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Emergence of the Novel Sixth Candida auris Clade VI in Bangladesh medRxiv. Infect. Dis. Pub Date : 2024-04-17 Tahsin Khan, Naimul Islam Faysal, Md Mobarok Hossain, Syeda Mah-E-Muneer, Arefeen Haider, Shovan Basak Moon, Debashis Sen, Dilruba Ahmed, Lindsay A. Parnell, Mohammad Jubair, Nancy A. Chow, Fahmida Chowdhury, Mustafizur Rahman
Candida auris, initially identified in 2009, has rapidly become a critical concern due to its antifungal resistance and significant mortality rates in healthcare-associated outbreaks. To date, whole-genome sequencing (WGS) has identified five unique clades of C. auris, with some strains displaying resistance to all primary antifungal drug classes. In this study, we presented the first WGS analysis
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Monitoring Report: Respiratory Viruses - March 2024 Data medRxiv. Infect. Dis. Pub Date : 2024-04-16 Samuel Gratzl, Brianna M Goodwin Cartwright, Patricia J Rodriguez, Charlotte Baker, Duy Do, Nicholas L Stucky
Background Few sources regularly monitor hospitalizations associated with respiratory viruses. This study provides current hospitalization trends associated with six common respiratory viruses: COVID-19, influenza, human metapneumovirus (HMPV), parainfluenza virus, respiratory syncytial virus (RSV), and rhinovirus.
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Precision medicine for pandemics: stratification of COVID-19 molecular phenotypes defined by topological analysis of global blood gene expression medRxiv. Infect. Dis. Pub Date : 2024-04-16 Rebekah Penrice-Randal, Fabio Strazzeri, Benoit Ernst, Brice Van Eeckhout, Julien Guiot, Anna Julie Peired, Cosimo Nardi, Erika Parkinson, Monique Henket, Alicia Staderoli, Elora Guglielmi, Anne-Françoise Dive, Laurie Giltay, Sara Tomassetti, Rebecca Baker, Kit Howard, Catherine Hartley, Tessa Prince, Thomas Kleyntssens, Tommaso Manciulli, Ratko Djukanovic, Tristan Clark, Diana Baralle, Scott S Wagers
Precision medicine offers a promising avenue for better therapeutic responses to pandemics such as COVID-19. This study leverages independent patient cohorts in Florence and Liège gathered under the umbrella of the DRAGON consortium for the stratification of molecular phenotypes associated with COVID-19 using topological analysis of global blood gene expression. Whole blood from 173 patients was collected
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Comparative evaluation of plasma biomarkers of Schistosoma haematobium infection in endemic populations from Burkina Faso medRxiv. Infect. Dis. Pub Date : 2024-04-16 Mireille Ouedraogo, Jana Christina Hey, Stan Hilt, Veronica Rodriguez Fernandez, Doris Winter, Ravo Razafindrakoto, Pytsje Hoekstra, Youssouf Kabore, Marco Fornili, Laura Baglietto, Issa Nebie, Govert J van Dam, Paul L Corstjens, Daniela Fusco, David Modiano, Fabrizio Bruschi, Valentina D Mangano
Infection with Schistosoma haematobium causes urogenital disease associated with organ disfunction, bleeding, pain, and higher susceptibility to infections and cancer. Timely and accurate diagnosis is crucial for prompt and appropriate treatment as well as surveillance efforts, and the use of plasma biomarkers offers important advantages over parasitological examination of urine, including increased
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Sustained Human Outbreak of a New MPXV Clade I Lineage in Eastern Democratic Republic of the Congo medRxiv. Infect. Dis. Pub Date : 2024-04-15 Emmanuel H. Vakaniaki, Cris Kacita, Eddy Kinganda-Lusamaki, Áine O’Toole, Tony Wawina-Bokalanga, Daniel Mukadi-Bamuleka, Adrienne Amuri Aziza, Nadine Malyamungu-Bubala, Franklin Mweshi Kumbana, Léandre Mutimbwa-Mambo, Freddy Belesi-Siangoli, Yves Mujula, Edyth Parker, Pauline-Chloé Muswamba-Kayembe, Sabin S. Nundu, Robert S. Lushima, Jean Claude Makangara Cigolo, Noella Mulopo-Mukanya, Elisabeth Pukuta
Background Monkeypox virus (MPXV) attracted global attention in 2022 during a widespread outbreak linked primarily to sexual contact. Clade I MPXV is prevalent in Central Africa and characterized by severe disease and high mortality, while Clade II is confined to West Africa and associated with milder illness. A Clade IIb MPXV emerged in Nigeria in 2017, with protracted human-to-human transmission
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Detection of Salmonella Typhi and blaCTX-M Genes in Drinking Water, Wastewater, and Environmental Biofilms in Sindh Province, Pakistan medRxiv. Infect. Dis. Pub Date : 2024-04-15 Ayesha Tajammul, L. Scott Benson, Jamil Ahmed, James VanDerslice, Windy Tanner
Typhoid fever poses a significant public health risk, particularly in low- and middle-income countries where access to clean water and improved sanitation may be limited. In Pakistan, this risk is especially serious given the emergence of an extensively drug-resistant (XDR) Salmonella Typhi strain, a strain attributed to S. Typhi acquisition of the blaCTX-M-15 gene. The now-dominant XDR S. Typhi strain
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A pragmatic pipeline for drug resistance identification in Mycobacterium tuberculosis using whole genome sequencing medRxiv. Infect. Dis. Pub Date : 2024-04-15 Linzy Elton, Alp Aydin, Neil Stoker, Sylvia Rofael, Letícia Muraro Wildner, Jabar Babatunde Pacome Agbo Achimi Abdul, John Tembo, Muzamil Abdel Hamid, Mfoutou Mapanguy Claujens Chastel, Julio Ortiz Canseco, Ronan Doyle, Giovanni Satta, Justin O’Grady, Adam Witney, Francine Ntoumi, Alimuddin Zumla, Timothy D McHugh
Background Delays in accurate diagnosis of drug resistant tuberculosis (DR-TB) can hinder treatment. Whole genome sequencing (WGS) provides more information than standard molecular and phenotypic testing, but commonly used platforms are expensive to implement, and data interpretation requires significant expertise.
