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<meta content="width=device-width, initial-scale=1.0, user-scalable=yes" name="viewport"/>
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<title>15 November, 2022</title>
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<title>Covid-19 Sentry</title><meta content="width=device-width, initial-scale=1.0" name="viewport"/><link href="styles/simple.css" rel="stylesheet"/><link href="../styles/simple.css" rel="stylesheet"/><link href="https://unpkg.com/aos@2.3.1/dist/aos.css" rel="stylesheet"/><script src="https://unpkg.com/aos@2.3.1/dist/aos.js"></script></head>
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<h1 data-aos="fade-down" id="covid-19-sentry">Covid-19 Sentry</h1>
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<h1 data-aos="fade-right" data-aos-anchor-placement="top-bottom" id="contents">Contents</h1>
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<li><a href="#from-preprints">From Preprints</a></li>
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<li><a href="#from-clinical-trials">From Clinical Trials</a></li>
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<li><a href="#from-pubmed">From PubMed</a></li>
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<li><a href="#from-patent-search">From Patent Search</a></li>
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<h1 data-aos="fade-right" id="from-preprints">From Preprints</h1>
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<li><strong>Sweden’s Coronavirus Fight Strategy And Bitter Memories Of Past Eugenic Practices</strong> -
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Herd immunity is one of the methods utilized by countries to combat the new coronavirus (SARS-CoV-2) pandemic. Sweden is the only country in Europe that pursues the practice of “herd immunity,” while the new coronavirus has spread throughout the country. As of April 27, 2020, the Johns Hopkins University Coronavirus Research Center reports that there have been 18,640 coronavirus cases in Sweden, resulting in 2,194 deaths. The ‘herd’ will survive, but in order for this to occur, other ‘weaker’ members of society must be sacrificed, according to some researchers. The goal of eugenics, in its simplest form, is to increase the genetic quality of a human population. People and organizations deemed inferior can be rejected or sacrificed for those deemed superior and able to live so that this improvement might occur. As we explained in our AVM analysis titled “Century-Old ‘White Supremacism’ and the Far-Rise Right’s in Sweden: A Credible Challenge to Progressive Values and Policies” published two years ago, the Scandinavian eugenics movement reached its zenith prior to the First World War and became operational during the 1930s and 1940s. Between 1934 and 1976, Sweden was the only country with a national eugenics society and employed sterilization regulations. The initial Swedish sterilisation statute went into effect in 1935 and was expanded in 1941. A Swedish government commission was established in 1997 to investigate sterilization operations from 1935 to 1975. According to international press accounts, Sweden’s present plan to combat the spread of the coronavirus is supported by the people at large. Time will tell if this strategy, which is pursued at the expense of vulnerable individuals (particularly the elderly), is worthwhile. Even if this technique currently supports Sweden’s interests, it will undoubtedly be subject to severe ethical objections in the future, similar to Sweden’s past eugenics activities.
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🖺 Full Text HTML: <a href="https://osf.io/zb2jn/" target="_blank">Sweden’s Coronavirus Fight Strategy And Bitter Memories Of Past Eugenic Practices</a>
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</div></li>
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<li><strong>Molecular autism research in Africa: a scoping review comparing publication outputs to Brazil, India, the UK, and the USA.</strong> -
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The increased awareness of autism spectrum disorders (ASD) is accompanied by burgeoning ASD research, and concerted research efforts are trying to elucidate the molecular ASD aetiology. However, much of this research is concentrated in the Global North, with recent reviews of research in Sub-Saharan Africa (SSA) highlighting the significant shortage of ASD publications from this region. The most limited focus area was molecular research with only two molecular studies ever published from SSA, both being from South Africa (SA). We examine the molecular ASD research publications from 2016 to 2021 from all African countries, with a special focus on SA. The SSA publications are compared to Brazil and India, two non-African, low-to-middle-income countries (LMICs), and to the UK and USA, two high-income countries (HICs). There were 228 publications across all regions of interest; only three publications were from SA. Brazil (n=29) and India (n=27) had almost 10 times more publications than SA. The HICs had more publications than the LMICs, with the UK (n=62) and the USA (n=74) having approximately 20 to 25 times more publications than SA, respectively. Given that SA has substantial research capacity as demonstrated by its recent research on SARS-CoV-2, we explore potential reasons for this deficit in molecular ASD publications from SA. We compare mental health research outputs, GDP per capita, research and development expenditure, and the number of psychiatrists and child psychiatrists per 100,000 people across all regions. The UK and the USA had significantly higher numbers for all these indicators, consistent with their higher publication output. Among the LMICs, SA can potentially produce more molecular ASD research, however, there are numerous barriers that need to be addressed to facilitate increased research capacity. These include cultural stigmas, challenges in accessing mental healthcare, shortages of specialists in the public sector, and the unreliability of ASD diagnostic tools across the 11 official SA languages. The unique genetic architecture of African populations presents an untapped reservoir for finding novel genetic loci associated with ASD. Therefore, addressing the disparity in molecular ASD research between the Global North and SSA is integral to global advancements in ASD research.
