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MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (1867)

ProteinN (508)

NSP5 (401)

ComplexRdRp (235)

ProteinE (135)


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SARS-CoV-2 Proteins
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    Multi-Omic Profiling of Plasma Identify Biomarkers and Pathogenesis of COVID-19 MESHD in Children

    Authors: Chong Wang; Xufang Li; Wanshan Ning; Sitang Gong; Fengxia Yang; Chunxiao Fang; Yu Gong; Di Wu; Muhan Huang; Yujie Gou; Shanshan Fu; Yujie Ren; Ruyi Yang; Yang Qiu; Yu Xue; Yi Xu; Xi Zhou

    doi:10.1101/2021.03.04.21252876 Date: 2021-03-06 Source: medRxiv

    Although children usually develop less severe disease responding to COVID-19 MESHD than adults, little is known about the pathogenesis of COVID-19 MESHD in children. Herein, we conducted the plasma proteomic and metabolomic profiling of a cohort of COVID-19 MESHD pediatric patients with mild symptoms. Our data show that numerous proteins and metabolites involved in immune as well as anti-inflammatory processes were up-regulated on a larger scale in children than in adults. By developing a machine learning-based pipeline, we prioritized two sets of biomarker combinations, and identified 5 proteins and 5 metabolites as potential children-specific COVID-19 MESHD biomarkers. Further study showed that these identified metabolites not only inhibited the expression of pro-inflammatory factors, but also suppressed coronaviral replication, implying that these factors played key roles in protecting pediatric patients from both viral infection MESHD and infection-induced inflammation MESHD. Together, our study uncovered a protective mechanism responding to COVID-19 MESHD in children, and sheds light on potential therapies.

    Longitudinal Analysis Reveals Distinct Antibody and Memory B Cell MESHD Responses in SARS-CoV2 Naive and Recovered Individuals Following mRNA Vaccination

    Authors: Rishi R Goel; Sokratis A Apostolidis; Mark M Painter; Divij Mathew; Ajinkya Pattekar; Oliva Kuthuru; Sigrid Gouma; Leticia Kuri-Cervantes; Wenzhao Meng; Sharon Adamski; Amy E Baxter; Josephine R Giles; Madison E Weirick; Christopher M McAllister; Amanda Hicks; Scott Korte; Jeanette Dougherty; Sherea Long; Kurt D'Andrea; Jacob T Hamilton; Eline T Luning Prak; Michael R Betts; Paul Bates; Scott E Hensley; Allison R Greenplate; E. John Wherry

    doi:10.1101/2021.03.03.21252872 Date: 2021-03-06 Source: medRxiv

    Novel mRNA vaccines for SARS-CoV2 have been authorized for emergency use and are currently being administered to millions of individuals worldwide. Despite their efficacy in clinical trials, there is limited data on vaccine-induced immune responses in individuals with a prior SARS-CoV2 infection MESHD compared to SARS-CoV2 naive subjects. Moreover, how mRNA vaccines impact the development of antibodies as well as memory B cells in COVID-19 MESHD experienced versus COVID-19 MESHD naive subjects remains poorly understood. In this study, we evaluated antibody responses and antigen-specific memory B cell responses over time in 33 SARS-CoV2 naive and 11 SARS-CoV2 recovered subjects. mRNA vaccination induced significant antibody and memory B cell responses against full-length SARS-CoV2 spike protein PROTEIN and the spike receptor binding domain (RBD). SARS-CoV2 naive individuals benefitted from both doses of mRNA vaccine with additional increases in antibodies and memory B cells following booster immunization. In contrast, SARS-CoV2 recovered individuals had a significant immune response after the first dose with no increase in circulating antibodies or antigen-specific memory B cells after the second dose. Moreover, the magnitude of the memory B cell response induced by vaccination was lower in older individuals, revealing an age-dependence to mRNA vaccine-induced B cell memory MESHD. Side effects also tended to associate with post-boost antibody levels, but not with post-boost memory B cells, suggesting that side effect severity may be a surrogate of short-term antibody responses. The frequency of pre-vaccine antigen-specific memory B cells in SARS-CoV2 recovered individuals strongly correlated with post-vaccine antibody levels, supporting a key role for memory B cells in humoral recall responses to SARS-CoV2. This observation may have relevance for future booster vaccines and for responses to viral variants that partially escape pre-existing antibodies and require new humoral responses to be generated from memory B cells. Finally, post-boost antibody levels were not correlated with post-boost memory responses in SARS-CoV2 naive individuals, indicating that short-term antibody levels and memory B cells are complementary immunological endpoints that should be examined in tandem when evaluating vaccine response. Together, our data provide evidence of both serological response and immunological memory MESHD following mRNA vaccination that is distinct based on prior SARS-CoV2 exposure. These findings may inform vaccine distribution in a resource-limited setting.

