Corpus overview


Overview

MeSH Disease

Human Phenotype

Transmission

Seroprevalence
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    The relative infectiousness of asymptomatic TRANS SARS-CoV-2 infected persons compared with symptomatic individuals: A rapid scoping review.

    Authors: David Mc Evoy; Conor G McAloon; Aine B Collins; Kevin Hunt; Francis Butler; Andrew W Byrne; Miriam Casey; Ann Barber; John M Griffin; Elizabeth A Lane; Patrick Wall; Simon J More

    doi:10.1101/2020.07.30.20165084 Date: 2020-08-01 Source: medRxiv

    Objectives: The aim of this study was to conduct a scoping review of estimates of the relative infectiousness of asymptomatic TRANS persons infected with SARS-CoV-2 compared with symptomatic individuals. Design: Rapid scoping review of literature available until 8th April 2020. Setting: International studies on the infectiousness of individuals infected with SARS-CoV-2 Participants: Studies were selected for inclusion if they defined asymptomatics TRANS as a separate cohort distinct from pre-symptomatics and if they provided a quantitative measure of the infectiousness of asymptomatics TRANS relative to symptomatics. Primary outcome measures: The relative number of secondary cases TRANS produced by an average primary case TRANS, the relative probability of transmitting infection MESHD upon contact, and the degree of viral shedding. Results: Very few studies reported estimates of relative infectiousness of asymptomatic TRANS compared with symptomatic individuals. Significant differences exist in the definition of infectiousness. Viral shedding studies in general show no difference in shedding levels between symptomatic and asymptomatic TRANS individuals but are likely to be impacted by insufficient statistical power. Two contact tracing TRANS studies provided estimates of 0.7 and 1.0, but differences in approach and definition preclude comparison across the two studies. Finally, two modelling studies suggest a relative infectiousness of around 0.5 but one of these was more reflective of the infectiousness of undocumented rather than asymptomatic TRANS cases. Importantly, one contact tracing TRANS study showing a very low level of infectiousness of asymptomatic TRANS was not included in the analysis at this point due difficulties interpreting the reported findings. Conclusions: The present study highlights the need for additional studies in this area as a matter of urgency. For the purpose of epidemiological modelling, we cautiously suggest that at present, asymptomatics TRANS could be considered to have a degree of infectiousness which is about 0.40-0.70 that of symptomatics. However, it must be stressed that this suggestion comes from a very low evidence base and that estimates exist that are close to zero and close to 1.

    Spinal Epidural Abscess MESHD Abscess HP in COVID-19 patients

    Authors: Giuseppe Talamonti; Davide Colistra; Francesco Crisà; Marco Cenzato; Pietro Giorgi; Giuseppe D'Aliberti

    doi:10.21203/rs.3.rs-38110/v1 Date: 2020-06-27 Source: ResearchSquare

    Objective: To report the peculiarities of spinal epidural abscess MESHD abscess HP in COVID-19 patients, because we observed an unusually high number of these patients following the outbreak of SARS-Corona Virus-2.Methods: We reviewed the clinical documentation of six consecutive COVID-19 patients with primary spinal epidural abscess MESHD abscess HP that we had to surgically manage during a two-month period. These cases were analyzed for what concerns both the viral infection MESHD and the spinal abscess MESHD abscess HP.Results: Abscess was primary in all cases TRANS meaning that no evident infective source was found. Primary abscess MESHD abscess HP represents the rarest form of spinal epidural abscess MESHD abscess HP, which is usually secondary to invasive procedures or spreading from adjacent infective sites, such as spondylodiscitis and generally occurs in patients with diabetes, obesity MESHD obesity HP, cancer, or other chronic disease MESHD. In all cases, there was mild lymphopenia MESHD lymphopenia HP but the spinal abscess MESHD abscess HP occurred regardless the severity of the viral disease MESHD, the immunologic state, and the presence of bacteremia MESHD bacteremia HP. Obesity MESHD Obesity HP was the only risk factor and was reported just in two patients. All patients but one were hypertensive. The preferred localizations were cervical and thoracic, whereas the classic abscess MESHD abscess HP generally occurs at lumbar level. No patient had history of pyogenic infection MESHD, even though previous asymptomatic TRANS bacterial contaminations were reported in three cases.Conclusion: We wonder about the concentration of this uncommon disease MESHD in a so short period. To our knowledge, cases of epidural spinal abscess MESHD abscess HP in COVID-19 patients have been not yet reported. Accordingly, we ignore if the SARS-Corona Virus-2 may really predispose to spinal epidural abscesses MESHD abscesses HP. However, we hypothesize that, in our patients, the spinal infection MESHD could have depended on the coexistence of an initially asymptomatic TRANS bacterial contamination. The well-known COVID-19-related endotheliitis might have created the conditions for retrograde bacterial invasion of the correspondent spinal epidural space. Anyway, the spinal epidural abscess MESHD abscess HP carries significantly high morbidity and mortality. It is difficult to diagnose, especially in compromised COVID-19 patients but it should be kept in mind because early diagnosis and treatment are crucial.

