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in category infectious diseases

4,256 results found. For more information, click each entry to expand.

3861: Thermal Effect On The Persistence Of SARS-CoV2 Egyptian Isolates As Measured By Quantitative RT-PCR
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Posted 15 Oct 2020

Thermal Effect On The Persistence Of SARS-CoV2 Egyptian Isolates As Measured By Quantitative RT-PCR
140 downloads medRxiv infectious diseases

M.G. Seadawy, A.F. Gad, M.F. Elhoseny, B. ELharty, M.S. EL Desoky, Y.A. Soliman

Coronavirus pandemic that caused by severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) appeared in China in 2019 then spread all over the world .COVID-19 firstly appeared in Egypt in Feb 2020. Studies on the thermal stability of the virus is crucial proper specimens transportation for molecular study. Oropharyngeal swabs were taken from recently infected military people with COVID-19 from Egypt during April 2020. Samples were aliquoted and the thermal stability of the virus was measured using quantitative real Time RT-PCR for samples treated at different temperature ranges from 20 {degrees}C to 70 {degrees}C for 2,4and 6 hours. Results shown that inactivation of the virus and significant reduction in the {Delta}Cq values begin at 40 {degrees}C/4h. Complete virus inactivation and loss of {Delta}Cq values were seen at 50 {degrees}C/6h and 60 {degrees}C. Tested samples showed no significant difference in thermal stability at any temp/time combinations tested.

3862: The impact of vaccination on Neisseria gonorrhoeae antimicrobial resistance and prevalence in men who have sex with men: a mathematical modelling study
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Posted 15 Sep 2020

The impact of vaccination on Neisseria gonorrhoeae antimicrobial resistance and prevalence in men who have sex with men: a mathematical modelling study
140 downloads medRxiv infectious diseases

Janneke CM Heijne, Maria Xiridou, Katy Turner, Maartje Basten, Maartje Visser, Birgit van Benthem, Nicola Low

Background. Neisseria gonorrhoeae (gonorrhoea) and antimicrobial-resistant (AMR) gonorrhoea infections disproportionately affect men who have sex with men (MSM). Vaccine development is challenging, but a N. meningitidis (group B) vaccine given to children and young adults was associated with a ca. 30% reduction in gonorrhoea diagnoses. We investigated the impact of vaccination on N. gonorrhoeae AMR development and transmission in MSM. Methods. We developed a compartmental model of N. gonorrhoeae transmission among MSM. AMR to ceftriaxone was incorporated as a stepwise increases in minimum inhibitory concentrations and eventual resistance (MIC drift). We estimated the impact of a partially protective vaccine (reducing susceptibility; 2-years protection) targeting high sexual activity MSM on AMR and prevalence until 2050. We performed sensitivity analyses assuming different levels of vaccine effectiveness (VE) and other modes of vaccine action. Findings. Gonorrhoea model prevalence was 3.4% (95% credible interval 3.2% - 3.8%) in all MSM, 12.5% (95% credible interval 12.1% - 12.7%) in high sexual activity MSM. A vaccine with 30% VE cannot prevent AMR, even with high uptake or durable protection. However, it increases time to AMR development by several years. For a fixed uptake of 40% a vaccine needs a minimum VE of 90% to prevent AMR development completely. A vaccine providing complete protection to infection for those vaccinated was most effective in reducing population prevalence and preventing AMR. Interpretation. A vaccine that has limited efficacy for the prevention of gonorrhoea could delay AMR development in MSM, providing time for developing new antimicrobials and more efficacious vaccines.

3863: An optimised protocol for detection of SARS-COV-2 in stool
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Posted 15 Jan 2021

An optimised protocol for detection of SARS-COV-2 in stool
140 downloads medRxiv infectious diseases

Tianqi Li, Enriqueta Garcia-Gutierrez, Jacob Scadden, Jade Davies, Chloe Hutchins, Alp Aydin, Stefano Romano, Lizbeth Sayavedra, Justin O'Grady, Arjan Narbad

Aim: SARS-CoV-2 has been detected in stool samples of COVID-19 patients, with potential implications for faecal-oral transmission. Compared to swab samples, the complexity of the stool matrix poses a challenge in the detection of the virus that has not yet been solved. The aim of this study was to establish a sensitive and reliable method for detecting SARS-CoV-2 in stool samples. Methods: Stool samples from individuals free of SARS-CoV-2 were homogenised in saline buffer and spiked with a known titre of inactivated virus ranging from 50 to 750 viral particles per 100 mg stool. Debris was removed via centrifugation and supernatants were concentrated by ultrafiltration. RNA was then extracted from the concentrated material using a commercial kit and SARS-CoV-2 was detected via real-time reverse-transcription polymerase chain reaction (RT-qPCR) using the CDC primers and probes. Results: The RNA extraction procedure we used allowed the detection of SARS-CoV-2 via RT-qPCR in most of the stool samples tested. We could detect as few as 50 viral particles per 100 mg of stool. However, high variability was observed across samples at low viral titres. The primer set targeting the N1 region provided more reliable and precise results and for this primer set our method had a limit of detection of 1 viral particle per mg of stool. Conclusions: Here we describe a sensitive method for detecting SARS-CoV-2 in stool samples. This method can be used to establish the persistence of SARS-CoV-2 in stool and ensure the safety of clinical practices such as faecal microbiota transplant (FMT).

