major concern, we aimed to evaluate which prognostic factors may impact repeated SARS-CoV-2 positivity (RSP) and their association with immunoglobulin detectability among recovered patients. A systematic literature search was performed on 5 April 2021. Cohort studies with risk factors for repeated RSP or information about the immunoglobulin response (immunoglobulin M (IgM) and/or immunoglobulin G (IgG)) were included in this analysis. The main examined risk factors were severity of the initial infection, body mass index (BMI), length of hospitalization (LOH), age, and gender, for which we pooled mean differences and odds ratios (ORs). Thirty-four cohort studies (N = 9269) were included in our analysis. We found that increased RSP rate might be associated with IgG positivity; IgG presence was higher in RSP patients (OR: 1.72, CI: 0.87–3.41, p = 0.117). Among the examined risk factors, only mild initial disease course showed a significant association with RSP (OR: 0.3, CI: 0.14–0.67, p = 0.003). Age, male gender, BMI, LOH, and severity of the first episode do not seem to be linked with repeated positivity. However, further prospective follow-up studies focusing on this topic are required.