    Incubation period TRANS and serial interval TRANS of Covid-19 in a chain of infections MESHD in Bahia Blanca (Argentina)

    Authors: Valentina Viego; Milva Geri; Juan Castiglia; Ezequiel Jouglard

    doi:10.1101/2020.06.18.20134825 Date: 2020-06-20 Source: medRxiv

    Objective: To estimate the incubation period TRANS and the serial interval TRANS of Covid-19 from a sample of symptomatic patients in Bahia Blanca city. Methods: We collected dates of illness onset for primary cases TRANS (infectors) and secondary cases TRANS (infectees) for the first 18 secondary patients infected with SARS-Cov-2 in Bahia Blanca (Argentina). We ranked the fiability of the data depending upon certainty about the identification of the infector and the date of exposition to infector. The sample has some missing values. In the case of incubation, as 3 patients were infected by other household members, we only have 15 observations with an observed date of exposition. For the estimation of serial interval TRANS, one patient became ill from close contact TRANS with an asymptomatic TRANS infectious. Also, estimations of both the incubation period TRANS and the serial interval TRANS were carried using the full sample and a subsample with higher certainty about the transmissor and date of exposition. By the time the dataset was prepared all infectors were recovered so estimations do need to take into account right censoring. Results: The mean incubation period TRANS for symptomatic patients is 7.9 days (95% CI: 4.6, 11.1) considering the sample of 15 cases patients and 7.5 days (95% CI: 4.1, 10.9) if the sample is restricted to the most certain cases (n=12). The median is 6.1 (95% CI: 4.1, 9.2) and 5.8 (95% CI: 3.6, 9.3) respectively. Moreover, 97.5% of symptomatic cases will develop symptoms after 13.6 days from exposition (95% CI 10.7, 16.5). The point estimation for the mean serial interval TRANS is 6.8 days (95% CI: 4.0-9.6). Considering only the most certain pairs, the mean serial interval TRANS is estimated at 5.5 days (95% CI: 2.8, 8.1). The estimated median serial intervals TRANS were 5.2 (95% CI: 3.0, 8.1) and 4.1 (95% CI: 2.0, 6.9) days respectively. Conclusions: Evidence from Bahia Blanca (Argentina) suggests that the median and mean serial interval TRANS of Covid-19 is shorter than the incubation period TRANS. This suggests that a pre-symptomatic transmission TRANS is not negligible. Comparisons with foreign estimates show that incubation period TRANS and serial interval TRANS could be longer in Bahia Blanca city than in other regions. That poses a signal of opportunity to attain more timely contact tracing TRANS and effective isolation.

    Seroprevalence SERO against COVID-19 and follow-up of suspected cases in primary TRANS health care in Spain

    Authors: Carlos Brotons; Jordi Serrano; Diana Fernandez; Carlos Garcia-Ramos; Begona Ichazo; Jeannine Lemaire; Patricia Montenegro; Irene Moral; Ricky Perez- Wienese; Marc Pitarch; Mireia Puig; Maria Teresa Vilella; Jaume Sellares