3864: Kankasha in Kassala: a prospective observational cohort study of the clinical characteristics, epidemiology, genetic origin, and chronic impact of the 2018 epidemic of Chikungunya virus infection in Kassala, Sudan
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Posted 24 Sep 2020

Kankasha in Kassala: a prospective observational cohort study of the clinical characteristics, epidemiology, genetic origin, and chronic impact of the 2018 epidemic of Chikungunya virus infection in Kassala, Sudan
140 downloads medRxiv infectious diseases

Hilary Bower, Mubarak el Karsany, Abd Alhadi Adam Hussein Hussein, Mubarak Ibrahim Idriss, Maaza Abasher al Zain, Mohamed Elamin Ahmed Alfakiyousif, Rehab Mohamed, Iman Mahmoud, Omer Albadri, Suha Abdulaziz Alnour Mahmoud, Orwa Ibrahim Abdalla, Mawahib Eldigail, Nuha Elagib, Ulrike Arnold, Bernardo Gutierrez, Oliver G Pybus, Daniel P Carter, Steven T Pullan, Shevin T Jacob, Tajeldin Mohammedein Abdallah, Benedict Gannon, Tom Fletcher

Background The public health impact of Chikungunya virus (CHIKV) is often underestimated. Usually considered a mild condition of short duration, recent outbreaks have reported greater incidence of severe illness, fatality, and longer-term disability. In 2018, Eastern Sudan experienced the largest epidemic of CHIKV in Africa to date, affecting an estimated 487,600 people. Known locally as Kankasha, this study examines the clinical characteristics, risk factors, and phylogenetics of the CHIKV epidemic in Kassala City. Methodology and Principal Findings A prospective cohort of 142 cases (102 adults, 40 children) were enrolled at Kassala Teaching Hospital in October 2018. Clinical information, socio-demographic data and sera samples were analysed to confirm diagnosis, characterise illness, and identify the viral strain. CHIKV infection was confirmed by real-time reverse transcription-PCR in 84{middle dot}5 percent of participants. Nine had concurrent CHIKV and Dengue virus (DENV) infection and 28{middle dot}8 percent had a positive Rapid Diagnostic Test for malaria. Five percent had haemorrhagic symptoms including two children with life-threatening haemorrhage. One CHIKV-positive participant died with acute renal injury. Ninety to 120 days post-illness, 63 percent of those followed-up were still experiencing arthralgia in one or more joints, and 11 percent remained moderately disabled using Rapid3 assessment. Phylogenetic analysis showed all CHIKV infections belonged to a single clade within the Indian Ocean Lineage (IOL) of the East-Central-South African (ECSA) genotype. History of contact with an infected person was the only socio-demographic factor associated with infection (p 0{middle dot}01), suggesting that vector transmission in households is important. Conclusions and Significance The epidemic is estimated to have affected approximately 50 percent of Kassala City's population. Substantial vulnerability to CHIKV remains here and elsewhere in Sudan due to widespread Aedes aegypti presence and mosquito-fostering household water storage methods. This study highlights the importance of increasing awareness of the severity and socio-economic impact of CHIKV outbreaks and the need for urgent actions to reduce transmission risk in households.

3865: Toward a COVID-19 testing policy: where and how to test when the purpose is to isolate silent spreaders
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Posted 24 Dec 2020

Toward a COVID-19 testing policy: where and how to test when the purpose is to isolate silent spreaders
140 downloads medRxiv infectious diseases

Ariel L Rivas, AL Hoogesteijn, JB Hittner, Marc H.V. van Regenmortel, Prakasha Kempaiah, P Vogazianos, A Antoniades, A Ioannidis, JL Febles, FO Fasina

BackgroundTo stop pandemics, such as COVID-19, infected individuals should be detected, treated if needed, and -to prevent contacts with susceptible individuals-isolated. Because most infected individuals may be asymptomatic, when testing misses such cases, epidemics may growth exponentially, inducing a high number of deaths. In contrast, a relatively low number of COVID-19 related deaths may occur when both symptomatic and asymptomatic cases are tested. MethodsTo evaluate these hypotheses, a method composed of three elements was evaluated, which included: (i) county- and country-level geo-referenced data, (ii) cost-benefit related considerations, and (iii) temporal data on mortality or test positivity (TP). TP is the percentage of infections found among tested individuals. Temporal TP data were compared to the tests/case ratio (T/C ratio) as well as the number of tests performed/million inhabitants (tests/mi) and COVID-19 related deaths/million inhabitants (deaths/mi). FindingsTwo temporal TP profiles were distinguished, which, early, displayed low ([~] 1 %) and/or decreasing TP percentages or the opposite pattern, respectively. Countries that exhibited >10 TP % expressed at least ten times more COVID-19 related deaths/mi than low TP countries. An intermediate pattern was identified when the T/C ratio was explored. Geo-referenced, TP-based analysis discovered municipalities where selective testing would be more cost-effective than alternatives. InterpretationsWhen TP is low and/or the T/C ratio is high, testing detects asymptomatic cases and the number of COVID-19 related deaths/mi is low. Geo-referenced TP data can support cost-effective, site-specific policies. TP promotes the prompt cessation of epidemics and fosters science-based testing policies. FundingNone Research in contextO_ST_ABSEvidence before this studyC_ST_ABSTo map this field, bibliographic searches were conducted in the Web of Science, which included the following results: (i) COVID-19 (95,133 hits), (ii) SARS COV-2 (33,680 hits), (iii) testing policy and COVID-19 (939 hits), (iv) testing policy and SARS COV-2 (340 hits), (v) testing policy and COVID-19 and asymptomatic (80 hits), (vi) testing policy and SARS COV-2 and asymptomatic (54 hits); (vii) test positivity and COVID-19 and validation (7 hits), and (viii) test positivity and SARS CoV-2 and validation (5 hits). Therefore, before this study, testing policy in relation to asymptomatic cases as well as test positivity represented a very low proportion (between [~]1 thousandth to [~] 1 ten thousandth) of all publications. While many articles distinguished between diagnostic and screening tests, no paper was found in which testing policy is mentioned as part of a process ultimately designed to isolate all infected individuals. The few articles that mentioned test positivity only investigated symptomatic cases. These quanti/qualitative assessments led the authors to infer that neither testing policy nor test positivity had been adequately validated and/or investigated. Added value of this studyWe provide the first validation of test positivity as an estimate of disease prevalence under rapidly changing conditions: in pandemics, disease prevalence may vary markedly within short periods of time. We also address a double limitation of control campaigns against COVID-19, namely: it is unknown who and where to test. Asymptomatic cases are not likely to seek medical assistance: while they feel well, they silently spread this pandemic. Because they represent approximately half of all infected individuals, they are a large, moving, and invisible target. Where to find them is also unknown because (i) randomized testing is likely to fail and (ii) testing is very limited. Usually, the locations where infected people reside are not randomly distributed but geographically clustered, and, up to now less than four persons per thousand inhabitants are tested on a given day. However, by combining geo-referenced test positivity data with cost-benefit considerations, we generate approaches not only likely to induce high benefits without increasing costs but also free of assumptions: we measure bio-geography as it is. Implications of all the available evidenceThe fact that asymptomatic cases were not tested in many countries may explain the exponential growth and much higher number of deaths observed in those countries. Ineffective testing (and, therefore, ineffective isolation) can also result from the absence of geo-referenced data analysis. Because the geographical location where people reside, work, study, or shop is not a random event, the analysis of small greographical areas is essential. Only when actual geographical relationships are observed, optimal (cost-benefit oriented) testing policies can be devised.

