Dimensional Structure of one-year Post-COVID-19 Neuropsychiatric and Somatic Sequelae and Association with Role Impairment (preprint)

This study examined the latent structure of the broad range of complex neuropsychiatric morbidities occurring one year after COVID-19 infection. As part of the CU-COVID19 study, 248 (response rate = 39·3%) of 631 adults hospitalized for COVID-19 infection in Hong Kong completed an online survey between 3-2021 and 1-2022. Disorder prevalence was compared against a random non-infected household sample (n = 1837). 248 surveys were received on average 321 days post-infection (Mean age: 48·9, 54% female, moderate/severe/critical infection: 58·2%). 32·4% were screened to have > = one mental disorder, 78·7% of whom had concurrent fatigue/subjective cognitive impairment (SCI). Only PTSD (19·1%) was significantly more common than control (14%, p = 0·047). Latent profile analysis classified individuals into P1(12·4%)-no current neuropsychiatric morbidities, P2 (23·1%)-SCI/fatigue, P3 (45·2%)-anxiety/PTSD, P4 (19·3%)-depression. SCI and fatigue pervaded in all profiles (P2-4) with neuropsychiatric morbidities one-year post-infection. SHAP: PTSD, anxiety and depressive symptoms were most important in differentiating P2-4. Past mental health and P4 independently predicted functional impairment. Neuropsychiatric morbidity was associated with past mental health, reduced resilience, financial problems, but not COVID-19 severity. Their confluence with depressive and anxiety symptoms predicted impairment and are associated with psychological and environmental factors.

Development and Implementation of a Simple and Rapid Extraction-Free Saliva SARS-CoV-2 RT-LAMP Workflow for Workplace Surveillance (preprint)

Effective management of the COVID-19 pandemic requires widespread and frequent testing of the population for SARS-CoV-2 infection. Saliva has emerged as an attractive alternative to nasopharyngeal samples for surveillance testing as it does not require specialized personnel or materials for its collection and can be easily provided by the patient. We have developed a simple, fast, and sensitive saliva-based testing workflow that requires minimal sample treatment and equipment. After sample inactivation, RNA is quickly released and stabilized in an optimized buffer, followed by reverse transcription loop-mediated isothermal amplification (RT-LAMP) and detection of positive samples using a colorimetric and/or fluorescent readout. The workflow was optimized using 1,670 negative samples collected from 172 different individuals over the course of 6 months. Each sample was spiked with 50 copies/L of inactivated SARS-CoV-2 virus to monitor the efficiency of viral detection. Using pre-defined clinical samples, the test was determined to be 100% specific and 97% sensitive, with a limit of detection comparable to commercially available RT-qPCR-based diagnostics. The method was successfully implemented in a CLIA laboratory setting for workplace surveillance and reporting. From April 2021-February 2022, more than 30,000 self-collected samples from 755 individuals were tested and 85 employees tested positive mainly during December and January, consistent with high infections rates in Massachusetts and nationwide. The rapid identification and isolation of infected individuals with trace viral loads before symptom onset minimized viral spread in the workplace.

The effect of Brahmi (Bacopa monnieri (L.) Pennell) on depression, anxiety and stress during Covid-19

Introduction: Despite overall impact on health during COVID-19, mental health was least explored to assess psychological wellbeing. Hence, this study to screen the symptoms of depression, anxiety, and stress among adolescents and adults and evaluate the effectiveness of Ayurveda herbal intervention becomes relevant. This study examined the effectiveness of Brahmi (Bacopa monnieri (L.) Pennell) in reducing depression, anxiety, and stress among populations aged between 12 to 60 years in COVID-19 negative patients Hassan district of Karnataka State, India after screening them for psychological distress. Methods: 198 eligible participants (140 female and 58 male) selected by Depression Anxiety and Stress Scale-21 (DASS-21) was used to evaluate depression, anxiety, and stress from 1657 screened participants at baseline. Two 500 mg capsule of Brahmi (Bacopa monnieri (L.) Pennell) was administered twice daily after food in morning and night for 30 days. Paired t-test, and Wilcoxon signed rank test was applied to see the change in each DASS-21 indicator after intervention. Results: At the DASS-21, 4.09% of the responders presented pathological levels of depression, 10.85% of anxiety, and 0.72% of stress among general population. Significant decrease in means were found for scales of depression, anxiety, stress and total DASS-21 after intervention (p<0.001) with Brahmi for a period of 1 month Conclusion: The population during COVID-19 experienced mild to moderate levels of anxiety, depression and stress. This study result highlights the effectiveness of Brahmi in improving the psychological health during COVID-19. These results have important implications in clinical practice in improving psychological health in the context of COVID-19 pandemic. Trial Registration: CTRI/2020/07/026952. Available at: http://www.ctri.nic.in. Keywords: COVID-19, DASS-21, psychological health, depression, anxiety, stress, Brahmi, Bacopa monnieri

Impact of COVID-19 on TB epidemiology in South Korea.

