Le infezioni in medicina : rivista periodica di eziologia, epidemiologia, diagnostica, clinica e terapia delle patologie infettive最新文献

{"title":"Phylogeographical and evolutionary history of variola major virus; a question of timescales?","authors":"A. Bergna, C. Ventura, Rossella Marzo, M. Ciccozzi, M. Galli, G. Zehender, A. Lai","doi":"10.20944/preprints202012.0310.v1","DOIUrl":"https://doi.org/10.20944/preprints202012.0310.v1","url":null,"abstract":"Aim of this study was to reconstruct the phylogeography of variola virus (VARV) in the XX century, using 47 VARV whole genome sequences available in public databases, through two different methods for ancestral character reconstruction: a frequently used Bayesian framework and a fast maximum-likelihood (ML) based method. The substitution rate of the whole VARV genome was estimated to be between 6.7×10-6 and 1.1×10-5 substitutions/site/year. Both ML and Bayesian methods gave similar trees topology, showing two distinct monophyletic groups: one (known as P1) including the great part of variola major and the second (P2) including West African and American (variola minor) isolates and close evolutionary rate estimations, between 6.73×10-6 and 1.1×10-5 for the whole genome. The phylogeographical reconstruction of P1 suggested that the common ancestor of the variola major circulating in the Old World between the 1940s and the 1970s most probably originated in the Far East in the first decades of the XX century, and then spread to Indian subcontinent in the 1920s. India represented a center of further spread of VARV to eastern Africa in the 1940s and to the Middle East in the 1960s. The phylogeographic scenario obtained by the maximum-likelihood based method was congruent with that obtained by Bayesian framework, but the analysis was faster indicating the usefulness of this method in the analyses of large viral genomes. Our results may help to explain the controversial reconstructions of the history of VARV obtained using long or short timescale for calibration.","PeriodicalId":17977,"journal":{"name":"Le infezioni in medicina : rivista periodica di eziologia, epidemiologia, diagnostica, clinica e terapia delle patologie infettive","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79906145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Association between RT-PCR Ct Values and COVID-19 New Daily Cases: A Multicenter Cross-Sectional Study","authors":"Abdulkarim Abdulrahman, Saad I. Mallah, A. Alawadhi, S. Perna, E. Janahi, M. Alqahtani","doi":"10.1101/2020.12.07.20245233","DOIUrl":"https://doi.org/10.1101/2020.12.07.20245233","url":null,"abstract":"Introduction: Proactive prediction of the epidemiologic dynamics of viral diseases and outbreaks of the likes of COVID-19 has remained a difficult pursuit for scientists, public health researchers, and policymakers. It is unclear whether RT-PCR Cycle Threshold (Ct) values of COVID-19 (or any other virus) as indicator of viral load, could represent a possible predictor for underlying epidemiological changes on a population level. Objectives: To investigate whether population-wide changes in SARS-CoV-2 RT-PCR Ct values over time are associated with the daily fraction of positive COVID-19 tests. In addition, this study analyses the factors that could influence the RT-PCR Ct values. Method: A retrospective cross-sectional study was conducted on 63,879 patients from May 4, 2020 to September 30, 2020, in all COVID-19 facilities in the Kingdom of Bahrain. Data collected included number of tests and newly diagnosed cases, as well as Ct values, age, gender nationality, and symptomatic status. Results: Ct values were found to be negatively and very weakly correlated with the fraction of daily positive cases in the population r = -0.06 (CI95%: -0.06; -0.05; p=0.001). The R-squared for the regression model (adjusting for age and number of daily tests) showed an accuracy of 45.3%. Ct Values showed an association with nationality (p=0.012). After the stratification, the association between Ct values and the fraction of daily positive cases was only maintained for the female gender and Bahraini-nationality. Symptomatic presentation was significantly associated with lower Ct values (higher viral loads). Ct values do not show any correlation with age (p=0.333) or gender (p=0.522). Conclusion: We report one of the first and largest studies to investigate the epidemiological associations of Ct values with COVID-19. Ct values offer a potentially simple and widely accessible tool to predict and model epidemiological dynamics on a population level. More population studies and predictive models from global cohorts are necessary.","PeriodicalId":17977,"journal":{"name":"Le infezioni in medicina : rivista