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Structural epitope profiling identifies antibodies associated with critical COVID-19 and long COVID medRxiv. Infect. Dis. Pub Date : 2024-04-15 Patrick K.A. Kearns, Charles Dixon, Mihaly Badonyi, Kim Lee, Rafal Czapiewski, Olivia Fleming, Prajitha Nadukkandy, Lukas Gerasimivicous, Rinal Sahputra, Bethany Potts, Sam Benton, Jacky Guy, Scott Neilson, Helen Wise, Sara Jenks, Kate Templeton, CIRCO, Christina Dold, Teresa Lambe, Andrew Pollard, Alexander J Mentzer, Julian C Knight, COMBAT, Susanna Dunachie, Paul Klenerman, Eleanor Barnes, Alan
Even within a single protein, antibody binding can have beneficial, neutral, or harmful effects during the response to infection. Resolving a polyclonal antibody repertoire across a pathogen’s proteome to specific epitopes may therefore explain much of the heterogeneity in susceptibility to infectious disease. However, the three-dimensional nature of antibody-epitope interactions makes the discovery
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Tongue Coating in COVID-19 Patients: A Case-Control Study medRxiv. Infect. Dis. Pub Date : 2024-04-15 Zhi Chun Wang, Xi Hong Cai, Jeremy Chan, Yi Yi Chan, Xiaotong Chen, Ching Wan Cheng, Donghui Huang, Bei-ni Lao, Xu-sheng Liu, Aiping Lu, Huixian Wang, Helen Zhang, Xuebin Zhang, Shi Ping Zhang
It has been suggested that COVID-19 patients have distinct tongue features, which may help to monitor the development of their condition. To determine if there was any specific tongue coating feature in COVID-19, this study investigated the difference in tongue coating between COVID-19 subjects and subjects with other acute inflammatory diseases characterized by fever. Tongue images taken with smartphones
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Bangladesh should engage the private sector for malaria elimination by 2030 medRxiv. Infect. Dis. Pub Date : 2024-04-14 Ryan Patrick McArdle, Ching Swe Phru, Mohammad Sharif Hossain, Mohammad Shafiul Alam, Kasturi Haldar
Bangladesh reduced malaria by 93% from 2008-2020 through the action of governmental and non-governmental organizations, yet ∼18 million people continue to live at risk of infection. For-profit private healthcare providers, catalytic for malaria elimination in many countries, have not yet been integrated into the national program. By imposing strict definitions on a large and complex literature surrounding
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SARS-CoV-2 Antigen Rapid Detection Tests: test performance during the COVID-19 pandemic and the impact of COVID-19 vaccination medRxiv. Infect. Dis. Pub Date : 2024-04-14 Isabell Wagenhäuser, Kerstin Knies, Tamara Pscheidl, Michael Eisenmann, Sven Flemming, Nils Petri, Miriam McDonogh, Agmal Scherzad, Daniel Zeller, Anja Gesierich, Anna Katharina Seitz, Regina Taurines, Ralf-Ingo Ernestus, Johannes Forster, Dirk Weismann, Benedikt Weißbrich, Johannes Liese, Christoph Härtel, Oliver Kurzai, Lars Dölken, Alexander Gabel, Manuel Krone
Introduction During the COVID-19 pandemic, SARS-CoV-2 antigen rapid detection tests (RDTs) emerged as point-of-care diagnostics in addition to the RT-qPCR as the gold standard for SARS-CoV-2 diagnostics. Facing the course of the COVID-19 pandemic to an endemic characterised by several SARS-CoV-2 virus variants of concern (VOC) and an increasing public COVID-19 vaccination rate the aim of the study
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Safety, effectiveness, and skin immune response in a controlled human infection model of sand fly transmitted cutaneous leishmaniasis medRxiv. Infect. Dis. Pub Date : 2024-04-13 Vivak Parkash, Helen Ashwin, Shoumit Dey, Jovana Sadlova, Barbora Vojtkova, Katrien Van Bocxlaer, Rebecca Wiggins, David Thompson, Nidhi Sharma Dey, Charles L. Jaffe, Eli Schwartz, Petr Volf, Charles J. N. Lacey, Alison M. Layton, Paul M. Kaye
The leishmaniases are globally important parasitic diseases for which no human vaccines are currently available. To facilitate vaccine development, we conducted an open label observational study to establish a controlled human infection model of sand fly-transmitted cutaneous leishmaniasis caused by L. major. Between 24th January and 12th August 2022, we exposed 14 (8F, 6M) participants to infected
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MONITORING OF RESPIRATORY VIRUS COINFECTION IN SOUTHERN BRAZIL DURING COVID-19 PANDEMIC medRxiv. Infect. Dis. Pub Date : 2024-04-12 Dayane Azevedo Padilha, Fernando Hartmann Barazzetti, Marcos André Schörner, Vilmar Benetti Filho, Eric Kazuo Kawagoe, Doris Sobral Marques Souza, Maria Luiza Bazzo, Glauber Wagner, Gislaine Fongaro