    REACT-1 round 9 final report: Continued but slowing decline of prevalence of SARS-CoV-2 during national lockdown in England in February 2021

    Authors: Steven Riley; Caroline E. Walters; Haowei Wang; Oliver Eales; David Haw; Kylie E. C. Ainslie; Christina Atchinson; Claudio Fronterre; Peter J. Diggle; Deborah Ashby; Christl A Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott

    doi:10.1101/2021.03.03.21252856 Date: 2021-03-06 Source: medRxiv

    Background England will start to exit its third national lockdown in response to the COVID-19 pandemic MESHD on 8th March 2021, with safe effective vaccines being rolled out rapidly against a background of emerging transmissible and immunologically novel variants of SARS-CoV-2. A subsequent increase in community prevalence of infection could delay further relaxation of lockdown if vaccine uptake and efficacy are not sufficiently high to prevent increased pressure on healthcare services. Methods The PCR self-swab arm of the REal-time Assessment of Community Transmission Study (REACT-1) estimates community prevalence of SARS-CoV-2 infection MESHD in England based on random cross-sections of the population ages five and over. Here, we present results from the complete round 9 of REACT-1 comprising round 9a in which swabs were collected from 4th to 12th February 2021 and round 9b from 13th to 23rd February 2021. We also compare the results of REACT-1 round 9 to round 8, in which swabs were collected mainly from 6th January to 22nd January 2021. Results Out of 165,456 results for round 9 overall, 689 were positive. Overall weighted prevalence of infection in the community in England was 0.49% (0.44%, 0.55%), representing a fall of over two thirds from round 8. However the rate of decline of the epidemic has slowed from 15 (13, 17) days, estimated for the period from the end of round 8 to the start of round 9, to 31 days estimated using data from round 9 alone (lower confidence limit 17 days). When comparing round 9a to 9b there were apparent falls in four regions, no apparent change in one region and apparent rises in four regions, including London where there was a suggestion of sub-regional heterogeneity in growth and decline. Smoothed prevalence maps suggest large contiguous areas of growth and decline that do not align with administrative regions. Prevalence fell by 50% or more across all age groups in round 9 compared to round 8, with prevalence (round 9) ranging from 0.21% in those aged 65 and over to 0.71% in those aged 13 to 17 years. Round 9 prevalence was highest among Pakistani participants at 2.1% compared to white participants at 0.45% and Black participants at 0.83%. There were higher adjusted odds of infection for healthcare and care home workers, for those working in public transport and those working in education, school, nursery or childcare and lower adjusted odds for those not required to work outside the home. Conclusions Community prevalence of swab-positivity has declined markedly between January and February 2021 during lockdown in England, but remains high; the rate of decline has slowed in the most recent period, with a suggestion of pockets of growth. Continued adherence to social distancing and public health measures is required so that infection rates fall to much lower levels. This will help to ensure that the benefits of the vaccination roll-out programme in England are fully realised.

    SARS-CoV-2 antibody magnitude and detectability are driven by disease severity, timing, and assay

    Authors: Michael J Peluso; Saki Takahashi; Jill Hakim; J. Daniel Kelly; Leonel Torres; Nikita S. Iyer; Keirstinne Turcios; Owen Janson; Sadie E. Munter; Cassandra Thanh; Christopher C. Nixon; Rebecca Hoh; Viva Tai; Emily Fehrman; Yanel Hernandez; Matthew A. Spinelli; Monica Gandhi; Mary-Ann Palafox; Ana Vallari; Mary A. Rodgers; John Prostko; John Hackett Jr.; Lan Trinh; Terri Wrin; Christos J. Petropoulos; Charles Y. Chiu; Philip J. Norris; Clara DiGermanio; Mars Stone; Michael P. Busch; Susanna K. Elledge; Xin X. Zhou; James A. Wells; Albert Shu; Theodore W. Kurtz; John E. Pak; Wesley Wu; Peter D. Burbelo; Jeffrey I Cohen; Rachel L. Rutishauser; Jeffrey N. Martin; Steven G. Deeks; Timothy J. Henrich; Isabel Rodriguez-Barraquer; Bryan Greenhouse