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🖺 Full Text HTML: <a href="https://www.biorxiv.org/content/10.1101/2022.11.11.516128v1" target="_blank">Molecular autism research in Africa: a scoping review comparing publication outputs to Brazil, India, the UK, and the USA.</a>
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<li><strong>Risk factors and symptom clusters for Long Covid: analysis of United Kingdom symptom tracker app data.</strong> -
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Background: Long Covid, characterised by symptoms after Covid-19 infection which persist for longer than 12 weeks, is becoming an important societal and economic problem. As Long Covid was novel in 2020, there has been debate regarding its aetiology and whether it is one, or multiple, syndromes. This study assessed risk factors associated with Long Covid and examined symptom clusters that might indicate sub-types. Methods: 4,040 participants reporting for >4 months in the Covid Symptom Study App were included. Multivariate logistic regression was undertaken to identify risk factors associated with Long Covid. Cluster analysis (K-modes and hierarchical agglomerative clustering) and factor analysis were undertaken to investigate symptom clusters. Results: Long Covid affected 13.6% of participants. Significant risk factors included being female (P < 0.01), pre-existing poor health (P < 0.01), and worse symptoms in the initial illness. A model incorporating sociodemographics, comorbidities, and health status predicted Long Covid with an accuracy (AUROC) of 76%. The three clustering approaches gave rise to different sets of clusters with no consistent pattern across methods. Conclusions: Our model of risk factors may help clinicians predict patients at higher risk of Long Covid, so these patients can rest more, receive treatments, or enter clinical trials; reducing the burden of this long-term and debilitating condition. No consistent subtypes were identified.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.11.14.22282285v1" target="_blank">Risk factors and symptom clusters for Long Covid: analysis of United Kingdom symptom tracker app data.</a>
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<li><strong>Protection conferred by Delta and BA.1/BA.2 infection against BA.4/BA.5 infection and hospitalization: A Retrospective Cohort Study</strong> -
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Background: SARS-CoV-2 immunity has declined with subsequent waves and accrual of viral mutations. In vitro studies raise concern for immune escape by BA.4/BA.5, and a study in Qatar showed moderate protection, but these findings have yet to be reproduced. Methods: This retrospective cohort study included individuals tested for COVID-19 by PCR during Delta or BA.1/BA.2 and retested during BA.4/BA.5. The preventable fraction (PF) was calculated as ratio of the infection/hospitalization rate for initially positive patients divided by infection/hospitalization rate for initially negative patients, stratified by age, and adjusted for age, gender, comorbidities, and vaccination using logistic regression. Results: 20,987 patients met inclusion criteria. Prior Delta infection provided no protection against BA.4/BA.5 infection (Adjusted PF: 11.9% (95% confidence interval [CI], 0.8-21.8); p=0.036) and minimal protection against hospitalization (Adjusted PF: 10.7% (95%CI, 4.9-21.7); p=0.003). In adjusted models, prior BA.1/BA.2 infection provided 45.9% (95%CI, 36.2-54.1) (p <0.001) protection against BA.4/BA.5 reinfection and 18.8% (95% CI, 10.3-28.3) (p<0.0001) protection against hospitalization. Up-to-date vaccination provided modest protection against reinfection with BA.4/BA.5 and hospitalization. Conclusions: Prior infection with BA.1/BA.2 and up-to-date vaccination provided modest protection against infection with BA.4/BA.5 and hospitalization, while prior Delta infection provided minimal protection against hospitalization, and no infection protection.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.11.14.22282310v1" target="_blank">Protection conferred by Delta and BA.1/BA.2 infection against BA.4/BA.5 infection and hospitalization: A Retrospective Cohort Study</a>
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<li><strong>Multi-omic spatial profiling reveals the unique virus-driven immune landscape of COVID-19 placentitis</strong> -
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COVID-19 placentitis, a rare complication of maternal SARS-CoV-2 infection, only shows detectable virus in the placenta of a subset of cases. We provide a deep multi-omic spatial characterisation of placentitis from obstetrically complicated maternal COVID-19 infection. We found that SARS-CoV-2 infected placentas have a distinct transcriptional and immunopathological signature. This signature overlaps with virus-negative cases supporting a common viral aetiology. An inverse correlation between viral load and disease duration suggests viral clearance over time. Quantitative spatial analyses revealed a unique microenvironment surrounding virus-infected trophoblasts characterised by PDL1-expressing macrophages, T-cell exclusion, and interferon blunting. In contrast to uninfected mothers, ACE2 was localised to the maternal side of the placental trophoblast layer of almost all mothers with placental SARS-CoV-2 infection, which may explain variable susceptibility to placental infection. Our results demonstrate a pivotal role for direct placental SARS-CoV-2 infection in driving the unique immunopathology of COVID-19 placentitis.