    doi:10.1101/2020.06.13.20130575 Date: 2020-06-16 Source: medRxiv

    Background During the coronavirus disease MESHD 2019 (COVID-19) pandemic little information has been available about patients with mild or moderate symptoms attended and followed in the primary care setting, most of whom had an unknown status for the severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) infection MESHD. Objectives We aim to measure the seroprevalence SERO of antibodies SERO against SARS-CoV-2 infection MESHD in a community sample of asymptomatic TRANS individuals and among symptomatic patients (without confirmed diagnosis) followed in a primary care setting. As a secondary objective, we estimated the proportions of symptomatic patients seeing at an emergency MESHD department (ED), hospitalized or dying, and identified the most important clinical symptoms associated with a positive infection MESHD. Methods From April 21 to April 24 2020, we selected a random sample of 600 individuals stratified by age groups TRANS, from a total population of 19,899 individuals from a community area in Barcelona (study population 1). From April 29 to May 5 2020, we also invited all the patients that had been followed by general practitioners (GPs) (study population 2). We used for both populations COVID-19 Rapid lateral flow immunoassay SERO which qualitatively assesses the presence of patient-generated IgG and IgM in approximately 10-15 minutes. The prevalence SERO (95% confidence intervals [CI]) of infection MESHD (past and current) was defined as the proportion of individuals with antibody SERO seropositivity. Odds ratios (ORs) for a positive test result were estimated using logistic regression analysis. Results Three hundred and eleven asymptomatic TRANS individuals from the randomly selected sample accepted to participate in the study. The overall mean age TRANS was 43.7 years (SD 21.79, range 1-94) and 55% were women. Seventeen individuals were seropositive for IgM and/or IgG, resulting an overall prevalence SERO of 5,47% (95% CI, 3.44-8.58). Six-hundred and thirty-four symptomatic patients were followed by GPs. The overall mean age TRANS was 46.97 years (SD 20.05, range 0-92) and 57.73% were women. Of these, 244 patients (38.49%) were seropositive for IgM and/or IgG. During the follow-up period, 27.13% of symptomatic patients attended the ED, 11.83% were hospitalized and about 2% died. Results of the multivariate logistic regression analysis showed that the OR for a positive test was significantly increased in patients who had fever MESHD fever HP (>38{degrees}C), ageusia MESHD and contact with a patient diagnosed with COVID-19. Conclusions The seroprevalence SERO of antibodies SERO against SARS-CoV-2 among asymptomatic TRANS individuals in the general population was lower than expected. Approximately 40% of the symptomatic patients followed by GPs during the peak months of the pandemic in Barcelona, were positive. Fever MESHD Fever HP (>38{degrees}C), anosmia HP, ageusia MESHD and contact with a patient diagnosed with COVID-19 were associated with a positive test result.

    Healthcare Worker COVID-19 Cases in Ontario, Canada: A Cross-sectional Study

    Authors: Kevin L Schwartz; Camille Achonu; Sarah A Buchan; Kevin A Brown; Brenda Lee; Michael Whelan; Julie HC Wu; Gary Garber

    doi:10.1101/2020.06.12.20129619 Date: 2020-06-14 Source: medRxiv

    Importance: Protecting healthcare workers (HCWs) from COVID-19 is a priority to maintain a safe and functioning healthcare system. The risk of transmitting COVID-19 to family members TRANS is a source of stress for many. Objective: To describe and compare HCW and non-HCW COVID-19 cases in Ontario, Canada, as well as the frequency of COVID-19 among HCWs household members. Design, Setting, and Participants: Using reportable disease MESHD data at Public Health Ontario which captures all COVID-19 cases in Ontario, Canada, we conducted a population-based cross-sectional study comparing demographic, exposure, and clinical variables between HCWs and non-HCWs with COVID-19 as of 14 May 2020. We calculated rates of infections MESHD over time and determined the frequency of within household transmissions TRANS using natural language processing based on residential address. Exposures and Outcomes: We contrasted age TRANS, gender TRANS, comorbidities, clinical presentation (including asymptomatic TRANS and presymptomatic), exposure histories including nosocomial transmission TRANS, and clinical outcomes between HCWs and non-HCWs with confirmed COVID-19. Results: There were 4,230 (17.5%) HCW COVID-19 cases in Ontario, of whom 20.2% were nurses, 2.3% were physicians, and the remaining 77.4% other specialties. HCWs were more likely to be between 30-60 years of age TRANS and female TRANS. HCWs were more likely to present asymptomatically TRANS (8.1% versus 7.0%, p=0.010) or with atypical symptoms (17.8% versus 10.5%, p<0.001). The mortality among HCWs was 0.2% compared to 10.5% of non-HCWs. HCWs commonly had exposures to a confirmed case TRANS or outbreak (74.1%), however only 3.1% were confirmed to be nosocomial. The rate of new infections MESHD was 5.5 times higher in HCWs than non-HCWs, but mirrored the epidemic curve. We identified 391 (9.8%) probable secondary household transmissions TRANS and 143 (3.6%) acquisitions. Children TRANS <19 years comprised 14.6% of secondary cases TRANS compared to only 4.2% of the primary cases TRANS. Conclusions and Relevance: HCWs represent a disproportionate number of COVID-19 cases in Ontario but with low confirmed numbers of nosocomial transmission TRANS. The data support substantial testing bias and under-ascertainment of general population cases. Protecting HCWs through appropriate personal protective equipment and physical distancing from colleagues is paramount.