    doi:10.1101/2021.03.03.21251639 Date: 2021-03-05 Source: medRxiv

    Serosurveillance studies are critical for estimating SARS-CoV-2 transmission and immunity, but interpretation of results is currently limited by poorly defined variability in the performance of antibody assays to detect seroreactivity over time in individuals with different clinical presentations. We measured longitudinal antibody responses to SARS-CoV-2 in plasma samples from a diverse cohort of 128 individuals over 160 days using 14 binding and neutralization assays. For all assays, we found a consistent and strong effect of disease severity on antibody magnitude, with fever MESHD, cough MESHD, hospitalization, and oxygen requirement explaining much of this variation. We found that binding assays measuring responses to spike protein PROTEIN had consistently higher correlation with neutralization than those measuring responses to nucleocapsid, regardless of assay format and sample timing. However, assays varied substantially with respect to sensitivity during early convalescence and in time to seroreversion. Variations in sensitivity and durability were particularly dramatic for individuals with mild infection, who had consistently lower antibody titers and represent the majority of the infected population, with sensitivities often differing substantially from reported test characteristics (e.g., amongst commercial assays, sensitivity at 6 months ranged from 33% for ARCHITECT IgG to 98% for VITROS Total Ig). Thus, the ability to detect previous infection by SARS-CoV-2 is highly dependent on the severity of the initial infection, timing relative to infection, and the assay used. These findings have important implications for the design and interpretation of SARS-CoV-2 serosurveillance studies.

    COVID Symptoms, Symptom Clusters, and Predictors for Becoming a Long-Hauler:Looking for Clarity in the Haze of the Pandemic

    Authors: Yong Huang; Melissa D Pinto; Jessica L Borelli; Milad Asgari Mehrabadi; Heather Abrihim; Nikil Dutt; Natalie Lambert; Erika L Nurmi; Rana Chakraborty; Amir M Rahmani; Charles Downs

    doi:10.1101/2021.03.03.21252086 Date: 2021-03-05 Source: medRxiv

    Emerging data suggest that the effects of infection with SARS-CoV-2 are far reaching extending beyond those with severe acute disease MESHD. Specifically, the presence of persistent symptoms after apparent resolution from COVID-19 MESHD have frequently been reported throughout the pandemic by individuals labeled as long-haulers. The purpose of this study was to assess for symptoms at days 0-10 and 61+ among subjects with PCR-confirmed SARS-CoV-2 infection MESHD. The UCCORDS dataset was used to identify 1407 records that met inclusion criteria. Symptoms attributable to COVID-19 MESHD were extracted from the electronic health record, Symptoms reported over the previous year prior to COVID-19 MESHD were excluded, using nonnegative matrix factorization (NMF) followed by graph lasso to assess relationships between symptoms. A model was developed predictive for becoming a long-hauler based on symptoms. 27% reported persistent symptoms after 60 days. Women were more likely to become long- haulers, and all age groups were represented with those aged 50 +/- 20 years comprising 72% of cases. Presenting symptoms included palpitations, chronic rhinitis MESHD, dysgeusia MESHD, chills, insomnia MESHD, hyperhidrosis MESHD, anxiety MESHD, sore throat, and headache MESHD among others. We identified 5 symptom clusters at day 61+: chest pain-cough MESHD, dyspnea-cough MESHD, anxiety-tachycardia MESHD, abdominal pain-nausea MESHD, and low back pain-joint pain MESHD. Long-haulers represent a very significant public health concern, and there are no guidelines to address their diagnosis and management. Additional studies are urgently needed that focus on the physical, mental, and emotional impact of long-term COVID-19 MESHD survivors who become long-haulers.

    SARS-CoV-2 Load does not Predict Transmissibility in College Students

    Authors: Di Tian; Zhen Lin; Ellie M. Kriner; Dalton J. Esneault; Jonathan Tran; Julia C. DeVoto; Naima Okami; Rachel Greenberg; Sarah Yanofsky; Swarnamala Ratnayaka; Nicholas Tran; Maeghan Livaccari; Marla Lampp; Noel Wong; Scott Tims; Patrick Norton; John Scott; Tony Y. Hu; Robert Garry; Patrice Delafontaine; Lee Hamm; Xiao-Ming Yin

    doi:10.1101/2021.03.02.21252105 Date: 2021-03-05 Source: medRxiv

    SARS-CoV2 is highly contagious and the global spread has caused significant medical, social and economic impacts. Other than vaccination, effective public health measures, including contact tracing, isolation and quarantine, is critical for deterring viral transmission, preventing infection progression and resuming normal activities. Viral transmission is affected by many factors but the viral load and vitality could be among the most important ones. Although in vitro culture studies have indicated that the amount of virus isolated from infected people determines the successful rate of virus isolation, whether the viral load carried at the individual level would affect the transmissibility was not known. We aimed to determine whether the Ct value, a measurement of viral load by RT-PCR assay, could differentiate the spreader from the non-spreader in a population of college students. Our results indicate that while at the population level the Ct value is lower, suggesting a higher viral load, in the symptomatic spreaders than the asymptomatic non-spreaders, there is a significant overlap in the Ct values between the two groups. Thus Ct values, or the viral load, at the individual level could not predict the transmissibility. Our studies also suggest that a sensitive method to detect the presence of virus is needed to identify asymptomatic persons who may carry a low viral load but can still be infectious.