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🖺 Full Text HTML: <a href="https://www.biorxiv.org/content/10.1101/2022.11.14.516398v1" target="_blank">Multi-omic spatial profiling reveals the unique virus-driven immune landscape of COVID-19 placentitis</a>
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<li><strong>Genetic and structural data on the SARS-CoV-2 Omicron BQ.1 variant reveal its low potential for epidemiological expansion</strong> -
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The BQ.1 SARS-CoV-2 variant, also known as Cerberus, is one of the most recent Omicron descendant lineages. Compared to its direct progenitor BA.5, BQ.1 carries out some additional spike mutations in some key antigenic site which confer it further immune escape ability over other circulating lineage. In such a context, here we performed a genome-based survey aimed to obtain an as complete as possible nuance of this rapidly evolving Omicron subvariant. Genetic data suggests that BQ.1 represents an evolutionary blind background, lacking of the rapid diversification which is typical of a dangerous lineage. Indeed, the evolutionary rate of BQ.1 is very similar to that of BA.5 (7.6 x 10-4 and 7 x 10-4 subs/site/year, respectively), which is circulating by several months. Bayesian Skyline Plot reconstruction, indicates low level of genetic variability, suggesting that the peak has been reached around September 3, 2022. Structure analyses performed by comparing the properties of BQ.1 and BA.5 RBD indicated that the impact of the BQ.1 mutations on the affinity for ACE2 may be modest. Likewise, immunoinformatic analyses showed modest differences between the BQ.1 and the BA5 potential B-cells epitope. In conclusion, genetic and structural analysis on SARS-CoV-2 BQ.1 suggest that, it does not show evidence about its particular dangerous or high expansion capability. The monitoring genome-based must continue uninterrupted for a better understanding of its descendant and all other lineages.
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🖺 Full Text HTML: <a href="https://www.biorxiv.org/content/10.1101/2022.11.11.516052v1" target="_blank">Genetic and structural data on the SARS-CoV-2 Omicron BQ.1 variant reveal its low potential for epidemiological expansion</a>
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<li><strong>Bispecific antibodies combine breadth, potency, and avidity of parental antibodies to neutralize sarbecoviruses</strong> -
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SARS-CoV-2 mutational variants evade humoral immune responses elicited by vaccines and current monoclonal antibody (mAb) therapies. Novel antibody-based treatments will thus need to exhibit broad neutralization against different variants. Bispecific antibodies (bsAbs) combine the specificities of two distinct antibodies into one antibody taking advantage of the avidity, synergy and cooperativity provided by targeting two different epitopes. Here we used controlled Fab-arm exchange (cFAE), a versatile and straightforward method, to produce bsAbs that neutralize SARS-CoV and SARS-CoV-2 variants, including Omicron and its subvariants, by combining potent SARS-CoV-2-specific neutralizing antibodies with broader but less potent antibodies that also neutralize SARS-CoV. We demonstrate that the parental IgG’s rely on avidity for their neutralizing activity by comparing their potency to bsAbs containing one irrelevant “dead” Fab arm. We used single particle mass photometry to measure formation of antibody:spike complexes, and determined that bsAbs increase binding stoichiometry compared to corresponding cocktails, without a loss of binding affinity. The heterogeneous binding pattern of bsAbs to spike (S), observed by negative-stain electron microscopy and mass photometry provided evidence for both intra- and inter-spike crosslinking. This study highlights the utility of cross-neutralizing antibodies for designing bivalent or multivalent agents to provide a robust activity against circulating variants, as well as future SARS-like coronaviruses.