periodica di eziologia, epidemiologia, diagnostica, clinica e terapia delle patologie infettive","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74997175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"After SARS-CoV-2, will H5N6 and other influenza viruses follow the pandemic path?","authors":"D. K. Bonilla-Aldana, Mateo Aguirre-Flórez, Rhuvi Villamizar-Peña, Estefanía Gutiérrez-Ocampo, Juan F Henao-Martínez, A. Cvetkovic-Vega, K. Dhama, A. Rabaan, R. Sah, A. Rodríguez-Morales, P. Schlagenhauf, A. Paniz‐Mondolfi","doi":"10.5167/UZH-198708","DOIUrl":"https://doi.org/10.5167/UZH-198708","url":null,"abstract":"While the world is focused on attending, controlling, and mitigating the current pandemic of COVID-19, caused by the SARS-CoV-2, other viral threats are possibly emerging and reemerging especially in Asia, posing a risk for the spread in that region and beyond. A predictable threat is the avian influenza virus, especially H5N6, which has recently led to significant outbreaks in China and the Philippines, deserving more attention and control. In the current review, we assess the history of this highly pathogenic reemerging virus, as well as the contemporary implications of poultry outbreaks occurring in some Asian countries. We also look at outbreaks due to other strains not only in Asia but also across Europe and Africa, according to recent reports from the World Organization of Animal Health (OIE).","PeriodicalId":17977,"journal":{"name":"Le infezioni in medicina : rivista periodica di eziologia, epidemiologia, diagnostica, clinica e terapia delle patologie infettive","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78073506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CURB-65 plus hypoalbuminemia: a new score system for prediction of the in-hospital mortality risk in patients with SARS-CoV-2 pneumonia.","authors":"A. Oliva, C. Borrazzo, F. Cancelli, C. Franchi, Martina Carnevalini, G. Galardo, M. Alessandroni, F. Urso, G. Ceccarelli, G. d’Ettorre, F. Pugliese, C. Mastroianni, M. Venditti","doi":"10.21203/rs.3.rs-74812/v1","DOIUrl":"https://doi.org/10.21203/rs.3.rs-74812/v1","url":null,"abstract":"INTRODUCTION\u0000There is the need of a simple but highly reliable score system for stratifying the risk of mortality and Intensive Care Unit (ICU) transfer in patients with SARS-CoV-2 pneumonia at the Emergency Room.\u0000\u0000\u0000PURPOSE\u0000In this study, the ability of CURB-65, extended CURB-65, PSI and CALL scores and C-Reactive Protein (CRP) to predict intra-hospital mortality and ICU admission in patients with SARS-CoV-2 pneumonia were evaluated.\u0000\u0000\u0000METHODS\u0000During March-May 2020, a retrospective, single-center study including all consecutive adult patients with diagnosis of SARS-CoV-2 pneumonia was conducted. Clinical, laboratory and radiological data as well as CURB-65, expanded CURB-65, PSI and CALL scores were calculated based on data recorded at hospital admission.\u0000\u0000\u0000RESULTS\u0000Overall, 224 patients with documented SARS-CoV-2 pneumonia were included in the study. As for intrahospital mortality (24/224, 11%), PSI performed better than all the other tested scores, which showed lower AUC values (AUC=0.890 for PSI versus AUC=0.885, AUC=0.858 and AUC=0.743 for expanded CURB-65, CURB-65 and CALL scores, respectively). Of note, the addition of hypoalbuminemia to the CURB-65 score increased the prediction value of intra-hospital mortality (AUC=0.905). All the tested scores were less predictive for the need of ICU transfer (26/224, 12%), with the best AUC for extended CURB-65 score (AUC= 0.708).\u0000\u0000\u0000CONCLUSION\u0000The addition of albumin level to the easy-to-calculate CURB-65 score at hospital admission is able to improve the quality of prediction of intra-hospital mortality in patients with SARS-CoV-2 pneumonia.","PeriodicalId":17977,"journal":{"name":"Le infezioni in medicina : rivista periodica di eziologia, epidemiologia, diagnostica, clinica e terapia delle patologie infettive","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73150685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"COVID 19 diagnostic multiplicity and its role in community surveillance and control.","authors":"V. Deshmukh, Satyendra C Tripathi, Ashlesh Patil, J. Tripathy","doi":"10.14293/s2199-1006.1.sor-.ppa94rc.v1","DOIUrl":"https://doi.org/10.14293/s2199-1006.1.sor-.ppa94rc.v1","url":null,"abstract":"Diagnosis of persons exposed to/infected with severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) is central to controlling the global pandemic of COVID-19. Currently, several diagnostic modalities are available for COVID-19, each with its own pros and cons. Although there is a global consensus to increase