3866: Practical considerations for Ultraviolet-C radiation mediated decontamination of N95 respirator against SARS-CoV-2 virus
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Posted 28 Nov 2020

Practical considerations for Ultraviolet-C radiation mediated decontamination of N95 respirator against SARS-CoV-2 virus
140 downloads medRxiv infectious diseases

Guillaume R Golovkine, Allison W Roberts, Chase Cooper, Sebastian Riano, Angela M Diciccio, Daniel L Worthington, Jeffrey P Clarkson, Michael Krames, Jianping Zhang, Ying Gao, Ling Zhou, Scott B. Biering, Sarah A. Stanley

Decontaminating N95 respirators for reuse could mitigate shortages during the COVID-19 pandemic. We tested a portable UV-C light-emitting diode disinfection chamber and found that decontamination efficacy depends on mask model, material and location on the mask. This emphasizes the need for caution when interpreting efficacy data of UV-C decontamination methods.

3867: Candida (Diutina) mesorugosa in Non-Albicans Candida Species Clinical Isolates in Southwest Nigeria
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Posted 26 Jul 2020

Candida (Diutina) mesorugosa in Non-Albicans Candida Species Clinical Isolates in Southwest Nigeria
140 downloads medRxiv infectious diseases

Oloche Owoicho, Judith Uche Oguzie, Tosin Segun Ogunbiyi, Toyin Abdulsalam, Philomena Eromon, Folarin Onikepe, Ernest Uzodimma Durugbo, Christian T. Happi

Introduction The emerging role of non-albicans Candida species (NACS) as causal agents of mild to life-threatening mycoses is increasingly being appreciated. Some NACS are known for intrinsic resistance or reduced susceptibility to some antifungal drugs. To inform therapeutic options and management of candidiasis, we embarked on Candida species surveillance in Southwest Nigeria. Method We obtained retrospective yeast isolates from urogenital samples of patients in a tertiary hospital in south western Nigeria. Among 47 isolates identified phenotypically, we encountered a yeast which failed to produce pseudohyphae in human serum but was morphologically similar to Candida albicans. We characterized this yeast by sequencing the internal transcribed spacer (ITS1-5.8S-ITS2) region of the ribosomal DNA. Results A BLAST search and sequence homology identified the yeast as Candida (Diutina) mesorugosa, with a strong bootstrap. Conclusion Candida mesorugosa, a rarely isolated yeast from clinical samples worldwide, should be considered among potentially relevant NACS in Nigerian clinics. To the best our knowledge, this is the first report of Candida mesorugosa from a patient sample in Nigeria. This finding confirms the need for more specific methods, such as DNA sequencing, for extensive surveillance of NACS. Key words: Candida mesorugosa, Candida rugosa complex, Non-albicans Candida species surveillance, ribosomal DNA sequencing, NACS

3868: The potential impact of human visceral leishmaniasis vaccines on population incidence
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Posted 08 May 2020

The potential impact of human visceral leishmaniasis vaccines on population incidence
140 downloads medRxiv infectious diseases