SETTING: Five referral hospitals, South Korea.OBJECTIVE: To assess epidemiological changes in TB before and during the COVID-19 pandemic.DESIGN: This was a multicentre cohort study of 3,969 patients diagnosed with TB.RESULTS: We analysed 3,453 patients diagnosed with TB prior to the COVID-19 pandemic (January 2016-February 2020) and 516 during the pandemic (March-November 2020). During the pandemic, the number of patients visits declined by 15% from the previous 4-year average, and the number of patients diagnosed with TB decreased by 17%. Patients diagnosed during the pandemic were older than those diagnosed before the pandemic (mean age, 60.2 vs. 56.6 years, P < 0.001). The proportion of patients to have primary TB at a younger age (births after 1980) among those diagnosed with TB was significantly lower during the pandemic than before (17.8% in 2020 vs. 23.5% in 2016, 24.0% in 2017, 22.5% in 2018, 23.5% in 2019; P = 0.005).CONCLUSIONS: The COVID-19 pandemic resulted in a reduction in the number of visits to respiratory departments, leading to fewer patients being diagnosed with TB. However, our results suggest that universal personal preventive measures help to suppress TB transmission in regions with intermediate TB burden.

Dynamics of mask use as a prevention strategy against SARS-Cov-2 in Panama (preprint)

BackgroundEarly in the SARS-CoV-2 pandemic, many national public health authorities implemented non-pharmaceutical interventions to mitigate disease outbreaks. Panama established mandatory mask use two months after its first documented case. Initial compliance was high, but diverse masks were used in public areas. We studied behavioral dynamics of mask use through the first two COVID waves in Panama, to improve implementation of effective, low-cost public health containment measures, when populations are exposed to novel air-borne pathogens. MethodsMask use behavior was recorded from pedestrians in four Panamanian populations (August to December 2020). We recorded facial coverings; and if used, the type of mask, and gender and estimated age of the wearer. FindingsPeople were highly compliant (> 95%) with mask mandates, and demonstrated important population-level behaviours: 1) decreasing use of cloth masks over time, and increasing use of surgical masks; 2) mask use was 3-fold lower in sub-urban neighborhoods than other public areas; and 3) young people were least likely to wear masks. InterpretationResults help focus highly-effective, low-cost, public health interventions for managing and controlling a pandemic. Considerations of behavioural preferences for different masks, relative to pricing and availability, are essential for optimizing public health policies. Policies to increase availability of effective masks, and behavioral nudges to increase acceptance, and to facilitate mask usage, during the on-going SARS-CoV-2 pandemic, and for future pandemics of respiratory pathogens, are key tools, especially for nations lagging in access to expensive vaccines and pharmacological approaches. Funding11-2020 SNI Grant, SENACYT.

Sustaining effective COVID-19 control in Malaysia through large-scale vaccination (preprint)

Introduction As of 3rd June 2021, Malaysia is experiencing a resurgence of COVID-19 cases. In response, the federal government has implemented various non-pharmaceutical interventions (NPIs) under a series of Movement Control Orders and, more recently, a vaccination campaign to regain epidemic control. In this study, we assessed the potential for the vaccination campaign to control the epidemic in Malaysia and four high-burden regions of interest, under various public health response scenarios. Methods A modified susceptible-exposed-infectious-recovered compartmental model was developed that included two sequential incubation and infectious periods, with stratification by clinical state. The model was further stratified by age and incorporated population mobility to capture NPIs and micro-distancing (behaviour changes not captured through population mobility). Emerging variants of concern (VoC) were included as an additional strain competing with the existing wild-type strain. Several scenarios that included different vaccination strategies (i.e. vaccines that reduce disease severity and/or prevent infection, vaccination coverage) and mobility restrictions were implemented. Results The national model and the regional models all fit well to notification data but underestimated ICU occupancy and deaths in recent weeks, which may be attributable to increased severity of VoC or saturation of case detection. However, the true case detection proportion showed wide credible intervals, highlighting incomplete understanding of the true epidemic size. The scenario projections suggested that under current vaccination rates complete relaxation of all NPIs would trigger a major epidemic. The results emphasise the importance of micro-distancing, maintaining mobility restrictions during vaccination roll-out and accelerating the pace of vaccination for future control. Malaysia is particularly susceptible to a major COVID-19 resurgence resulting from its limited population immunity due to the historical success of the country in maintaining control throughout much of 2020.