the testing capacity, it is also essential to prudently utilize these tests to control the pandemic. In this paper, we have reviewed the current array of diagnostics for SARS-CoV-2, highlighted the gaps in current diagnostic modalities, and their role in community surveillance and control of the pandemic. The different modalities of COVID-19 diagnosis discussed are: clinical and radiological, molecular based (laboratory based and point-of-care), Immunoassay based (ELISA, rapid antigen and antibody detection tests) and digital diagnostics (artificial intelligence based algorithms). The role of rapid antigen/antibody detection tests in community surveillance has also been described here. These tests can be used to identify asymptomatic persons exposed to the virus and in community based seroprevalence surveys to assess the epidemiology of spread of the virus. However, there are few concerns about the accuracy of these tests which needs to evaluated beforehand.","PeriodicalId":17977,"journal":{"name":"Le infezioni in medicina : rivista periodica di eziologia, epidemiologia, diagnostica, clinica e terapia delle patologie infettive","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85814433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MERS-CoV and SARS-CoV infections in animals: a systematic review and meta-analysis of prevalence studies.","authors":"D. K. Bonilla-Aldana, María C. Cardona-Trujillo, Alejandra García-Barco, Yeimer Holguin-Rivera, Isabella Cortés-Bonilla, H. A. Bedoya-Arias, Leidy Jhoana Patiño-Cadavid, Juan David Tamayo-Orozco, A. Paniz‐Mondolfi, L. Zambrano, K. Dhama, R. Sah, A. Rabaan, G. J. Balbin-Ramon, A. Rodríguez-Morales","doi":"10.20944/preprints202003.0103.v1","DOIUrl":"https://doi.org/10.20944/preprints202003.0103.v1","url":null,"abstract":"INTRODUCTION\u0000Coronaviruses are zoonotic viruses that include human epidemic pathogens such as the Middle East Respiratory Syndrome virus (MERS-CoV), and the Severe Acute Respiratory Syndrome virus (SARS-CoV), among others (e.g., COVID-19, the recently emerging coronavirus disease). The role of animals as potential reservoirs for such pathogens remains an unanswered question. No systematic reviews have been published on this topic to date.\u0000\u0000\u0000METHODS\u0000We performed a systematic literature review with meta-analysis, using three databases to assess MERS-CoV and SARS-CoV infection in animals and its diagnosis by serological and molecular tests. We performed a random-effects model meta-analysis to calculate the pooled prevalence and 95% confidence interval (95%CI).\u0000\u0000\u0000RESULTS\u00006,493articles were retrieved (1960-2019). After screening by abstract/title, 50 articles were selected for full-text assessment. Of them, 42 were finally included for qualitative and quantitative analyses. From a total of 34 studies (n=20,896 animals), the pool prevalence by RT-PCR for MERS-CoV was 7.2% (95%CI 5.6-8.7%), with 97.3% occurring in camels, in which pool prevalence was 10.3% (95%CI 8.3-12.3). Qatar was the country with the highest MERS-CoV RT-PCR pool prevalence: 32.6% (95%CI 4.8-60.4%). From 5 studies and 2,618 animals, for SARS-CoV, the RT-PCR pool prevalence was 2.3% (95%CI 1.3-3.3). Of those, 38.35% were reported on bats, in which the pool prevalence was 14.1% (95%CI0.0-44.6%).\u0000\u0000\u0000DISCUSSION\u0000A considerable proportion of infected animals tested positive, particularly by nucleic acid amplification tests (NAAT). This essential condition highlights the relevance of individual animals as reservoirs of MERS-CoV and SARS-CoV. In this meta-analysis, camels and bats were found to be positive by RT-PCR in over 10% of the cases for both; thus, suggesting their relevance in the maintenance of wild zoonotic transmission.","PeriodicalId":17977,"journal":{"name":"Le infezioni in medicina : rivista periodica di eziologia, epidemiologia, diagnostica, clinica e terapia delle patologie infettive","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78659900","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diabetic calcaneal osteomyelitis.","authors":"Felix W. A. Waibel, I. Uçkay, Kati Sairanen, Lorenz Waibel, M. Berli, T. Böni, K. Gariani, Benjamin A Lipsky","doi":"10.5167/UZH-181767","DOIUrl":"https://doi.org/10.5167/UZH-181767","url":null,"abstract":"Diabetic foot infection (DFI), a multi-facetted disease requiring a multidisciplinary approach for successful treatment, mostly affects the forefoot. Calcaneal osteomyelitis (CO) is an uncommon presentation of DFI with a somewhat different epidemiology, clinical features, and approach to management. These patients, compared to those with non-calcaneal DFI, more often require special surgical techniques and off-loading approaches. In