Since December 2019, the COVID-19 pandemic caused by SARS-CoV-2 has reached approximately 769 million people, leading to more than 7 million deaths worldwide. Faced with the possible presence of other respiratory pathogens that could co-infect and modify the clinical response of patients detected for SARS-CoV-2, some researchers have explored this line of investigation. The relationship between these
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Modeling the interplay between disease spread, behaviors, and disease perception with a data-driven approach medRxiv. Infect. Dis. Pub Date : 2024-04-12 Alessandro De Gaetano, Alain Barrat, Daniela Paolotti
Individuals’ perceptions of disease influence their adherence to preventive measures, shaping the dynamics of disease spread. Despite extensive research on the interaction between disease spread, human behaviors, and interventions, few models have incorporated real-world behavioral data on disease perception, limiting their applicability. This study novelly integrates disease perception, represented
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Incidence and Risk of Post-COVID-19 Thromboembolic Disease and the Impact of Aspirin Prescription; Nationwide Observational Cohort at the US Department of Veteran Affairs medRxiv. Infect. Dis. Pub Date : 2024-04-12 Anna D Ware, Zachary P Veigulis, Peter J Hoover, Terri L Blumke, George N Ioannou, Edward J Boyko, Thomas F Osborne
Introduction COVID-19 triggers prothrombotic and proinflammatory changes, with thrombotic disease prevalent in up to 30% SARS-CoV-2 infected patients. Early work suggests that aspirin could prevent COVID-19 related thromboembolic disorders in some studies but not others. This study leverages data from the largest integrated healthcare system in the United States to better understand this association
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On the parameterization of mathematical models of infectious disease transmission structured by age at the start of the epidemic spread medRxiv. Infect. Dis. Pub Date : 2024-04-12 Santiago Sarratea, Gabriel Fabricius
Estimation of transmission and contact rate parameters among individuals in different age groups is a key point in the mathematical modeling of infectious disease transmission. Several approaches exist for this task but, given the complexity of the problem, the obtained values are always approximate estimations that hold in particular conditions. Our goal is to contribute to this task in the event
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Safety and immunogenicity of PHH-1V as booster vaccination through the Omicron era: results from a phase IIb open-label extension study up to 6 months medRxiv. Infect. Dis. Pub Date : 2024-04-12 M.J. Lopez, M.M. Vazquez, M. Alvarez, J.R. Arribas, E. Arana-Arri, P. Muñoz, J. Navarro-Pérez, R. Ramos, J. Molto, S. Otero-Romero, I. Esteban, E. Aurrecoechea, R. Pomarol, M. Plana, R Perez-Caballero, L. Bernad, J.G. Prado, L. Riera-Sans, A. Soriano
Background Phase IIb HIPRA-HH-2 study results showed that PHH-1V as first booster dose elicited a strong and sustained neutralising antibody response against various SARS-CoV-2 variants. Here, we report the safety and immunogenicity of a fourth booster dose of PHH-1V against the most prevalent Omicron SARS-CoV-2 variants in Spain.
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Effectiveness of the 2023-2024 Omicron XBB.1.5-containing mRNA COVID-19 vaccine (mRNA-1273.815) in preventing COVID-19-related hospitalizations and medical encounters among adults in the United States: An interim analysis medRxiv. Infect. Dis. Pub Date : 2024-04-12 Hagit Kopel, Andre B. Araujo, Alina Bogdanov, Ni Zeng, Isabelle Winer, Jessamine Winer-Jones, Tianyi Lu, Morgan A. Marks, Mac Bonafede, Van Hung Nguyen, David Martin, James A. Mansi
Background/Objectives COVID-19 continues to pose a significant burden that impacts public health and the healthcare system as the SARS-CoV-2 virus continues to evolve. Regularly updated vaccines are anticipated to boost waning immunity and provide protection against circulating variants. This study evaluated vaccine effectiveness (VE) of mRNA-1273.815, a 2023-2024 Omicron XBB.1.5-containing mRNA COVID-19
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Association of current Schistosoma mansoni, S. japonicum, and S. mekongi infection status and intensity with periportal fibrosis: a systematic review and meta-analysis medRxiv. Infect. Dis. Pub Date : 2024-04-12 Adanna Ewuzie, Lauren Wilburn, Dixa B. Thakrar, Nia Roberts, Reem Malouf, Goylette F. Chami
Background Periportal fibrosis (PPF) is a severe morbidity caused by both current and past exposure to intestinal schistosomes. We assessed the association between current/active infection status and intensity of Schistosoma mansoni, S. japonicum, or S. mekongi with PPF.