Epke A Le Rutte, Luc E Coffeng, Stefano Malvolti, Paul M Kaye, Sake J de Vlas

Background: Human visceral leishmaniasis (VL) vaccines are currently under development and there is a need to understand their potential impact on population wide VL incidence. Methodology / Principal Findings: We implement four characteristics from different human VL vaccine candidates into two published VL transmission model variants to estimate the potential impact of these vaccine characteristics on population-wide anthroponotic VL incidence on the Indian subcontinent (ISC). The vaccines that are simulated in this study 1) reduce the infectiousness of infected individuals towards sand flies, 2) reduce risk of developing symptoms after infection, 3) reduce the risk of developing post-kala-azar dermal leishmaniasis (PKDL), or 4) lead to the development of transient immunity. We also compare and combine a vaccine strategy with current interventions to identify their potential role in elimination of VL as public health problem. We show that the first two simulated vaccine characteristics can greatly reduce VL incidence. For these vaccines, an approximate 60% vaccine efficacy would lead to achieving the ISC elimination target (<1 VL case per 10,000 population per year) within 10 years' time in a moderately endemic setting when vaccinating 100% of the population. Vaccinating VL cases to prevent the development of PKDL is a promising tool to sustain the low incidence elimination target after regular interventions are halted. Vaccines triggering the development of transient immunity protecting against infection lead to the biggest reduction in VL incidence, but booster doses are required to achieve perduring impact. Conclusions / Significance: Even though vaccines are not yet available for implementation, their development should be pursued as their potential impact on transmission can be substantial, both in decreasing incidence at the population level as well as in sustaining the ISC elimination target when other interventions are halted.

3869: A systematic review and meta-analysis on the safety and efficacy of tocilizumab in the management of COVID-19
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Posted 29 Jan 2021

A systematic review and meta-analysis on the safety and efficacy of tocilizumab in the management of COVID-19
139 downloads medRxiv infectious diseases

Gollapalle Lakshminarayanashastry Viswanatha, CH K V L S N Anjana Male, Hanumanthappa Shylaja

Background: This systematic review and meta-analysis was aimed to evaluate the therapeutic benefits and safety of tocilizumab (TCZ) in treating severe coronavirus disease 2019 (COVID-19) and associated health complications. Methods: The electronic search was performed using PubMed, Scopus, CENTRAL (Cochrane Central Register of Controlled Trials (RCTs), and Google scholar databases to identify the retrospective observational reports. The studies published from 01 January 2020 to 30th September 2020 involving comparison of TCZ group with SOC/control treatment group were included. The studies included in this work involve RT-PCR confirmed cases of COVID-19 (Population), having tocilizumab and corresponding SOC/control as interventions (Intervention), comparison between tocilizumab versus SOC/control (Comparison) for the parameter of interest. Mortality, incidences of ICU admission, need of mechanical ventilation (MV), length of stay in the hospital (LOS), and length of stay in the ICU (LOS-ICU), and the incidences of super-infection, bacteraemia, fugleman, pneumonia, and pulmonary thrombosis were evaluated as the primary outcomes. The comparison will be between TCZ versus standard of care (SOC)/placebo. Results: Based on the inclusion criteria there were 24 retrospective studies involving 5686 subjects were included. The outcomes of the meta-analysis have revealed that the TCZ has reduced the mortality (Mantel-Haenszel (M-H), random effects risk difference (RE-RD) of -0.11 (-0.18 to -0.04), at 95% CI, p = 0.001, I2 = 88%) and increased the incidences of super-infections (M-H, RE-Risk ratio (RR) of 1.49 (1.13 to 1.96) at 95% CI, p=0.004, I2 = 47%). However, there is no significant difference in ICU admissions rate (M-H, RE-RD of -0.06 (-0.23 to 0.12) at 95% CI, p=0.54, I2 = 93%), need of MV (M-H, RE-RD of 0.00 (-0.06 to 0.07) at 95% CI, p=0.96, I2 = 74%), LOS (Inverse variance (IV): -2.86 (-0.91 to 3.38) at 95% CI, p=0.37, I2 = 100%), LOS-ICU (IV: -3.93 (-12.35 to 4.48) at 95% CI, p=0.36, I2 = 100%), and incidences of pulmonary thrombosis (M-H, fixed effect odds ratio (FE-OR) of 1.01 (0.45 to 2.26) at 95% CI, p=0.99, I2 = 0%) compared to SOC/control. Conclusion: This meta-analysis was performed using retrospective clinical reports on the use of tocilizumab in COVID-19 and based on the outcomes of the meta-analysis we can conclude that administration of TCZ would reduce the risk of mortality, and however there is no much difference observed between the TCZ and SOC/control groups in other parameters such as ICU admission rate, need of mechanical ventilation and length of hospital stay (ICU and Non-ICU). On the other hand, TCZ treated subjects possess higher chances of super-infections and pneumonia compared with SOC/control group. However, there is a need for multi-centric randomized trials to determine the potential therapeutic role of TCZ in mitigating COVID-19 and associated health complications.

3870: The experience of European hospital-based healthcare workers on following infection prevention and control procedures for COVID-19
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Posted 24 Dec 2020

The experience of European hospital-based healthcare workers on following infection prevention and control procedures for COVID-19
139 downloads medRxiv infectious diseases

Denise van Hout, Paul Hutchinson, Marta Wanat, Caitlin Pilbeam, Herman Goossens, Sibyl Anthierens, Sarah Tonkin-Crine, Nina Gobat