    Age-dependent immune response to the Biontech/Pfizer BNT162b2 COVID-19 MESHD vaccination

    Authors: Lisa Müller; Marcel Andree; Wiebke Moskorz; Ingo Drexler; Lara Walotka; Ramona Grothmann; Johannes Ptok; Jonas Hillebrandt; Anastasia Ritchie; Denise Rabl; Philipp Niklas Ostermann; Rebekka Robitzsch; Sandra Hauka; Andreas Walker; Christopher Menne; Ralf Grutza; Jörg Timm; Ortwin Adams; Heiner Schaal

    doi:10.1101/2021.03.03.21251066 Date: 2021-03-05 Source: medRxiv

    Background: The SARS-CoV-2 pandemic has led to the development of various vaccines. Real-life data on immune responses elicited in the most vulnerable group of vaccinees over 80 years old is still underrepresented despite the prioritization of the elderly in vaccination campaigns. Methods: We conducted a cohort study with two age groups, young vaccinees below the age of 60 and elderly vaccinees over the age of 80, to compare their antibody responses to the first and second dose of the BNT162b2 COVID-19 MESHD vaccination. Results: While the majority of participants in both groups produced specific IgG antibody titers against SARS-CoV-2 spike PROTEIN protein, titers were significantly lower in elderly participants. Although the increment of antibody levels after the second immunization was higher in elderly participants, the absolute mean titer of this group remained lower than the <60 group. After the second vaccination, 31.3 % of the elderly had no detectable neutralizing antibodies in contrast to the younger group, in which only 2.2% had no detectable neutralizing antibodies. Conclusion: Our data suggests that lower frequencies of neutralizing antibodies after BNT162b2 vaccination in the elderly population may require earlier revaccination to ensure strong immunity and protection against infection.

    Just 2% of SARS-CoV-2-positive individuals carry 90% of the virus circulating in communities

    Authors: Qing Yang; Tassa K Saldi; Erika Lasda; Carolyn J Decker; Camille L Paige; Denise G Muhlrad; Patrick K Gonzales; Morgan R Fink; Kimngan L Tat; Cole R Hager; Jack C Davis; Christopher D Ozeroff; Nicholas R Meyerson; Stephen K Clark; Will T Fattor; Alison R Gilchrist; Arturo Barbachano-Guerrero; Emma R Worden-Sapper; Sharon S Wu; Gloria R Brisson; Matthew B McQueen; Robin D Dowell; Leslie A Leinwand; Roy R Parker; Sara Sawyer

    doi:10.1101/2021.03.01.21252250 Date: 2021-03-05 Source: medRxiv

    We analyze data from the Fall 2020 pandemic response efforts at the University of Colorado Boulder (USA), where more than 72,500 saliva samples were tested for SARS-CoV-2 using quantitative RT-PCR. All samples were collected from individuals who reported no symptoms associated with COVID-19 MESHD on the day of collection. From these, 1,405 positive cases were identified. The distribution of viral loads within these asymptomatic individuals was indistinguishable from what has been previously reported in symptomatic individuals. Regardless of symptomatic status, approximately 50% of individuals who test positive for SARS-CoV-2 seem to be in non-infectious phases of the disease, based on having low viral loads in a range from which live virus has rarely been isolated. We find that, at any given time, just 2% of individuals carry 90% of the virions circulating within communities, serving as viral super-carriers and possibly also super-spreaders.

    Clinical course and risk factors for in-hospital mortality of 205 patients with SARS-CoV-2 pneumonia MESHD in Como, Lombardy Region, Italy