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🖺 Full Text HTML: <a href="https://www.biorxiv.org/content/10.1101/2022.11.11.516125v1" target="_blank">Bispecific antibodies combine breadth, potency, and avidity of parental antibodies to neutralize sarbecoviruses</a>
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<li><strong>SARS-CoV-2 vaccination of laboratory rhesus monkeys (Macaca mulatta): Monitoring and efficacy</strong> -
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The availability of effective vaccines and a high vaccination rate allowed the recent mitigation, or even withdrawal, of many protective measures for containing the SARS CoV-2 pandemic. At the same time, new and highly mutated variants of the virus are found to have significantly higher transmissibility and reduced vaccine efficacy, thus causing high infection rates during the third year of the pandemic. The combination of reduced measures and increased infectivity poses a particular risk for unvaccinated individuals, including animals susceptible to the virus. Among the latter, non-human primates (NHPs) are particularly vulnerable. They serve as important models in various fields of biomedical research and because of their cognitive capabilities, they receive particular attention in animal welfare regulations around the world. Yet, although they played an extraordinarily important role for developing and testing vaccines against SARS-CoV-2, the protection of captive rhesus monkeys against Covid-19 has rarely been discussed. We here report upon twofold mRNA vaccination of a cohort of 19 rhesus monkeys (Macaca mulatta) against infection by SARS-CoV-2. All animals were closely monitored on possible side effects of vaccination, and were tested for neutralising antibodies against the virus. The data show that vaccination of rhesus monkeys is a safe and reliable measure to protect these animals against SARS-CoV-2.
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🖺 Full Text HTML: <a href="https://www.biorxiv.org/content/10.1101/2022.11.11.516206v1" target="_blank">SARS-CoV-2 vaccination of laboratory rhesus monkeys (Macaca mulatta): Monitoring and efficacy</a>
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<li><strong>Serology assays used in SARS-CoV-2 seroprevalence surveys worldwide: a systematic review and meta-analysis of assay features, testing algorithms, and performance</strong> -
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Background: Many serological assays to detect SARS-CoV-2 antibodies were developed during the COVID-19 pandemic. Differences in the detection mechanism of SARS-CoV-2 serological assays limited the comparability of seroprevalence estimates for populations being tested. Methods: We conducted a systematic review and meta-analysis of serological assays used in SARS-CoV-2 population seroprevalence surveys, searching for published articles, preprints, institutional sources, and grey literature between January 1, 2020, and November 19, 2021. We described features of all identified assays and mapped performance metrics by the manufacturers, third-party head-to-head, and independent group evaluations. We compared the reported assay performance by evaluation source with a mixed-effect beta regression model. A simulation was run to quantify how biased assay performance affects population seroprevalence estimates with test adjustment. Results: Among 1807 included serosurveys, 192 distinctive commercial assays and 380 self-developed assays were identified. According to manufacturers, 28.6% of all commercial assays met WHO criteria for emergency use (sensitivity [Sn.] >= 90.0%, specificity [Sp.] >= 97.0%). However, manufacturers overstated the absolute values of Sn. of commercial assays by 1.0% [0.1, 1.4%] and 3.3% [2.7, 3.4%], and Sp. by 0.9% [0.9, 0.9%] and 0.2% [-0.1, 0.4%] compared to third-party and independent evaluations, respectively. Reported performance data was not sufficient to support a similar analysis for self-developed assays. Simulations indicate that inaccurate Sn. and Sp. can bias seroprevalence estimates adjusted for assay performance; the error level changes with the background seroprevalence. Conclusions: The Sn. and Sp. of the serological assay are not fixed properties, but varying features depending on the testing population. To achieve precise population estimates and to ensure the comparability of seroprevalence, serosurveys should select assays with high performance validated not only by their manufacturers and adjust seroprevalence estimates based on assured performance data. More investigation should be directed to consolidating the performance of self-developed assays.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.10.13.22280957v2" target="_blank">Serology assays used in SARS-CoV-2 seroprevalence surveys worldwide: a systematic review and meta-analysis of assay features, testing algorithms, and performance</a>