BackgroundWorking under pandemic conditions exposes health care workers (HCWs) to infection risk and psychological strain. Protecting the physical and psychological health of HCWs is a key priority. This study assessed the perceptions of European hospital HCWs of local infection prevention and control (IPC) procedures during the COVID-19 pandemic and the impact on their emotional wellbeing. MethodsWe performed two rounds of an international cross-sectional survey, between 31 March and 17 April 2020 via existing research networks (round 1), and between 14 May and 31 August 2020 via online convenience sampling (round 2). Main outcome measures were (1) behavioural determinants of HCW adherence with IPC procedures, (2) WHO-5 Well-Being Index, a validated scale of 0-100 reflecting emotional wellbeing. The WHO-5 was interpreted as a score below or above 50 points, a cut-off score used in previous literature to screen for depression. Results2,289 HCWs (round 1: n=190, round 2: n=2,099) from 40 countries in Europe participated. Mean age of respondents was 42 ({+/-}11) years, 66% were female, 47% and 39% were medical doctors and nurses, respectively. 74% (n=1699) of HCWs were directly treating patients with COVID-19, of which 32% (n=527) reported they were fearful of caring for these patients. HCWs reported high levels of concern about COVID-19 infection risk to themselves (71%) and their family (82%) as a result of their job. 40% of HCWs considered that getting infected with COVID-19 was not within their control. This was more common among junior than senior HCWs (46% versus 38%, P value <.01). Sufficient COVID-19-specific IPC training, confidence in PPE use and institutional trust were positively associated with the feeling that becoming infected with COVID-19 was within their control. Female HCWs were more likely than males to report a WHO-5 score below 50 points (aOR 1.5 (95% confidence interval (CI) 1.2-1.8). ConclusionsIn Europe, the COVID-19 pandemic has had a differential impact on those providing direct COVID-19 patient care, junior staff and women. Health facilities must be aware of these differential impacts, build trust and provide tailored support for this vital workforce during the current COVID-19 pandemic.

3871: A quantitative exploration of symptoms in COVID-19 patients: an observational cohort study
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Posted 27 Oct 2020

A quantitative exploration of symptoms in COVID-19 patients: an observational cohort study
139 downloads medRxiv infectious diseases

Gaojing Qu, Junwen Chen, Guoxin Huang, Meiling Zhang, Hui Yu, Haoming Zhu, Lei Chen, Dengru Wang, Bin Pei

BackgroundAs the spreading of the COVID-19 around the global, we investigated the characteristics and changes of symptoms in COVID-19 patients. MethodsThis was an ambispective observational cohort study, and 133 confirmed COVID-19 patients were included and all symptoms over the course were analyzed qualitatively. The symptoms, their changes over the course in the cohort and in the different clinical types, etc. were illustrated. Differences in different periods and severities were analyzed through Chi square test, association with severity was analyzed through LASSO binomial logistic regression analysis. Inter-correlation and classification of symptoms were completed. Major symptoms were screened and their changes were illustrated. ResultsA total of 43 symptoms with frequencies as 6067 in this cohort. Differences of symptoms in different stages and clinical types were significant. Expectoration, shortness of breath, dyspnea, diarrhea, poor appetite were positively but vomiting, waist discomfort, pharyngeal discomfort, acid reflux were negatively correlated with the combined-severe and critical type; dyspnea was correlated with the critical type. The 17 major symptoms were identified. The average daily frequency of symptoms per case was decreased continuously before the transition into the severe type and increased immediately one day before the transition and then decreased. It was decreased continuously before the transition date of the critical type and increased from the transition into the critical type to the next day and decreased thereafter. Dyspnea (P<0.001), shortness of breath (P<0.01) and chest distress (P<0.05) were correlated with death and their corresponding coefficient was 0.393, 0.258, 0.214, respectively. ConclusionThe symptoms of COVID-19 patients mainly related to upper respiratory tract infection, cardiopulmonary function, and digestive system. The mild type and the early stage in other types mainly related to upper respiratory tract infection. The cardiopulmonary function and digestive system associated symptoms were found in all other types and stages. Dyspnea was correlated with critical type and dyspnea, shortness of breath, and chest distress were correlated with death. Respiratory dysfunction (or incompleteness) associated symptoms were the characteristic symptoms. The changes of symptoms did not synchronously with the changes of severity before the transition into the severe or critical type.

3872: Extraction of Viral Nucleic Acids with Carbon Nanotubes Increases SARS-CoV-2 RT-qPCR Detection Sensitivity
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Posted 26 Jan 2021

Extraction of Viral Nucleic Acids with Carbon Nanotubes Increases SARS-CoV-2 RT-qPCR Detection Sensitivity
139 downloads medRxiv infectious diseases

Sanghwa Jeong, Eduardo G Grandio, Nicole Navarro, Rebecca L Pinals, Francis Ledesma, Darwin Yang, Markita P Landry

The global SARS-CoV-2 coronavirus pandemic has led to a surging demand for rapid and efficient viral infection diagnostic tests, generating a supply shortage in diagnostic test consumables including nucleic acid extraction kits. Here, we develop a modular method for high-yield extraction of viral single-stranded nucleic acids by using capture ssDNA sequences attached to carbon nanotubes. Target SARS-CoV-2 viral RNA can be captured by ssDNA-nanotube constructs via hybridization and separated from the liquid phase in a single-tube system with minimal chemical reagents, for downstream quantitative reverse transcription polymerase chain reaction (RT-qPCR) detection. This nanotube-based extraction method enables 100% extraction yield of target SARS-CoV-2 RNA from phosphate buffered saline in comparison to ~20% extraction yield when instead using a commercial silica-column kit. Notably, carbon nanotubes enable extraction of nucleic acids directly from 50% human saliva, bypassing the need for further biofluid purification and avoiding the use of DNA/RNA extraction kits. Carbon nanotube-based extraction of viral nucleic acids facilitates high-yield and high-sensitivity identification of viral nucleic acids such as the SARS-CoV-2 viral genome with reduced reliance on reagents affected by supply chain obstacles.