[Autoptical display of the nasopharyngeal space in cases of suspected SARS-Co2 infection]. / Autoptische Darstellung des Nasen-Rachen-Raumes bei Verdacht auf SARS-CoV2-Infektion.

This paper deals with a dissection technique in order to display the nasopharyngeal space. It consists of a parafrontal saw cut through the base of the skull at the level of the sella turcica. In this way the ventral part of the nasopharyngeal space can be separated from the cervical spine and the posterior base of the skull within an anatomically preformed border region. Apart from a comprehensive overview of the nasopharyngeal space, this technique also enables samples to be correctly taken. The time required takes approximately 2-3 min, the external appearance of the deceased is not affected and the preparation of the body is not complicated.

Direct measurement of B lymphocyte gene expression biomarkers in peripheral blood enables early prediction of seroconversion after vaccination (preprint)

Vaccination is a common and efficient means to reduce the mortality and morbidity of emerging infectious diseases. Among responders, injected antigen induces acquired immunity pathways and leads to the final production of antigen-specific antibodies. The whole process may take weeks to months, depending on the antigen. Typically, seroconversion to influenza vaccine is expected after one month with a responder rate of ~50%. An early biomarker to predict response is desirable. Peripheral blood gene expression (or transcript abundance, TA) datasets in the public domain were analyzed for early biomarkers among responders. As peripheral blood samples (such as peripheral blood mononuclear cells, PBMC) are cell mixture samples containing various blood cell-types (leukocyte subpopulations, LS). We first develop a model that enables the determination of TA in B lymphocytes of certain genes directly in PBMC samples without the need of prior cell isolation. These genes are called B cell informative genes. Then a ratio of two B cell informative genes (a target gene and a stably expressed reference gene) measured in PBMC was used as a new biomarker to gauge the target gene expression in B lymphocytes. This method having an obvious advantage over conventional methods by eliminating the tedious procedure of cell sorting and enables directly determining TA of a leukocyte subpopulation in cell mixture samples is called Direct LS-TA method. By using a B lymphocyte-specific gene such as TNFRSF17 or TXNDC5 as target genes with either TNFRSF13C or FCRLA as reference genes, the B cell biomarkers were determined directly in PBMC which was highly correlated with TA of target genes in purified B lymphocytes. These Direct LS-TA biomarkers in PBMC increased significantly early after vaccination in both the discovery dataset and a meta-analysis of 7 datasets. Responders had almost a 2-fold higher Direct LS-TA biomarker level of TNFRSF17 (SMD=0.84, 95% CI=0.47-1.21 after log2). And Direct LS-TA biomarkers of TNFRSF17 and TXNDC5 measured at day 7 predict responder with sensitivity values of higher than 0.7. The Area-under curves (AUC) in receiver operation curve (ROC) analysis were over 0.8. Here, we report a straightforward approach to directly analyses B lymphocyte gene expression in PBMC, which could be used in a routine clinical setting as it avoids the labor-intensive procedures of B lymphocyte isolation. And the method allows the practice of precision medicine in the prediction of vaccination response. Furthermore, response to vaccination could be predicted as early as on day 7. As vaccination response is based on the similar acquired immunology pathway in the upcoming worldwide vaccination campaign against COVID-19, these biomarkers could also be useful to predict seroconversion for individuals.

Temporal Landscape of Human Gut Virome in SARS-CoV-2 Infection and Severity (preprint)