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WITHDRAWN: Unravelling the transcriptome of the human tuberculosis lesion and its clinical implications medRxiv. Infect. Dis. Pub Date : 2024-04-12 Albert Despuig, Kaori L. Fonseca, Dominic Habgood-Coote, Álvaro Del RíoÁlvarez, Juan Carrillo-Reixach, Lilibeth Arias, Nino Gogichadze, Aaron Goff, Leticia Muraro Wildner, Shota Gogishvili, Keti Nikolaishvili, Natalia Shubladze, Zaza Avaliani, Pere-Joan Cardona, Federico Martinón-Torres, Antonio Salas, Alberto Gómez- Carballa, Simon J Waddell, Carolina Armengol, Sergo Vashakidze, Myrsini Kaforou, Cristina
The authors have withdrawn their manuscript owing to a more in-depth analysis of the bioinformatics data. This has substantially reshaped the manuscript’s structure, affecting key findings, methodology, figures, and overall narrative, as well as the authorship. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding
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A randomized double-blind Phase IIb trial to evaluate the efficacy of ChAd63-KH for the treatment of post kala-azar dermal leishmaniasis medRxiv. Infect. Dis. Pub Date : 2024-04-11 Brima M. Younis, Rebecca Wiggins, Eltahir A.G. Khalil, Mohamed Osman, Francesco Santoro, Chiara Sonnati, Ada Keding, Maria Novedrati, Giorgio Montesi, Ali Noureldein, Elmukashfi T. A. Elmukashfi, Ala Eldin Mustafa, Mohammed Alamin, Mohammed Saeed, Khalid Salman, Ahmed J. Suliman, Amin E.A. Musa, Alison M. Layton, Charles J. N. Lacey, Paul M. Kaye, Ahmed M. Musa
Background In a recent Phase IIa clinical trial, the candidate leishmaniasis vaccine ChAd63-KH was shown to be safe and immunogenic in Sudanese patients with post kala-azar dermal leishmaniasis (PKDL). However, its value as a stand-alone therapeutic was unknown.
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Adverse outcomes and their predictors of dengue fever in pregnancy; a cross sectional study with a follow up medRxiv. Infect. Dis. Pub Date : 2024-04-10 Oshadhi Nallaperuma, Hematha Senanayake, Janaka Godevithana
Antenatal dengue infection presents substantial risks to maternal, fetal, and neonatal health, particularly in dengue-endemic regions such as Sri Lanka. This retrospective cross-sectional study with a follow up aimed to investigate the adverse outcomes of antenatal dengue infection and identify predictive parameters associated with maternal, fetal, and neonatal complications. A total of 115 pregnant
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Parallel Trends in an Unparalleled Pandemic Difference-in-differences for infectious disease policy evaluation medRxiv. Infect. Dis. Pub Date : 2024-04-10 Shuo Feng, Alyssa Bilinski
Researchers frequently employ difference-in-differences (DiD) to study the impact of public health interventions on infectious disease outcomes. DiD assumes that treatment and non-experimental comparison groups would have moved in parallel in expectation, absent the intervention (“parallel trends assumption”). However, the plausibility of parallel trends assumption in the context of infectious disease
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Low pre-infection levels of neutralizing antibody in breakthrough infections after bivalent BA.4-5 vaccine and practical application of dried blood spots medRxiv. Infect. Dis. Pub Date : 2024-04-10 Hitoshi Kawasuji, Yoshitomo Morinaga, Hideki Tani, Hiroshi Yamada, Yoshihiro Yoshida, Masayoshi Ezaki, Yuki Koshiyama, Yusuke Takegoshi, Makito Kaneda, Yushi Murai, Kou Kimoto, Kentaro Nagaoka, Hideki Niimi, Yoshihiro Yamamoto
The level of neutralizing antibodies required to confer protection against COVID-19 breakthrough infections (BIs) is unclear, and the ability to know the immune status of individuals against the rapidly changing endemic variants is limited. We assessed longitudinal serum anti-RBD antibody levels and neutralizing activities (NTs) against Omicron BA.5 and XBB.1.5 in healthcare workers following the fourth
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Meta-analysis on safety of standard vs prolonged infusion of beta-lactams medRxiv. Infect. Dis. Pub Date : 2024-04-09 Hunter Rolain, Zachary Schwartz, Raymond Jubriail, Kevin Downes, Lisa Hong, Alireza Fakhri Ravari, Nathaniel J. Rhodes, Marc H. Scheetz
Background Efficacy for prolonged infusion beta-lactam dosing schemes has been previously described, but there has been less focus on the safety of standard vs prolonged infusion protocols of beta-lactams. This study explored differences in adverse drug reactions (ADRs) reported for beta-lactams between each of these infusion protocols.