    Power Laws in Superspreading Events: Evidence from Coronavirus Outbreaks and Implications for SIR Models

    Authors: Masao Fukui; Chishio Furukawa

    doi:10.1101/2020.06.11.20128058 Date: 2020-06-12 Source: medRxiv

    While they are rare, superspreading events (SSEs), wherein a few primary cases TRANS infect an extraordinarily large number of secondary cases TRANS, are recognized as a prominent determinant of aggregate infection MESHD rates ( R0 TRANS). Existing stochastic SIR models incorporate SSEs by fitting distributions with thin tails, or finite variance, and therefore predicting almost deterministic epidemiological outcomes in large populations. This paper documents evidence from recent coronavirus outbreaks, including SARS, MERS, and COVID-19, that SSEs follow a power law distribution with fat tails, or infinite variance. We then extend an otherwise standard SIR model with estimated power law distributions, and show that idiosyncratic uncertainties in SSEs will lead to large aggregate uncertainties in infection MESHD dynamics, even with large populations. That is, the timing and magnitude of outbreaks will be unpredictable. While such uncertainties have social costs, we also find that they on average decrease the herd immunity thresholds and the cumulative infections MESHD because per-period infection MESHD rates have decreasing marginal effects. Our findings have implications for social distancing interventions: targeting SSEs reduce not only the average rate of infection MESHD ( R0 TRANS) but also its uncertainty. To understand this effect, and to improve inference of the average reproduction numbers TRANS under fat tails, estimating the tail distribution of SSEs is vital.

    Detecting the Emergent or Re-Emergent COVID-19 Pandemic in a Country: Modelling Study of Combined Primary Care and Hospital Surveillance

    Authors: Nick Wilson; Markus Schwehm; Ayesha J Verrall; Matthew Parry; Michael G Baker; Martin Eichner

    doi:10.1101/2020.05.13.20100743 Date: 2020-05-19 Source: medRxiv

    Aims: We aimed to determine the effectiveness of surveillance using testing for SARS-CoV-2 to identify an outbreak arising from a single case of border control failure at a country level. Methods: A stochastic version of the SEIR model CovidSIM v1.1 designed specifically for COVID-19 was utilised. It was seeded with New Zealand (NZ) population data and relevant parameters sourced from the NZ and international literature. Results: For what we regard as the most plausible scenario with an effective reproduction number TRANS of 2.0, the results suggest that 95% of outbreaks from a single imported case would be detected in the period up to day 33 after introduction. At the time point of detection, there would be a median number of 6 infected cases in the community (95%UI: 1-68). To achieve this level of detection, an on-going programme of 7,800 tests per million people per week for the NZ population would be required. The vast majority of this testing (96%) would be of symptomatic cases in primary TRANS care settings and the rest in hospitals. Despite the large number of tests required, there are plausible strategies to enhance testing yield and cost-effectiveness eg, (i) adjusting the eligibility criteria via symptom profiles; (ii) and pooling of test samples. Conclusions: This model-based analysis suggests that a surveillance system with a very high level of routine testing is probably required to detect an emerging or re-emerging SARS-CoV-2 outbreak within one month of a border control failure in a nation.

    Self-reported loss of smell and taste in SARS-CoV-2 patients: primary care data to guide future early detection strategies 

    Authors: Benoit Tudrej; Paul Sebo; Julie Lourdaux; Clara Cuzin; Martin Floquet; Dagmar M Haller; Hubert Maisonneuve

    doi:10.21203/rs.3.rs-28701/v1 Date: 2020-05-13 Source: ResearchSquare

    The early identification of new cases of SARS-CoV-2 infection MESHD in primary care is of outmost importance in the current pandemia. We conducted a preliminary study involving 816 primary care patients undergoing RT-PCR testing for a suspicion of COVID-19. We examined the association between smell or taste disorders MESHD and a positive SARS-CoV-2 test, and computed the performance SERO of these symptoms in predicting a positive test. Smell or taste disorders MESHD were significantly associated with positive RT-PCR with an adjusted OR=6.3 (95%CI 5.2-7.5). Once confinement measures are lifted, our data could further inform triage and early identification of new clusters of cases through primary TRANS care.