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<li><strong>Immune response of primary and booster immunity of SARS-CoV-2 vaccination among patients with chronic liver disease: a real-world study</strong> -
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Aim: The present study discussed the humoral immune response and antibody dynamics after primary and booster immunity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines among patients with chronic liver disease (CLD) in the real world. Thus, it provided data to develop SARS-CoV-2 vaccination strategy. Methods: Patients with confirmed CLD and completed primary or booster immunity of SARS-CoV-2 vaccines were enrolled. Serological specimens were collected after primary or booster immunity of SARS-CoV-2 vaccines to detect novel coronavirus neutralizing antibody (nCoV NTAb) and novel coronavirus spike receptor-binding domain antibody (nCoV S-RBD). Thus, we could evaluate the humoral immune response and antibody dynamics after primary and booster immunity of SARS-CoV-2 vaccines among patients with CLD. Simultaneously, baseline demographics, liver disease-related situations, comorbidity-related situations, SARS-CoV-2 vaccination information, and laboratory examination-related indicators of patients were collected. Results: A total of 315 patients received SARS-CoV-2 vaccines, including 223 patients who completed the primary immunity of SARS-CoV-2 vaccines, 114 patients who completed booster immunity of SARS-CoV-2 vaccines, and 22 patients who underwent the antibody detection of SARS-CoV-2 vaccines after both primary and booster immunities. The positive rate of nCoV NTAb was 59.64% in Primary and 87.72% in Booster (P<0.001). The median level of nCoV NTAb was 11.53 AU/mL in Primary and 31.98 AU/mL in Booster (P<0.001). The positive rate of nCoV S-RBD was 69.06% in Primary and 91.23% in Booster (P<0.001). The median level of nCoV S-RBD was 21.60AU/mL in Primary and 112.65 AU/mL in Booster (P<0.001). After booster immunity of SARS-CoV-2 vaccines in 22 patients, the positive rate of nCoV NTAb increased from 59.09% to 86.36%, and that of nCoV S-RBD increased from 68.18% to 90.91%. The median level of nCoV NTAb increased from 11.24 AU /mL to 59.14 AU /mL after booster immunity. The median level of nCoV S-RBD increased from 27.28 AU/mL to 219.10 AU/mL. Compared to the antibody level of primary immunity, the median level of nCoV NTAb and nCoV S-RBD in 22 patients was increased by 5.26 and 8.03 times, respectively. Among 22 patients, 9 were negative for nCoV NTAb after primary immunity, while 6 were transformed positive after booster immunity, and the positive conversion rate of nCoV NTAb was 66.7%. On the other hand, 7 patients were negative for nCoV S-RBD after primary immunity, while 5 were transformed positive after booster immunity, and the positive conversion rate of nCoV S-RBD was 71.4%. Conclusion: Patients with CLD show improved humoral immune response after completing primary and booster immunity of SARS-CoV-2 vaccines, while booster immunity further improves the positive rate and antibody level of patients with CLD. Finally, the positive conversion rate among patients with primary immunity failure also can be improved after booster immunity. Keywords: immune response; primary and booster immunity; SARS-CoV-2 vaccination; chronic liver disease
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.11.12.22282242v1" target="_blank">Immune response of primary and booster immunity of SARS-CoV-2 vaccination among patients with chronic liver disease: a real-world study</a>
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<li><strong>COVID Seq as Laboratory Developed Test (LDT) for diagnosis of SARS-CoV-2 Variants of Concern (VOC)</strong> -
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Rapid classification and detection of SARS-CoV-2 variants have been critical in comprehending the virus9s transmission dynamics. Clinical manifestation of the infection is influenced by comorbidities such as age, immune status, diabetes, and the infecting variant. Thus, clinical management may differ for new variants. For example, some monoclonal antibody treatments are variant-specific. Yet, an FDA-approved test for detecting the SARS-CoV-2 variant is unavailable. A laboratory-developed test (LDT) remains a viable option for reporting the infecting variant for clinical intervention or epidemiological purposes. Accordingly, we have validated the Illumina COVID-Seq assay as an LDT according to the guidelines prescribed by the College of American Pathologists (CAP) and Clinical Laboratory Improvement Amendments (CLIA). The limit of detection (LOD) of this test is Ct<30 (~15 viral copies) and >200X genomic coverage, and the test is 100% specific in the detection of existing variants. The test demonstrated 100% precision in inter-day, intra-day, and intra-laboratory reproducibility studies. It is also 100% accurate, defined by reference strain testing and split sample testing with other CLIA laboratories. Advanta Genetics LDT COVID Seq has been reviewed by CAP inspectors and is under review by FDA for Emergency Use Authorization.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.11.11.22282032v1" target="_blank">COVID Seq as Laboratory Developed Test (LDT) for diagnosis of SARS-CoV-2 Variants of Concern (VOC)</a>