3873: SARS-CoV-2 Control on a Large Urban College Campus Without Mass Testing
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Posted 25 Jan 2021

SARS-CoV-2 Control on a Large Urban College Campus Without Mass Testing
139 downloads medRxiv infectious diseases

Christopher P O'Donnell, Katherine Brownlee, Elise Martin, Joe Suyama, Steven Middle Name(s)/Initial(s) Albert, Steven Anderson, Sai H Bhatte, Kenyon Bonner, Chad Burton, Micaela F Corn, Heather Eng, Bethany J Flage, Jay Frerotte, Goundappa K Balasubramani, Catherine L Haggerty, Joel Haight, Lee H. Harrison, Amy Hartman, Thomas Hitter, Wendy C King, Kate Ledger, Jane W. Marsh, Margaret C McDonald, Bethany R Miga, Kimberly D Moses, Anne W Newman, Meg Ringler, Mark S Roberts, Terrie Sax, Anantha Shekhar, Matthew Sterne, Tyler J Tenney, Marian Vanek, Alan Wells, Sally Wenzel, John V Williams

Objective. A small percentage of universities and colleges conduct mass SARS-CoV-2 testing. However, universal testing is resource-intensive, strains national testing capacity, and false negative tests can encourage unsafe behaviors. Participants. A large urban university campus. Methods. Virus control centered on three pillars: mitigation, containment, and communication, with testing of symptomatic and a random subset of asymptomatic students. Results. Random surveillance testing demonstrated a prevalence among asymptomatic students of 0.4% throughout the term. There were two surges in cases that were contained by enhanced mitigation and communication combined with targeted testing. Cumulative cases totaled 445 for the term, most resulting from unsafe undergraduate student behavior and among students living off-campus. A case rate of 232/10,000 undergraduates equaled or surpassed several peer institutions that conducted mass testing. Conclusions. An emphasis on behavioral mitigation and communication can control virus transmission on a large urban campus combined with a limited and targeted testing strategy.

3874: Machine learning based prognostic model and mobile application software platform for predicting infection susceptibility of COVID-19 using health care data
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Posted 12 Oct 2020

Machine learning based prognostic model and mobile application software platform for predicting infection susceptibility of COVID-19 using health care data
139 downloads medRxiv infectious diseases

R Srivatsan, Prithviraj N Indi, Swapnil Agrahari, Siddharth Menon, S Denis Ashok

From public health perspectives of COVID-19 pandemic, accurate estimates of infection severity of individuals are extremely valuable for the informed decision making and targeted response to an emerging pandemic. This paper presents machine learning based prognostic model for providing early warning to the individuals for COVID-19 infection using the health care data set. In the present work, a prognostic model using Random Forest classifier and support vector regression is developed for predicting the Infection Susceptibility Probability (ISP) score of COVID-19 and it is applied on an open health care data set containing 27 field values. The typical fields of the health care data set include basic personal details such as age, gender, number of children in the household, marital status along with medical data like Coma score, Pulmonary score, Blood Glucose level, HDL cholesterol etc. An effective preprocessing method is carried out for handling the numerical, categorical values (non-numerical), missing data in the health care data set. The correlation between the variables in the health care data is analyzed using the correlation coefficient and heat map with a color code is used to identify the influencing factors on the Infection Susceptibility Probability (ISP) score of COVID-19. Based on the accuracy, Precision, Sensitivity and F-scores, it is noted that the random forest classifier provides an improved classification performance as compared to Support vector regression for the given health care data set. Android based mobile application software platform is developed using the proposed prognostic approach for enabling the healthy individuals to predict the susceptibility infection score of COVID-19 to take the precautionary measures. Based on the results of the proposed method, clinicians and government officials can focus on the highly susceptible people for limiting the pandemic spread MethodsIn the present work, Random Forest classifier and support vector regression techniques are applied to a medical health care dataset containing 27 variables for predicting the susceptibility score of an individual towards COVID-19 infection and the accuracy of prediction is compared. An effective preprocessing is carried for handling the missing data in the health care data set. Correlation analysis using heat map is carried on the health care data for analyzing the influencing factors of Infection Susceptibility Probability (ISP) score of COVID-19. A confusion matrix is calculated for understanding the performance of classification of the based on the number of True-Positives, True-Negatives, False-Positives and False-Negatives. These values further used to calculate the accuracy, Precision, Sensitivity and F-scores. ResultsFrom the classification results, it is noted that the Random Forest classifier provides an classification accuracy of 99.7% precision of 99.8%, sensitivity of 98.8% and F-score of 99.29% for the given medical data set. ConclusionProposed machine learning approach can help the individuals to take additional precautions for protecting people from the COVID-19 infection, clinicians and government officials can focus on the highly susceptible people for limiting the pandemic spread. Abbreviation Table O_TBL View this table: org.highwire.dtl.DTLVardef@1e7968aorg.highwire.dtl.DTLVardef@14c462eorg.highwire.dtl.DTLVardef@938d3dorg.highwire.dtl.DTLVardef@11dd674org.highwire.dtl.DTLVardef@1ea99d8_HPS_FORMAT_FIGEXP M_TBL C_TBL

3875: The use of germicidal ultraviolet light, vaporised hydrogen peroxide and dry heat to decontaminate face masks and filtering respirators contaminated with an infectious norovirus
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Posted 09 Sep 2020

The use of germicidal ultraviolet light, vaporised hydrogen peroxide and dry heat to decontaminate face masks and filtering respirators contaminated with an infectious norovirus
139 downloads medRxiv infectious diseases