    Authors: Mauro Turrini; Angelo Gardellini; Livia Beretta; Lucia Buzzi; Stefano Ferrario; Sabrina Vasile; Raffaella Clerici; Andrea Colzani; Luigi Liparulo; Giovanni Scognamiglio; Gianni Imperiali; Giovanni Corrado; Antonella Strada; Marco Galletti; Nunzio Castiglione; Claudio Zanon

    doi:10.1101/2021.02.25.20134866 Date: 2021-03-05 Source: medRxiv

    Importance: With randomized clinical trials ongoing and vaccine still a long distance away, efforts to repurpose old medications used for other diseases provide hope for treatment of COVID-19 MESHD. Objectives: To examine the risk factors for in-hospital mortality and describe the effectiveness of different treatment strategies in a real-life setting of patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia MESHD. Design: Real-life single-center study during the Lombardy COVID-19 MESHD outbreak. Setting: Valduce Hospital in Como, Lombardy Region, Italy. Participants: 205 laboratory-confirmed patients presenting with SARS-Cov-2 pneumonia MESHD requiring hospitalization. Interventions: All patients received best supportive care and, based on their clinical needs and comorbidities, specific interventions that included the main drugs being tested for repurposing to treat COVID-19 MESHD, such as hydroxychloroquine, anticoagulation, antiviral drugs, steroids or interleukin-6 HGNC pathway inhibitors. Main outcomes and measures: Clinical, laboratory and treatment characteristics were analyzed with univariate and multivariate logistic regression methods to explore their impact on in-hospital mortality and compared with current literature data. Results: Univariate analyses for clinical variables showed prognostic significance for age equal or greater than 70 years (estimated 28-days survival: 21.4 vs 67.4%; p<0.0001), presence of 2 or more relevant comorbidities (35.3 vs 61.8%; p=0.0008), ratio of arterial oxygen partial pressure to fractional inspired oxygen (P/F) less than 200 at presentation (21-days survival: 14.7 vs 52.4%;p<0.0001), high levels of lactate dehydrogenase (LDH) (26.4 vs 65.3%; p=0.0001), and elevated C-reactive protein HGNC (CRP) values (25.4 vs 74.9%; p=0.0001), while no statistical significance was found for all the other clinical variables tested. At univariate analysis for the different treatment scheduled, prognostic significance for survival was showed for intermediate or therapeutic-dose anticoagulation (estimated 28-days survival: 37.1 vs 23.4%; p=0.0001), hydroxychloroquine (35.7 vs 27.3%; p=0.0029), early antiviral therapy with lopinavir/ritonavir (60.1 vs 22.4%; p<0.0001), late short-course of steroids (47.9 vs 18.2%; p<0.0001) or tocilizumab therapy (69.4 vs 29.4%; p=0.0059). Multivariable regression confirmed increasing odds of in-hospital death associated with age older than 70 years (odds ratio 3.26, 95% CI 1.81 - 5.86; p<0.0001) and showed a reduction in mortality for patients treated with anticoagulant (-0.37, 0.49 - 0.95; p=0.0273), antiviral (-1.22, 0.16 - 0.54; p<0.0001), or steroids (-0.59, 0.35 - 0.87; p=0.0117) therapy.

    Dramatic Rise of Seroprevalence Rates of SARS-CoV-2 Antibodies among Healthy Blood Donors: The evolution of a Pandemic

    Authors: Maher A Sughayer; Asem Mansour; Abeer Al Nuirat; Lina Souan; Mohammad Ghanem; Mahmoud Siag

    doi:10.1101/2021.03.02.21252448 Date: 2021-03-05 Source: medRxiv

    Background: The coronavirus disease 2019 MESHD ( COVID-19 MESHD) pandemic has resulted in more than 106 million cases of confirmed infection and more than 2.3 million deaths worldwide as of February 11th 2021. Seroprevalence studies are extremely useful in studying and assessing the epidemiological status in the community and the degree of spread. They help decision makers in implementing or relaxing mitigating measures to contain the disease in addition to other benefits. Objective: To study the seroprevalence rates of SARS-CoV-2 antibodies among healthy blood donors in Jordan, at various points of time as the pandemic evolves in the community. Methods: A total of 1374 blood donor were tested for the SARS-CoV-2 antibodies in 3 groups. The first group of 746 and the second of 348 individuals were tested in June and September of 2020 respectively. The 3rd group of 292 were tested in early February of 2021. We utilized a qualitative assay that uses Electrochemiluminescence method (ECLIA) that has a specificity and sensitivity of 99.8% and 100% respectively. Results: The first 2 groups representing the months of January to September of 2020, where the number of confirmed Covid-19 MESHD cases were several hundred to 3000 showed a seroprevalence rate of 0% (95% CI 0.00%, 0.51%). The 3rd group representing late January and early February 2021 when the number of reported confirmed case has reached 100 folds the numbers of September 2020, showed a seroprevalence of 27.4% (95% CI 22.5% and 32.9%). Conclusions: a dramatic rise in seroprevalence of SARS-CoV-2 antibodies was seen among healthy blood donors in Jordan in parallel with wide-spread intracommunity transmission of the disease. This information is useful to assess the degree of herd immunity and provides for better understanding of the pandemic.

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MeSH Disease
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