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Integrative Systems Immunology Analysis Reveals Elevated Anti-AGTR1 Levels with Accumulating COVID-19 Symptoms medRxiv. Infect. Dis. Pub Date : 2024-04-09 Dennyson Leandro M Fonseca, Maj Jäpel, Igor Salerno Filgueiras, Gabriela Crispim Baiochi, Yuri Ostrinski, Gilad Halpert, Yael Bublil Lavi, Elroy Vojdani, Juan Carlo Santos e Silva, Júlia Nakanishi Usuda, Paula P. Freire, Adriel Leal Nóbile, Anny Silva Adri, Pedro Barcelos Marçal, Yohan Lucas Gonçalves Corrêa, Fernando Yuri Nery do Vale, Letícia Oliveira Lopes, Solveig Lea Schmidt, Xiaoqing Wang, Carl
The coronavirus disease 2019 (COVID-19) displays a broad spectrum of symptoms, with the underlying reasons for this variability still not fully elucidated. Our study investigates the potential association between specific autoantibodies (AABs), notably those that targeting G protein-coupled receptors (GPCRs) and renin-angiotensin system (RAS) related molecules, and the diverse clinical manifestations
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Gut resident Escherichia coli profile predicts the eighteen-month probability and antimicrobial susceptibility of urinary tract infections medRxiv. Infect. Dis. Pub Date : 2024-04-09 Veronika Tchesnokova, Lydia Larson, Irina Basova, Yulia Sledneva, Debarati Choudhury, Thalia Solyanik, Jennifer Heng, Teresa Cristina Bonilla, Isaac Pasumansky, Victoria Bowers, Sophia Pham, Lawrence T. Madziwa, Erika Holden, Sara Y. Tartof, James D. Ralston, Evgeni V. Sokurenko
Background Community-acquired UTI is the most common bacterial infection managed in general medical practice that can lead to life-threatening outcomes. While UTIs are primarily caused by Escherichia coli colonizing the patient’s gut, it is unclear whether the gut resident E. coli profiles can predict the person’s risks for UTI and optimal antimicrobial treatments. Thus, we conducted an eighteen-month
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N-protein vaccine Convacell® is effective against COVID-19: phase 3, randomized, double-blind, placebo-controlled clinical trial medRxiv. Infect. Dis. Pub Date : 2024-04-09 Sevastyan O. Rabdano, Ellina A. Ruzanova, Anastasiya E. Vertyachikh, Valeriya A. Teplykh, Alla B. Emelyanova, German O. Rudakov, Sergei A. Arakelov, Iuliia V. Pletyukhina, Nikita S. Saveliev, Anna A. Lukovenko, Liliya N. Fakhretdinova, Ariana S. Safi, Ekaterina N. Zhirenkina, Irina N. Polyakova, Natalia S. Belozerova, Vladislav V. Klykov, Arina P. Savelieva, Aleksey A. Ekimov, Vadim A. Merkulov, Sergei
We have developed a Convacell®, a COVID-19 vaccine based on the conservative viral nucleocapsid (N) protein. The N protein is evolutionary conservative and is abundantly expressed on the surface of infected cells, allowing anti-N immune response generated by Convacell® to rapidly clear infected cells and provide long-lasting protection against COVID-19. Convacell® has been demonstrated to be safe and
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Transcriptome landscape of high and low responders to an inactivated COVID-19 vaccine after 4 months using single-cell sequencing medRxiv. Infect. Dis. Pub Date : 2024-04-08 Zhongyi Zhu, Yaling Huang, Jiatong Sun, Meirong Li, Yong Chen, Lei Zhang, Fubaoqian Huang, Chuanyu Liu, Weijun Chen, Jinmin Ma
Background Variability in antibody responses among individuals following vaccination is a universal phenomenon. Single-cell transcriptomics offers a potential avenue to understand the underlying mechanisms of these variations and improve our ability to evaluate and predict vaccine effectiveness.