Constance Wielick, Louisa F. Ludwig-Begall, Lorene Dams, Ravo Michele Razafimahefa, Pierre-Francois Demeuldre, Aurore Napp, Jan Laperre, Olivier Jolois, Frederic Farnir, Eric Haubruge, Etienne Thiry

In the context of the SARS-CoV-2 pandemic, reuse of surgical masks and filtering facepiece respirators has been recommended. Their reuse necessitates procedures to inactivate contaminating human respiratory and oral pathogens. We previously demonstrated decontamination of masks and respirators contaminated with an infectious SARS-CoV-2 surrogate via ultraviolet germicidal irradiation, vaporised hydrogen peroxide, and use of dry heat. Here, we show that these same methods efficiently inactivate a more resistant, non-enveloped oral virus; decontamination of infectious murine norovirus-contaminated masks and respirators reduced viral titres by over four orders of magnitude on mask or respirator coupons.

3876: Localized skin inflammation during cutaneous leishmaniasis drives a chronic, systemic IFN-γ signature
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Posted 04 Dec 2020

Localized skin inflammation during cutaneous leishmaniasis drives a chronic, systemic IFN-γ signature
138 downloads medRxiv infectious diseases

Camila Farias Amorim, Fernanda O. Novais, Ba T. Nguyen, Mauricio T. Nascimento, Jamile Lago, Alexsandro S. Lago, Lucas P. Carvalho, Daniel P. Beiting, Phillip Scott

Cutaneous leishmaniasis is a localized infection controlled by CD4+ T cells that produce IFN-{gamma} within lesions. Phagocytic cells recruited to lesions, such as monocytes, are then exposed to IFN-{gamma} which triggers their ability to kill the intracellular parasites. Consistent with this, a transcriptional analysis of lesions from patients identified the presence of a strong interferon stimulated gene (ISG) signature. To determine what systemic responses are occurring that might influence the disease, we performed RNA sequencing (RNA-seq) on the blood of L. braziliensis-infected patients, as well as healthy controls. Functional enrichment analysis identified a transcriptional ISG signature as the dominant response in the blood of patients. An increase in monocytes and macrophages in the blood, estimated from our RNA-seq dataset, was positively correlated with this ISG signature. Consistent with this result, patients had circulating IFN-{gamma} in their serum. A cytotoxicity signature, which is a dominant feature in the lesions, was also found in the blood and correlated with an increased abundance of cytolytic cells. Thus, two transcriptional signatures present in lesions were found systemically, although with a substantially reduced number of differentially expressed genes (DEGs). Finally, we found that the number of DEGs and ISGs in leishmaniasis was similar to tuberculosis - another localized infection - but significantly less than observed in malaria. In contrast, the cytolytic signature and increased cytolytic cell abundance was not found in tuberculosis or malaria. Our results indicate that systemic signatures can reflect what is occurring in leishmanial lesions. Furthermore, the presence of an ISG signature in blood monocytes and macrophages suggests a mechanism to limit systemic spread of the parasite, as well as enhance parasite control by pre-activating cells prior to lesion entry.

3877: Analysis of genome characteristics and transmission of SARS-CoV-2 strains in North-East of Romania during the first COVID-19 outbreak
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Posted 24 Dec 2020

Analysis of genome characteristics and transmission of SARS-CoV-2 strains in North-East of Romania during the first COVID-19 outbreak
137 downloads medRxiv infectious diseases

Andrei Lobiuc, Mihai Dimian, Roxana Gheorghita, Olga Sturdza, Mihai Covasa

Romania officially declared its first SARS-CoV-2 case on February 26, 2020. The first and largest COVID-19 outbreak in Romania was recorded in Suceava, N/E region of the country, and originated at the Suceava regional county hospital. Following sheltering-in-place measures, infection rates decreased, only to rise again after relaxation of measures. This study describes the incursion of SARS-CoV-2 in Suceava and other parts of Romania and analyzes the mutations and their association with clinical manifestation of the disease during the period of COVID-19 outbreak. Phylogenetic analysis indicated multiple sites of origin for SARS-CoV-2 strains in Suceava, specifically from Spain, Italy and Russia, but also other strains related to those from Czech Republic, Belgium and France. Most Suceava samples contained mutations common to European lineages, such as A20268G, however aproximately 10% of samples were missing such mutations, indicating a possible different origin. While overall genome regions ORF1ab, S and ORF7 were subject to most mutations, several recurring mutations such as C27707T were identified, and these were mainly present in severe forms of the disease. Non-synonymous mutations, such as C3225A (Thr987Asn in NSP3a domain), associated with changes in a protein responsible for decreasing viral tethering in human host were also present. Patients with diabetes and hypertension exhibited eight and three time,s respectively, higher odds ratios of acquiring severe forms of the disease and these were mainly related to C27707T mutation. These results will aid in tracing virus movement throughout Romania and identification of infectivity, virulence and pathogenicity.