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<li><strong>Acute and Post-Acute COVID-19 Outcomes Among Immunologically Naïve Adults During Delta Versus Omicron Waves</strong> -
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Importance: The U.S. arrival of the Omicron variant led to a rapid increase in SARS-CoV-2 infections. While numerous studies report characteristics of Omicron infections among vaccinated individuals and/or persons with a prior history of infection, comprehensive data describing infections among immunologically naïve adults is lacking. Objective: To examine COVID-19 acute and post-acute clinical outcomes among a well-characterized cohort of unvaccinated and previously uninfected adults who contracted SARS-CoV-2 during the Omicron (BA.1/BA.2) surge, and to compare outcomes with infections that occurred during the Delta wave. Design: A prospective cohort undergoing high-resolution symptom and virologic monitoring between June 2021 and September 2022 Setting: Multisite recruitment of community-dwelling adults in 8 U.S. states Participants: Healthy, unvaccinated adults between 30 to 64 years of age without an immunological history of SARS-CoV-2 who were at high-risk of infection were recruited. Participants were followed for up to 48 weeks, submitting regular COVID-19 symptom surveys and nasal swabs for SARS-CoV-2 PCR testing. Exposure(s): Omicron (BA.1/BA.2 lineages) versus Delta SARS-CoV-2 infection, defined as a positive PCR that occurred during a period when the variant represented ≥50% of circulating SARS-CoV-2 variants in the participant9s geographic region. Main Outcome(s) and Measure(s): The main outcomes examined were the prevalence and severity of acute (≤28 days post-onset) and post-acute (≥5 weeks post-onset) symptoms. Results: Among 274 immunologically naïve participants, 166 (61%) contracted SARS-CoV-2. Of these, 137 (83%) and 29 (17%) infections occurred during the Omicron- and Delta-predominant periods, respectively. Asymptomatic infections occurred among 6.7% (95% CI: 3.1%, 12.3%) of Omicron cases and 0.0% (95% CI: 0.0%, 11.9%) of Delta cases. Healthcare utilization among Omicron cases was 79% (95% CI: 43%, 92%, P=0.001) lower relative to Delta cases. Relative to Delta, Omicron infections also experienced a 56% (95% CI: 26%, 74%, P=0.004) and 79% (95% CI: 54%, 91%, P<0.001) reduction in the risk and rate of post-acute symptoms, respectively. Conclusions and Relevance: These findings suggest that among previously immunologically naïve adults, few Omicron (BA.1/BA.2) and Delta infections are asymptomatic, and relative to Delta, Omicron infections were less likely to seek healthcare and experience post-acute symptoms.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.11.13.22282222v1" target="_blank">Acute and Post-Acute COVID-19 Outcomes Among Immunologically Naïve Adults During Delta Versus Omicron Waves</a>
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<li><strong>Successful Detection of Delta and Omicron Variants of SARS-CoV-2 by Veterinary Diagnostic Laboratory Participants in an Interlaboratory Comparison Exercise</strong> -
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Background: Since the beginning of the COVID-19 pandemic veterinary diagnostic laboratories have tested diagnostic samples for SARS-CoV-2 not only in animals, but in over five million human samples. An evaluation of the performance of those laboratories is needed using blinded test samples to ensure that laboratories report reliable data to the public. This interlaboratory comparison exercise (ILC3) builds on two prior exercises to assess whether veterinary diagnostic laboratories can detect Delta and Omicron variants spiked in canine nasal matrix or viral transport medium. Methods: Inactivated Delta variant at levels of 25 to 1,000 copies per 50 microliters of nasal matrix were prepared for participants by the ILC organizer, an independent laboratory, for blinded analysis. Omicron variant at 1,000 copies per 50 microliters of transport medium was also included. Feline infectious peritonitis virus (FIPV) RNA was used as a confounder for specificity assessment. A total of 14 test samples were prepared for each participant. Participants used their routine diagnostic procedures for RNA extraction and real-time RT-PCR. Results were analyzed according to International Organization for Standardization (ISO) 16140 - 2:2016. Results: The overall results showed 93% detection for Delta and 97% for Omicron at 1,000 copies per 50 microliters (22-200 copies per reaction). The overall specificity was 97% for blank samples and 100% for blank samples with FIPV. No differences in Ct values were significant for samples with the same virus levels between N1 and N2 markers, nor between the two variants. Conclusions: The results indicated that all ILC3 participants were able to detect both Delta and Omicron variants. The canine nasal matrix did not significantly affect SARS-CoV-2 detection.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.11.08.22282084v1" target="_blank">Successful Detection of Delta and Omicron Variants of SARS-CoV-2 by Veterinary Diagnostic Laboratory Participants in an Interlaboratory Comparison Exercise</a>