Background: Coronavirus Disease 2019 (COVID-19) caused by the enveloped RNA virus SARS-CoV-2 primarily affects the respiratory and gastrointestinal tracts.SARS-CoV-2 was isolated from faecal samples and active viral replication was reported in human intestinal cells. The human gut also harbors an enormous amount of resident viruses (collectively known as virome) that play a role in regulating host immunity and pathophysiology.Understanding gut virome perturbation that underlies SARS-CoV-2 infection and severity is an unmet need.Methods: We enrolled 98 COVID-19 patients with varying disease severity (3 asymptomatic, 53 mild, 34 moderate, 5 severe, 3 critical) and 78 non-COVID-19 controls matched for gender and co-morbidities. All study subjects had faecal specimens sampled at inclusion. Blood specimens were sampled for COVID-19 patients at admission to test for inflammatory markers and white cell counts. Among COVID-19 cases, 37 (38%) patients had serially faecal samples collected 2 to 3 times per week from time of hospitalization until after discharge. Using shotgun metagenomics sequencing, we sequenced and profiled the faecal RNA and DNA virome respectively. We investigated alterations and longitudinal dynamics of the gut virome in association with disease severity and blood parameters.Findings: Patients with COVID-19 showed underrepresentation of P epper mild mottle virus (RNA virus) and multiple bacteriophage lineage s (DNA viruses) and enrichment of environment-derived eukaryotic DNA viruses in faecal samples, compared to non-COVID-19 subjects. Such gut virome dysbiosis persisted up to 30 days after disease resolution. Faecal virome in SARS-CoV-2 infection harboured more stress-, inflammation- and virulence-associated gene encoding capacities including those pertaining to bacteriophage integration, DNA repair, and metabolism and virulence associated with their bacterial host. Human faecal baseline abundance of 9 virus species (1 RNA virus, Pepper chlorotic spot virus, and 8 DNA virus species) inversely correlated with disease severity of COVID-19. These viruses were also inversely associated with blood levels of pro-inflammatory proteins, white cells and neutrophils. Among the 9 COVID-19 severity-associated virus species, 4 showed inverse correlation with age; 5 showed persistent lower abundance both during disease course and after disease resolution relative to non-COVID-19 subjects. Interpretation: Both enteric RNA and DNA viromes were perturbed in COVID-19, which prolonged even after disease resolution. Gut virome may calibrate host immunity and regulate severity to SARS-CoV-2 infection. Our observation that gut viruses inversely correlated with both severity of COVID-19 and host age partly explains that older subjects are prone to severe and unfavorable COVID-19 outcomes. Our data altogether highlight the significance of human gut virome in COVID-19 disease course and potentially therapeutics.Funding Statement: This work was supported by The D. H. Chen Foundation, Center for Gut Microbiota Research (Faculty of Medicine, The Chinese University of Hong Kong) and Health and Medical Research Fund (Hong Kong, China).Declaration of Interests: None.Ethics Approval Statement: This study was approved by the Joint Chinese University of Hong Kong–New Territories East Cluster Clinical Research Ethics Committees (Reference number: 2020.076). All subjects provided informed consent to participate in this study and agreed for publication of the research results.

Temporal landscape of human gut RNA and DNA virome in SARS-CoV-2 infection and severity (preprint)

Background: Coronavirus Disease 2019 (COVID-19) caused by the enveloped RNA virus SARS-CoV-2 primarily affects the respiratory and gastrointestinal tracts. SARS-CoV-2 was isolated from faecal samples and active viral replication was reported in human intestinal cells. The human gut also harbors an enormous amount of resident viruses (collectively known as the virome) that play a role in regulating host immunity and disease pathophysiology. Understanding gut virome perturbation that underlies SARS-CoV-2 infection and severity is an unmet need.Methods: We enrolled 98 COVID-19 patients with varying disease severity (3 asymptomatic, 53 mild, 34 moderate, 5 severe, 3 critical) and 78 non-COVID-19 controls matched for gender and co-morbidities. All subjects had faecal specimens sampled at inclusion. Blood specimens were collected for COVID-19 patients at admission to test for inflammatory markers and white cell counts. Among COVID-19 cases, 37 (38%) patients had serial faecal samples collected 2 to 3 times per week from time of hospitalization until after discharge. Using shotgun metagenomics sequencing, we sequenced and profiled the faecal RNA and DNA virome. We investigated alterations and longitudinal dynamics of the gut virome in association with disease severity and blood parameters.Results: Patients with COVID-19 showed underrepresentation of Pepper mild mottle virus (RNA virus) and multiple bacteriophage lineages (DNA viruses) and enrichment of environment-derived eukaryotic DNA viruses in faecal samples, compared to non-COVID-19 subjects. Such gut virome alterations persisted up to 30 days after disease resolution. Faecal virome in SARS-CoV-2 infection harboured more stress-, inflammation- and virulence-associated gene encoding capacities including those pertaining to bacteriophage integration, DNA repair, and metabolism and virulence associated with their bacterial host. Baseline fecal abundance of 10 virus species (1 RNA virus, Pepper chlorotic spot virus, and 9 DNA virus species) inversely correlated with disease COVID-19 severity. These viruses inversely correlated with blood levels of pro-inflammatory proteins, white cells and neutrophils. Among the 10 COVID-19 severity-associated DNA virus species, 4 showed inverse correlation with age; 5 showed persistent lower abundance both during disease course and after disease resolution relative to non-COVID-19 subjects.Conclusions: Both enteric RNA and DNA virome in COVID-19 patients were different from non-COVID-19 subjects, which persisted after disease resolution of COVID-19. Gut virome may calibrate host immunity and regulate severity to SARS-CoV-2 infection. Our observation that gut viruses inversely correlated with both severity of COVID-19 and host age may partly explain that older subjects are prone to severe and worse COVID-19 outcomes. Altogether our data highlight the importance of human gut virome in severity and potentially therapeutics of COVID-19.