    A SARS-CoV-2 Coronavirus Antigen-Detecting Half-Strip Lateral Flow Assay Towards the Development of Point of Care Tests Using Commercially Available Reagents

    Authors: Benjamin D. Grant; Caitlin E. Anderson; John R Williford; Luis F. Alonzo; Veronika A. Glukhova; David S. Boyle; Bernhard H. Weigl; Kevin P Nichols

    doi:10.26434/chemrxiv.12250142.v1 Date: 2020-05-07 Source: ChemRxiv

    The SARS-CoV-2 pandemic has created an unprecedented need for rapid diagnostic testing to enable the efficient treatment and mitigation of COVID-19. The primary diagnostic tool currently employed is reverse transcription polymerase chain reaction (RT-PCR), which can have good sensitivity SERO and excellent specificity. Unfortunately, implementation costs and logistical problems with reagents during the global SARS-CoV-2 pandemic have hindered its universal on demand adoption. Lateral flow assays (LFAs) represent a class of diagnostic that, if sufficiently clinically sensitive, may fill many of the gaps in the current RT-PCR testing regime, especially in low- and middle-income countries (LMICs). To date, many serology LFAs have been developed, though none meet the performance SERO requirements necessary for diagnostic use cases, primarily TRANS due to the relatively long delay between infection MESHD and seroconversion. However, based on previously reported results from SARS-CoV-1, antigen-based SARS-CoV-2 assays may have significantly better clinical sensitivity SERO than serology assays. To date, only a very small number of antigen-detecting LFAs have been developed. Development of a half-strip LFA is a useful first step in the development of any LFA format. In this paper we present a half-strip LFA using commercially available antibodies SERO for the detection of SARS-CoV-2. We have tested this LFA in buffer and measured an LOD of 0.62 ng/mL using an optical reader with sensitivity SERO equivalent to a visual read. Further development, including evaluating the appropriate sample matrix, will be required for this assay approach to be made useful in a point of care setting, though this half-strip LFA may serve as a useful starting point for others developing similar tests.

    Exit strategies: optimising feasible surveillance for detection, elimination and ongoing prevention of COVID-19 community transmission TRANS

    Authors: Kamalini Lokuge; Emily Banks; Stephanie Davis; Leslee Roberts; Tatum Street; Grazia Caleo; Kathryn Glass

    doi:10.1101/2020.04.19.20071217 Date: 2020-04-23 Source: medRxiv

    Background Following successful implementation of strong containment measures by the community, Australia is now close to the point of eliminating detectable community transmission TRANS of COVID-19. We aimed to develop an efficient, rapid and scalable surveillance strategy for detecting all remaining COVID-19 community transmission TRANS through exhaustive identification of every active transmission chain TRANS. We also identified measures to enable early detection and effective management of any reintroduction of transmission TRANS once containment measures are lifted to ensure strong containment measures do not need to be reinstated. Methods We compared efficiency and sensitivity SERO to detect community transmission chains TRANS through testing of: hospital cases; primary TRANS care fever MESHD fever HP and cough MESHD cough HP patients; or asymptomatic TRANS community members, using surveillance evaluation methods and mathematical modelling, varying testing capacities and prevalence SERO of COVID-19 and non-COVID-19 fever MESHD fever HP and cough MESHD cough HP, and the reproduction number TRANS. System requirements for increasing testing to allow exhaustive identification of all transmission chains TRANS, and then enable complete follow-up of all cases and contacts within each chain, were assessed per million population. Findings Assuming 20% of cases are asymptomatic TRANS and all symptomatic COVID-19 cases present to primary care, with high transmission TRANS (R=2.2) there are a median of 13 unrecognised community cases (5 infectious) when a transmission chain TRANS is identified through hospital surveillance versus 3 unrecognised cases (1 infectious) through primary care surveillance. 3 unrecognised community upstream community cases themselves are estimated to generate a further 22-33 contacts requiring follow-up. The unrecognised community cases rise to 5 if only 50% of symptomatic cases present to primary care. Screening for asymptomatic disease MESHD asymptomatic TRANS in the community cannot exhaustively identify all transmission TRANS under any of the scenarios assessed. The additional capacity required to screen all fever MESHD fever HP and cough MESHD cough HP primary care patients would be approximately 2,000 tests/million population per week using 1/16 pooling of samples. Interpretation Screening all syndromic fever MESHD fever HP and cough MESHD cough HP primary care presentations, in combination with exhaustive and meticulous case and contact identification and management, enables appropriate early detection and elimination of community transmission TRANS of COVID-19. If testing capacity is limited, interventions such as pooling allow increased case detection, even given reduced test sensitivity SERO. Wider identification and testing of all upstream contacts, (i.e. potential sources of infection MESHD for identified cases, and their related transmission chains TRANS) is critical, and to be done exhaustively requires more resources than downstream contact tracing TRANS. The most important factor in determining the performance SERO of such a surveillance system is community participation in screening and follow up, and as such, appropriate community engagement, messaging and support to encourage presentation and compliance is essential. We provide operational guidance on implementing such a system.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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