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Comparative Application of the Fluctuation Test to the data of Morbidity by COVID-19 in United States of America, United Kingdom, Taiwan and China 2020-2023 medRxiv. Infect. Dis. Pub Date : 2024-04-08 Anyi Yannire López-Ramírez, Hilda Cristina Grassi, Efrén de Jesús Andrades, Jesús Enrique Andrades-Grassi
In this work the Luria and Delbruck Fluctuation Test was comparatively applied to the data of Morbidity by COVID-19 in the United States of America (USA), United Kingdom (UK), Taiwan and China from 2020 to 2023. Three types of data were used: es.statista.com, datosmacro.expansion.com and larepublica.co without modification, but trying to avoid and justify the anomalies and inconsistencies observed
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Improved limit of detection for zoonotic Plasmodium knowlesi and P. cynomolgi surveillance using reverse transcription for total nucleic acid preserved samples or dried blood spots medRxiv. Infect. Dis. Pub Date : 2024-04-08 Kamil A Braima, Kim A Piera, Inke ND Lubis, Rintis Noviyanti, Giri S Rajahram, Pinkan Kariodimedjo, Irbah RA Nainggolan, Ranti Permatasari, Leily Trianty, Ristya Amalia, Sitti Saimah binti Sakam, Angelica F Tan, Timothy William, Jacob AF Westaway, PingChin Lee, Sylvia Daim, Henry Surendra, Nathaniel Christy, Andrew G Letizia, Christopher L Peatey, Mohd Arshil Moideen, Bridget E Barber, Colin J Sutherland
Background Zoonotic P. knowlesi and P. cynomolgi symptomatic and asymptomatic infections occur across endemic areas of Southeast Asia. Most infections are low-parasitemia, with an unknown proportion below routine microscopy detection thresholds. Molecular surveillance tools optimizing the limit of detection (LOD) would allow more accurate estimates of zoonotic malaria prevalence.
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Re-assessing thermal response of schistosomiasis transmission risk: evidence for a higher thermal optimum than previously predicted medRxiv. Infect. Dis. Pub Date : 2024-04-07 Ibrahim Halil Aslan, Julie D. Pourtois, Andrew J. Chamberlin, Kaitlyn R. Mitchell, Lorenzo Mari, Kamazima M. Lwiza, Chelsea L. Wood, Erin A. Mordecai, Yu Ao, Roseli Tuan, Raquel Gardini Sanches Palasio, Antônio M.V. Monteiro, Devin Kirk, Tejas S. Athni, Susanne H. Sokolow, Eliezer K. N’Goran, Nana R. Diakite, Mamadou Ouattara, Marino Gatto, Renato Casagrandi, David C. Little, Reed W. Ozretich, Rachael
The geographical range of schistosomiasis is affected by the ecology of schistosome parasites and their obligate host snails, including their response to temperature. Previous models predicted schistosomiasis’ thermal optimum at 21.7 °C, which is not compatible with the temperature in sub-Saharan Africa (SSA) regions where schistosomiasis is hyperendemic. We performed an extensive literature search
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Laboratory validation of a simplified DNA extraction protocol followed by a portable qPCR detection of M. tuberculosis DNA suitable for point of care settings medRxiv. Infect. Dis. Pub Date : 2024-04-07 Tainá dos Santos Soares, Graziele Lima Bello, Ianca Moraes dos Santos Petry, Maria Rita Castilho Nicola, Larissa Vitoria da Silva, Regina Bones Barcellos, Joana Morez Silvestri, Maria Lucia Rossetti, Alexandre Dias Tavares Costa
Tuberculosis, caused by Mycobacterium tuberculosis, is a treatable and curable disease, and yet remains one of the leading causes of death worldwide. Diagnosis is essential to reducing the number of cases and starting treatment, but costly tests and equipments that require complex infrastructure hamper their widespread use as a tool to contain the disease in vulnerable populations as well countries
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Analytical Validation of a Highly Accurate and Reliable Next-Generation Sequencing-Based Urine Assay medRxiv. Infect. Dis. Pub Date : 2024-04-07 Mara Couto-Rodriguez, David C Danko, Heather L Wells, Sol Rey, Xavier Jirau Serrano, John Papciak, P Ford Combs, Gabor Fidler, Christopher E. Mason, Caitlin Otto, Niamh B. O’Hara, Dorottya Nagy-Szakal
Culture is currently the gold standard for diagnosis of urinary tract infections (UTIs); however, it has poor sensitivity detecting urogenital pathogens, especially if patients have already initiated antimicrobial therapy, or have an infection from an organism that is not commonly cultured. False negative urine culture results can lead to the inappropriate use of antimicrobial therapies or to the progression
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Effectiveness of BNT162b2 XBB vaccine in the US Veterans Affairs Healthcare System medRxiv. Infect. Dis. Pub Date : 2024-04-07 Aisling R. Caffrey, Haley J. Appaneal, Vrishali V. Lopes, Laura Puzniak, Evan J. Zasowski, Luis Jodar, Kerry L. LaPlante, John M. McLaughlin
Data evaluating effectiveness of XBB.1.5-adapted vaccines against JN.1-related endpoints are scarce. We performed a nationwide test-negative case-control study within the US Veterans Affairs Healthcare System to estimate vaccine effectiveness (VE) of BNT162b2 XBB.1.5-adapted vaccine compared to not receiving an XBB vaccine of any kind against COVID-19 hospitalization, emergency department or urgent