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<li><strong>Exploration of wastewater surveillance for Monkeypox virus</strong> -
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The sudden emergence and spread of Monkeypox in non-endemic parts of the world is currently not well understood. Infections are often mis-diagnosed and surveillance strategies are scarce. Wastewater-based surveillance (WBS) of human Monkeypox virus (MPXV) can help supplement our current clinical surveillance and mitigation efforts. WBS has shown to be an effective tool in monitoring the spread of other infectious pathogens, such as SARS-CoV-2 and its variants, and has helped guide public health actions. In this study, we describe how WBS can be used to detect MPXV in wastewater. We conducted WBS for MPXV in 22 wastewater treatment plants (WWTPs) over a period of 14 weeks. Nucleic acids were extracted using the MagAttract PowerMicrobiome DNA/RNA extraction kit. Three real-time qPCR assays were assessed for the detection of MPXV in wastewater. These included the G2R assays (G2R_WA and G2R_G) developed by the Centers for Disease Control and Prevention (CDC) in 2010, as well as an in-house-developed assay (G2R_NML). The G2R_WA assay was designed to detect the West African clade of viruses while the G2R_G (generic) assay was designed to detect both the Congo and West African clades (re-named to clades 1 and 2 respectively). The G2R_NML assay was designed using reference genomes of the 2022 MPXV outbreak. Our results show that all three assays have similar limits of detection and are all able to detect the presence of MPXV in wastewater. Following detection through real time qPCR, Sanger sequencing was performed on the resulting amplicon products, with the assembled contigs then undergoing analysis using nucleotide Basic Local Alignment Search Tool (BLAST). Due in part to the longer amplicon size of the G2R_NML assay, a significantly greater number of positive detections were identified as originating from MPXV compared to the CDC G2R assays. The ability to detect trace amounts of MPXV in wastewater as well as obtain Sanger sequence confirmation, has allowed for the successful surveillance of this virus in wastewater.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.11.10.22282091v1" target="_blank">Exploration of wastewater surveillance for Monkeypox virus</a>
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<li><strong>Early prone positioning does not improve the outcome of patients with mild pneumonia due to SARS-CoV-2: results from an open-label, randomized controlled trial (the EPCoT Study).</strong> -
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Background Prone positioning (PP) is routinely used among patients with COVID-19 requiring mechanical ventilation. However, its utility among spontaneously breathing patients is still debated. Methods In an open-label randomized controlled trial, we enrolled patients hospitalized with mild COVID-19 pneumonia, whose PaO2/FiO2 ratio was >200 mmHg and who did not require mechanical ventilation (MV) or non-invasive ventilation (NIV) at hospital admission. Patients were randomized 1:1 to PP on top of standard of care (intervention group) versus standard of care only (controls). The primary composite outcome included death, MV, NIV and PaO2/FiO2 <200 mmHg; secondary outcomes were oxygen weaning and hospital discharge. Results Sixty-one subjects were enrolled, 29 adjudicated to PP and 32 to the control group. By day 28, 11 patients required NIV, 4 MV and 3 died. Overall, 24/61 (39.3%) met the primary outcome. Using an intention-to-treat approach, 15/29 patients in PP group versus 9/32 controls met the primary outcome, corresponding to a significantly higher risk of progression among those randomized to PP (HR 2.38 95%CI 1.04-5.43; P=0.040). Using an as-treated approach, which included in the intervention group only patients who maintained PP for ≥3 hours/day, no significant differences were found between the two groups (HR 1.77; 95%CI 0.79-3.94; P=0.165). Also, we did not find any statistically difference in terms of time to oxygen weaning or hospital discharge between study arms, in any of the analyses conducted. Conclusions We observed no clinical benefit from awake PP among spontaneously breathing patients with COVID-19 pneumonia requiring conventional oxygen therapy.