3878: Visual Scoring of Chest CT at Hospital Admission Predicts Hospitalization Time and Intensive Care Admission in Covid-19
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Posted 03 Nov 2020

Visual Scoring of Chest CT at Hospital Admission Predicts Hospitalization Time and Intensive Care Admission in Covid-19
137 downloads medRxiv infectious diseases

Erik Ahlstrand, Sara Cajander, Per Cajander, Edvin Ingberg, Erika Löf, Matthias Wegener, Mats Lidén

BackgroundThe extent and character of lung involvement on chest computerized tomography (CT) have a prognostic value in covid-19 but there is lack of consensus on how to assess and stage CT features. A scoring system of lung involvement in covid-19, Orebro covid-19 Scale (OCoS) was implemented in clinical routine on April 1 2020 in Orebro Region, Sweden. The OCoS-severity score measures the extent of lung involvement while OCoS-temporal stage characterizes the parenchymal involvement. The objective of the present study was to evaluate the OCoS scores in relation to clinical outcome of covid-19. MethodsPopulation based study including data from all hospitalized patients with covid-19 in Orebro Region during March to July 2020. Chest CT scores at the time of hospital admission and ICU admission were analyzed in relation to hospital and intensive care unit (ICU) length of stay, time to ICU admission and admission to ICU or death. FindingsIn the 381 included patients, there was a close correlation of the OCoS-severity score on admittance to hospital and the hospital length of stay. The OCoS-severity score on hospital admittance was a strong predictor for both a severe outcome in regards to ICU admittance or death and the time to ICU admittance. On admittance to ICU, both OCoS-severity score and temporal stage were correlated with the ICU length of stay. InterpretationChest CT visual scoring on admission to hospital predicts the clinical course in covid-19 pneumonia. FundingThis work was supported by the Orebro Region, Sweden.

3879: How Timing of Stay-home Orders and Mobility Reductions Impacted First-Wave COVID-19 Deaths in US Counties
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Posted 28 Nov 2020

How Timing of Stay-home Orders and Mobility Reductions Impacted First-Wave COVID-19 Deaths in US Counties
137 downloads medRxiv infectious diseases

Michelle Audirac, Mauricio Tec, Spencer J. Fox, Lauren Ancel Meyers, Corwin Matthew Zigler

SARS-CoV-2 transmission continues to evolve in the United States following the large second wave in the Summer. Understanding how location-specific variations in non-pharmaceutical epidemic control policies and behaviors contributed to disease transmission will be key for designing effective strategies to avoid future resurgences. We offer a statistical analysis of the relative effectiveness of the timing of both official stay-at-home orders and population mobility reductions, offering a distinct (but complementary) dimension of evidence gleaned from more traditional mechanistic models of epidemic dynamics. Specifically, we use a Bayesian hierarchical model fit to county-level mortality data from the first wave of the pandemic from Jan 21 2020 through May 10 2020 to establish how timing of stay-at-home orders and population mobility changes impacted county-specific epidemic growth. We find that population mobility reductions generally preceded stay-at-home orders, and among 356 counties with a pronounced early local epidemic between January 21 and May 10 (representing 195 million people and 32,000 observed deaths), a 10 day delay in population mobility reduction would have added 16,149 (95% credible interval [CI] 9,517 24,381) deaths by Apr 20, whereas shifting mobility reductions 10 days earlier would have saved 13,571 (95% CI 8,449 16,930) lives. Analogous estimates attributable to the timing of explicit stay-at-home policies were less pronounced, suggesting that mobility changes were the clearer drivers of epidemic dynamics. Our results also suggest that the timing of mobility reductions and policies most impacted epidemic dynamics in larger, urban counties compared with smaller, rural ones. Overall, our results suggest that community behavioral changes had greater impact on curve flattening during the Spring wave compared with stay at home orders. Thus, community engagement and buy-in with precautionary policies may be more important for predicting transmission risk than explicit policies.

3880: Seroprevalence of SARS-CoV-2 IgG in healthcare workers and other staff at North Bristol NHS Trust: a sociodemographic analysis
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Posted 16 Nov 2020

Seroprevalence of SARS-CoV-2 IgG in healthcare workers and other staff at North Bristol NHS Trust: a sociodemographic analysis
137 downloads medRxiv infectious diseases

Christopher R. Jones, Fergus W Hamilton, Ameeka Thompson, Tim T. Morris, Ed Moran

Structured summaryO_ST_ABSBackgroundC_ST_ABSHealthcare workers (HCWs) are at increased risk of infection with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). There are limited data exploring the relative impact of geographical and socioeconomic factors on risk of SARS-CoV-2 infection among HCWs. AimTo estimate and explore SARS-CoV-2 IgG antibody seroprevalence in HCWs and support staff at a hospital in South West England. MethodsWe conducted a nested cross-sectional study from May-July 2020. Inverse probability weighted regression was used to estimate seroprevalence of SARS-CoV-2 and associations with demographic and socioeconomic risk factors that were robust to selection into testing. FindingsAttendance for testing varied by demographic and socioeconomic factors. The overall rate of SARS-CoV-2 IgG seroprevalence among tested staff was 9.3% (638/6858). The highest seroprevalence was found in wards associated with SARS-CoV-2 outbreaks and among junior staff with patient-facing roles. Black, Asian and Minority Ethnic (BAME) staff had increased odds of SARS-CoV-2 seroprevalence (adjusted OR: 1.99, 95%CI: 1.69, 2.34; p<0.001) relative to White staff, except for those categorised as Medical/Dental. We found a significant association between neighbourhood deprivation and seroprevalence (p<0.01). Seroprevalence ranged from 12% in staff residing in areas with the greatest relative deprivation to 8.4% in the least deprived. ConclusionTransmission between staff groups is evident within the healthcare setting. BAME individuals were at increased risk of infection with SARS-CoV-2. Work role, area of residence, and neighbourhood deprivation all contribute to SARS-CoV-2 infection risk. As hospitals introduce routine staff SARS-CoV-2 testing they should consider differential uptake of testing among staff groups.

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