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Discovery of a novel antibiotic, Transitmycin, from Streptomyces sp unveils highly efficient activities against tuberculosis and human immunodeficiency virus medRxiv. Infect. Dis. Pub Date : 2024-04-07 Vanaja Kumar, Balagurunathan Ramsamy, Mukesh Doble, Radhakrishnan Manikkam, Luke Elizabeth Hanna, Gandarvakottai senthilkumar Arumugam, Kannan DOmodharan, Suresh Ganesan, Azger Dusthakeer, Precilla Lucia, Shainaba A Saadhali, Shanthi John, Selvakumar Nagamiah, Jaleel UCA, Rakhila M, Ayisha Safeeda, Sathish S
HIV is identified as a factor that aggravates tuberculosis disease pathogenesis and its progression to latent TB. While, TB is declared as one of the major causes for AIDS-associated mortality. So there is a dire need for new drugs to combat such ailments that have a synergistic interaction.This has led us to study a novel antibiotic purified from a marine Streptomyces sp isolated from the coral reef
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When should lockdown be implemented? Devising cost-effective strategies for managing epidemics amid vaccine uncertainty medRxiv. Infect. Dis. Pub Date : 2024-04-05 Nathan J. Doyle, Fergus Cumming, Robin N. Thompson, Michael J. Tildesley
During an infectious disease outbreak, public health policy makers are tasked with strategically implementing control interventions whilst balancing competing objectives. To provide a quantitative framework that can be used to guide these decisions, it is helpful to devise a clear and specific objective function that can be evaluated to determine the optimal outbreak response. In this study, we have
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Evaluating biomedical feature fusion on machine learning’s predictability and interpretability of COVID-19 severity types medRxiv. Infect. Dis. Pub Date : 2024-04-05 Haleigh West-Page, Kevin McGoff, Harrison Latimer, Isaac Olufadewa, Shi Chen
Background Accurately differentiating severe from non-severe COVID-19 clinical types is critical for the healthcare system to optimize workflow, as severe patients require intensive care. Current techniques lack the ability to accurately predict COVID-19 patients’ clinical type, especially as SARS-CoV-2 continues to mutate.
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Increased fibrinaloid microclot counts in platelet-poor plasma are associated with Long COVID medRxiv. Infect. Dis. Pub Date : 2024-04-05 Caroline F. Dalton, Madalena IR de Oliveira, Prachi Stafford, Nicholas Peake, Binita Kane, Andrew Higham, Dave Singh, Natalie Jackson, Helen E. Davies, David A. Price, Rae Duncan, Nicola Tattersall, Amanda Barnes, David P. Smith
Outcomes following SARS-CoV-2 infection are variable; whilst the majority of patients recover without serious complications, a subset of patients develop prolonged illness termed Long COVID or post-acute sequelae of SARS-CoV-2 infection (PASC). The pathophysiology underlying Long COVID remains unclear but appears to involve multiple mechanisms including persistent inflammation, coagulopathy, autoimmunity
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Traditional Healers’ Knowledge, Attitudes, and Perceptions About Tuberculosis and Collaboration with the Conventional Health System in the Kereyu Pastoralist Area of Ethiopia: A Cross-Sectional Study medRxiv. Infect. Dis. Pub Date : 2024-04-05 Bezawit Temesgen Sima, Tefera Belachew, Gunnar Bjune, Fekadu Abebe
Background Traditional Healers (THs) hold significant roles in many developing countries, often sought for ailments like tuberculosis (TB). However, their knowledge, attitude, and practice (KAP) regarding TB, particularly in Ethiopia’s pastoralist areas, remains unexamined. This study evaluates THs’ KAP on TB and their perceptions to collaborate with conventional health systems on TB control.
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Mutational alterations in the QRDR regions associated with fluoroquinolone resistance in Pseudomonas aeruginosa of clinical origin from Savar, Dhaka medRxiv. Infect. Dis. Pub Date : 2024-04-05 Md. Shamsul Arefin, Meftahul Jannat Mitu, Shomaia Yasmin Mitu, Azmeri Noorjahan, Mir Mobin, Shamsun Nahar, Hasnain Anjum, M. Hasibur Rahman
Bacterial DNA gyrase and topoisomerase IV are the major targets of quinolone antibiotic, and mutational alterations in quinolone resistance determining regions (QRDR) serve as major mechanism of resistance in most bacterial species, including P. aeruginosa. The present investigation was aimed to study the molecular mechanism of fluoroquinolone resistance among clinical P. aeruginosa isolated from Dhaka
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Incidence and risk factors of omicron variant SARS-CoV-2 breakthrough infection among vaccinated and boosted individuals medRxiv. Infect. Dis. Pub Date : 2024-04-05 Fabiola M. Moreno-Echevarria, Mathew T. Caputo, Daniel M. Camp, Susheel Reddy, Chad J. Achenbach
Background SARS-CoV-2 vaccines have been shown to be safe and effective against infection and severe COVID-19 disease worldwide. Certain co-morbid conditions cause immune dysfunction and may reduce immune response to vaccination. In contrast, those with co-morbidities may practice infection prevention strategies. Thus, the real-world clinical impact of co-morbidities on SARS-CoV-2 infection in the