this narrative review targeted to non-surgical clinicians, we explore how CO differs from other types of DFI affecting other anatomical locations. Based on our review of the literature and personal experience, we also highlight important issues regarding the management of CO osteomyelitis, including the need for specialized surgical approaches.","PeriodicalId":17977,"journal":{"name":"Le infezioni in medicina : rivista periodica di eziologia, epidemiologia, diagnostica, clinica e terapia delle patologie infettive","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79307446","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"[Prion diseases].","authors":"R. Doria, F. Menichetti","doi":"10.1201/9781315382715-24","DOIUrl":"https://doi.org/10.1201/9781315382715-24","url":null,"abstract":"The prion diseases or transmissible spongiform encephalopathies (TSE) constitute a group of hereditary or acquired neurodegenerative disorders. The Authors evaluate the etiopathogenetic background, the clinical features and the current concerns with special attention to bovine spongiform encephalopathy and new variant Creutzfeldt Jacob disease.","PeriodicalId":17977,"journal":{"name":"Le infezioni in medicina : rivista periodica di eziologia, epidemiologia, diagnostica, clinica e terapia delle patologie infettive","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2018-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75905406","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prevalence of zoonotic and non-zoonotic genotypes of Giardia intestinalis in cats: a systematic review and meta-analysis.","authors":"Sebastián Ramírez-Ocampo, Juan David Cotte-Alzate, A. Escobedo, A. Rodríguez-Morales","doi":"10.26226/morressier.56d6be7cd462b80296c9591a","DOIUrl":"https://doi.org/10.26226/morressier.56d6be7cd462b80296c9591a","url":null,"abstract":"There are no meta-analyses specifically describing the prevalence of zoonotic and non-zoonotic genotypes of Giardia intestinalis in cats, which would be useful in defining the importance of cats as a source of zoonotic transmission. We performed a systematic review of the literature in three databases (PubMed, Scopus and SciELO) to assess the proportion of cats that were infected with specific G. intestinalis genotypes. A meta-analysis using a random effects model was performed to calculate the pooled prevalence and 95% confidence intervals (95%CI). A 2-tailed alpha level of 5% was used for hypothesis testing. Measures of heterogeneity, including Cochran's Q statistic, the I2 index, and the tau-squared test, were estimated and reported. Subgroup analyses were conducted by geographic area and animal origin, as well as coinfection. Publication bias was assessed using a funnel-plot. Up to November 1, 2015, the literature search yielded 780 articles, of which 29 studies were valid for analysis. The pooled prevalence rate was higher for genotype F (19 studies, n=368 cats) with 55.8% [95%CI (42.8%-68.7%), τ2=0.0463]. For genotype A (21 n=409) it was 38.7% [95%CI (29.0%-48.4%), τ2=0.0527], for genotype D (7, n=276) 8.9% [95%CI (2.1%-15.8%), τ2=0.0024], for genotype C (2, n=212) 3.1% [95%CI (2.5%-3.5%), τ2=0.0001], for genotype E (3, n=187) 2.9% [95%CI (0.0%-8.1%), τ2=0.0009], and for genotype B (4, n=230) it was 2.8% [95%CI (0.0%-5.7%), τ2=0.0002]. Genotypes A and B of G. intestinalis are present in a wide range of hosts, including humans and cats, whilst genotype E has been reported in bovines, ovines, caprine and porcine animals, as well as in dogs and cats; and genotype F is almost exclusive to cats. Thus genotypes A and B are the most important for zoonotic transmission. In this study, after genotype F (55.5%), genotype A yielded more than 38% in cats (95%CI 29-48). This has interesting possible implications in zoonotic transmission of giardiasis between cats and humans.","PeriodicalId":17977,"journal":{"name":"Le infezioni in medicina : rivista periodica di eziologia, epidemiologia, diagnostica, clinica e terapia delle patologie infettive","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74896533","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Four cases with Kawasaki disease and viral infection: aetiology or association.","authors":"T. Giray, S. Biçer, Ö. Küçük, D. Çöl, Zerrin Yalvaç, Y. Gürol, G. Yılmaz, Ahmet Saç, Yiğit Moğol","doi":"10.1007/978-3-319-31526-3_6","DOIUrl":"https://doi.org/10.1007/978-3-319-31526-3_6","url":null,"abstract":"","PeriodicalId":17977,"journal":{"name":"Le infezioni in medicina : rivista periodica di eziologia, epidemiologia, diagnostica, clinica e terapia delle patologie infettive","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91537596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}