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🖺 Full Text HTML: <a href="https://www.medrxiv.org/content/10.1101/2022.11.12.22282252v1" target="_blank">Early prone positioning does not improve the outcome of patients with mild pneumonia due to SARS-CoV-2: results from an open-label, randomized controlled trial (the EPCoT Study).</a>
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<h1 data-aos="fade-right" id="from-clinical-trials">From Clinical Trials</h1>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>COVID-19 Bivalent Booster Megastudy</strong> - <b>Condition</b>: COVID-19<br/><b>Intervention</b>: Behavioral: COVID Booster text messages<br/><b>Sponsor</b>: University of Pennsylvania<br/><b>Enrolling by invitation</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>A Study on Utilization, Adherence, and Acceptability of Voluntary Routine COVID-19 Self-testing Among Students, Staff and Health Workers at Two Institutions in Mizoram, India.</strong> - <b>Condition</b>: COVID-19 Pandemic<br/><b>Intervention</b>: Diagnostic Test: COVID-19 Self testing and related messaging<br/><b>Sponsors</b>: PATH; UNITAID; Zoram Medical College; Pacchunga University College; ALERT India; Government of Mizoram<br/><b>Not yet recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Using a Community-level Just-in-Time Adaptive Intervention to Address COVID-19 Testing Disparities</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Behavioral: Multi-Level Multi-Component Intervention (MLI); Behavioral: Community Just-In-Time Adaptive Intervention (Community JITAI)<br/><b>Sponsors</b>: The University of Texas Health Science Center, Houston; National Center for Advancing Translational Sciences (NCATS)<br/><b>Active, not recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Examining How a Facilitated Self-Sampling Intervention and Testing Navigation Intervention Influences COVID-19 Testing</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Behavioral: Facilitated Self-Sampling Intervention (FSSI); Behavioral: Testing Navigation Intervention (TNI).; Behavioral: Control<br/><b>Sponsors</b>: The University of Texas Health Science Center, Houston; National Center for Advancing Translational Sciences (NCATS)<br/><b>Not yet recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Assessing Performance of the Testing Done Simple Covid 19 Antigen Test</strong> - <b>Condition</b>: COVID-19<br/><b>Intervention</b>: Diagnostic Test: Testing Done Simple SARS CoV-2 Antigen Test<br/><b>Sponsors</b>: Testing Done Simple; Nao Medical Urgent Care<br/><b>Recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>A Phase III of COVID-19 Vaccine EuCorVac-19 in Healthy Adults Aged 18 Years and Older</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Biological: EuCorVac-19; Biological: ChAdOx1<br/><b>Sponsor</b>: EuBiologics Co.,Ltd<br/><b>Recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Open Multicentre Study of the Safety and Efficacy Against COVID-19 of Nirmatrelvir/Ritonavir in the Adult Population</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Drug: nirmatrelvir/ritonavir; Drug: Standard of care<br/><b>Sponsors</b>: Promomed, LLC; Sponsor GmbH<br/><b>Completed</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Study Evaluating GS-5245 in Participants With COVID-19 Who Have a High Risk of Developing Serious or Severe Illness</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Drug: GS-5245; Drug: GS-5245 Placebo<br/><b>Sponsor</b>: Gilead Sciences<br/><b>Recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>The LAVA (Lateral Flow Antigen Validation and Applicability) 2 Study for COVID-19</strong> - <b>Condition</b>: SARS-CoV-2 Infection<br/><b>Intervention</b>: Diagnostic Test: Innova Lateral Flow Test<br/><b>Sponsor</b>: Alder Hey Children’s NHS Foundation Trust<br/><b>Completed</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Q-POC COVID-19 Clinical Evaluation</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Diagnostic Test: RT-PCR Test; Diagnostic Test: Real-time PCR Test<br/><b>Sponsors</b>: QuantuMDx Group Ltd; EDP Biotech; Paragon Rx Clinical; PathAI; PRX Research and Development<br/><b>Not yet recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>A Phase I/II Study of GLB-COV2-043 as a COVID-19 Vaccine Booster</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Drug: GLB-COV2-043; Drug: BNT162b2/COMIRNATY®<br/><b>Sponsor</b>: GreenLight Biosciences, Inc.<br/><b>Not yet recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Enhancing Protection Against Influenza and COVID-19 for Pregnant Women and Medically at Risk Children</strong> - <b>Conditions</b>: Influenza; COVID-19<br/><b>Intervention</b>: Behavioral: Nudge<br/><b>Sponsor</b>: University of Adelaide<br/><b>Recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>Safety and Efficacy of Intranasal Administration of Avacc 10 Vaccine Against COVID-19 in Healthy Volunteers</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Biological: Avacc 10; Combination Product: Outer Membrane Vesicles (OMV) : OMV alone in vehicle; Other: Placebo<br/><b>Sponsors</b>: Intravacc B.V.; Novotech (Australia) Pty Limited<br/><b>Not yet recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>COVID-19 Antibody Responses in Cystic Fibrosis</strong> - <b>Conditions</b>: COVID-19; Cystic Fibrosis<br/><b>Intervention</b>: Biological: Blood sample<br/><b>Sponsors</b>: Hospices Civils de Lyon; Queen’s University, Belfast<br/><b>Recruiting</b></p></li>
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<li data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><p data-aos="fade-left" data-aos-anchor-placement="bottom-bottom"><strong>The Phase Ⅱ/Ⅲ Trial of LYB001</strong> - <b>Condition</b>: COVID-19<br/><b>Interventions</b>: Biological: LYB001; Biological: Placebo<br/><b>Sponsor</b>: Yantai Patronus Biotech Co., Ltd.<br/><b>Not yet recruiting</b></p></li>
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<h1 data-aos="fade-right" id="from-pubmed">From PubMed</h1>
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<h1 data-aos="fade-right" id="from-patent-search">From Patent Search</h1>
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