Sentinel Coronavirus Environmental Monitoring Can Contribute to Detecting Asymptomatic SARS-CoV-2 Virus Spreaders and Can Verify Effectiveness of Workplace COVID-19 Controls (preprint)

Detecting all workplace asymptomatic COVID-19 virus spreaders would require daily testing of employees, which is not practical. Over a two week period, nine workplace locations were chosen to test employees for SARS-CoV-2 infection (841 tests) and high-frequency-touch point environmental surfaces (5,500 tests) for Coronavirus using Eurofins COVID-19 SentinelTM RT-PCR methods. Of the 9 locations, 3 had one or employees infected with SARS-CoV-2, neither of whom had symptoms at the time of testing nor developed symptoms. Locations with Coronavirus contaminated surfaces were 10 times more likely to have clinically positive employees than locations with no or very few positive surfaces. Break room chairs, workbenches, and door handles were the most frequently contaminated surfaces. Coronavirus RNA was detected at very low concentrations (RT-PCR 34 to 38 Cq). Environmental monitoring can be used to validate intervention strategies and be useful to verify the effectiveness of such strategies on a regular basis.

Students’ Perception and Preference for Online Education in India During COVID -19 Pandemic (preprint)

Educational institutes across the world have closed due to the COVID-19 pandemic jeopardizing the academic calendars. Most educational institutes have shifted to online learning platforms to keep the academic activities going. However, the questions about the preparedness, designing and effectiveness of e-learning is still not clearly understood, particularly for a developing country like India, where the technical constraints like suitability of devices and bandwidth availability poses a serious challenge. In this study, we focus on understanding Agricultural Student’s perception and preference towards the online learning through an online survey of 307 students. We also explored the student’s preferences for various attributes of online classes, which will be helpful to design effective online learning environment. The results indicated that majority of the respondents (70%) are ready to opt for online classes to manage the curriculum during this pandemic. Majority of the students preferred to use smart phone for online learning. Using content analysis, we found that students prefer recorded classes with quiz at the end of each class to improve the effectiveness of learning. The students opined that flexibility and convenience of online classes makes it attractive option, whereas broadband connectivity issues in rural areas makes it a challenge for students to make use of online learning initiatives.Funding: This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.Competing Interest: We whole-heartedly acknowledge all the respondents for spending their valuable time on filling our questionnaire

How much India detecting SARS-CoV-2 Infections? A model-based estimation (preprint)

Background and Rationale: Amid SARS-CoV-2 outbreak, the low number of infections for a population size of 1.38 billion is widely discussed, but with no definite answers. Methods: We used the model proposed by Bommer and Vollmer to assess the quality of official case records. The infection fatality rates were taken from Verity et al (2020). Age distribution of the population for India and states are taken from the Census of India (2011). Reported number of deaths and SARS-CoV-2 confirmed cases from https://www.covid19india.org. The reported numbers of samples tests were collected from the reports of the Indian Council for Medical Research (ICMR). Results: The findings suggest that India is detecting just 3.6% of the total number of infections with a huge variation across its states. Among 13 states which have more than 100 COVID-19 cases, the detection rate varies from 81.9% (of 410 estimated infections) in Kerala to 0.8% (of 35487 estimated infections) in Madhya Pradesh and 2.4% (of 7431 estimated infections) in Gujarat. Conclusion: As the study reports a lower number of deaths and higher recovery rates in the states with a high detection rate, thus suggest that India must enhance its testing capacity and go for widespread testing. Late detection puts patients in greater need of mechanical ventilation and ICU care, which imposes greater costs on the health system. The country should also adopt population-level random testing to assess the prevalence of the infection.