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Alternative Approaches for Monitoring and Evaluation of Lymphatic Filariasis Following Mass Drug Treatment with Ivermectin, Diethylcarbamazine and Albendazole in East New Britain Province, Papua New Guinea medRxiv. Infect. Dis. Pub Date : 2024-04-04 Krufinta Bun, Benedict Mode, Melinda Susapu, Catherine Bjerum, Michael Payne, Daniel Tisch, Makoto Sekihara, Emanuele Giorgi, Gary J. Weil, Peter U Fischer, Leanne Robinson, Moses Laman, Christopher L. King
Background WHO recommends two annual rounds of mass drug administration (MDA) with ivermectin, diethylcarbamazine, and albendazole (IDA) for lymphatic filariasis (LF) elimination in treatment naïve areas that are not co-endemic for onchocerciasis such as Papua New Guinea (PNG). Whether two rounds of MDA are necessary or sufficient and the optimal sampling strategies and endpoints for stopping MDA remain
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A Randomized, Placebo-Controlled Trial to Evaluate the Safety and Efficacy of VIR-2482 in Healthy Adults for Prevention of Influenza A Illness (PENINSULA) medRxiv. Infect. Dis. Pub Date : 2024-04-04 Susanna K. Tan, Deborah Cebrik, David Plotnik, Maria L. Agostini, Keith Boundy, Christy M. Hebner, Wendy W. Yeh, Phillip S. Pang, Jaynier Moya, Charles Fogarty, Manuchehr Darani, Frederick G. Hayden
Background Influenza A results in significant morbidity and mortality. VIR-2482, an engineered human monoclonal antibody with extended half-life, targets a highly conserved epitope on the stem region of influenza A hemagglutinin, and may protect against seasonal and pandemic influenza.
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Molecular epidemiology of invasive Group A Streptococcal infections before and after the COVID-19 pandemic in Switzerland medRxiv. Infect. Dis. Pub Date : 2024-04-03 Angeliki M. Andrianaki, Jessica Franz, Federica Andreoni, Judith Bergada-Pijuan, Thomas C. Scheier, Tanja Duwe, Marc Pfister, Helena Seth-Smith, Tim Roloff, Natalia Kolesnik-Goldmann, Sara H. Burkhard, Alexia Cusini, Urs Karrer, Christian Rüegg, Adrian Schibli, Jacques Schrenzel, Stefano Musumeci, Roger D. Kouyos, Adrian Egli, Silvio D. Brugger, Annelies S. Zinkernagel
Group A Streptococcus (GAS, aka Streptococcus pyogenes) poses a significant public health concern, causing a diverse spectrum of infections with high mortality rates. Following the COVID-19 pandemic, a resurgence of invasive GAS (iGAS) infections has been documented, necessitating efficient outbreak detection methods. Whole genome sequencing (WGS) serves as the gold standard for GAS molecular typing
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After Reaching Its Highest Levels since 1950s, Incidence of Syphilis Among US Adults Declined in 2023 medRxiv. Infect. Dis. Pub Date : 2024-04-03 Duy Do, Patricia J. Rodriguez, Samuel Gratzl, Brianna M. Goodwin Cartwright, Charlotte Baker, Nicholas L Stucky
Recent reports showed that the incidence of syphilis in the US reached a 70-year high. Using 2019-2023 data from Truveta, this study demonstrated that while the incidence of syphilis increased from 2020 to 2022, it started to decline in 2023. The decline was driven by population subgroups that are commonly considered higher-risk for syphilis infection. Findings also highlighted growing trends among
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Machine learning-driven COVID-19 early triage and large-scale testing strategies based on the 2021 Costa Rican Actualidades survey medRxiv. Infect. Dis. Pub Date : 2024-04-03 Carlos Pasquier, Maikol Solís, Vivian Vilchez, Santiago Núñez-Corrales
The COVID-19 pandemic underscored the importance of mass testing in mitigating the spread of the virus. This study presents mass testing strategies developed through machine learning models, which predict the risk of COVID-19 contagion based on health determinants. Using the data from the 2021 “Actualidades” survey in Costa Rica, we trained models to classify individuals by contagion risk. After theorize
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Bacterial etiologies, antimicrobial susceptibility profiles and associated factors among patients with otitis media referred to Nekemte Public Health Research and Referral Laboratory Center, Western Ethiopia: A prospective cross-sectional study medRxiv. Infect. Dis. Pub Date : 2024-04-03 Endalu Tesfaye Guteta, Fedassan Alemu Abdi, Seifu Gizaw Feyisa, Belay Merkeb Zewudie, Betrearon Sileshi Kinfu, Hunduma Feyisa Geleta, Tadesse Bekele Tafesse
Background Otitis media is among the leading causes of illnesses responsible for causing hearing problems and adding significant costs to the public health system. Bacteria are the most common causative agents for otitis media. Currently, there is little information on the prevalence and antimicrobial susceptibility patterns of pathogenic bacterial isolates from patients with otitis media in Ethiopia
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Spatio-temporal distribution of rhinovirus types in Kenya: A retrospective analysis, 2014 medRxiv. Infect. Dis. Pub Date : 2024-04-03 John Mwita Morobe, Everlyn Kamau, Martha M. Luka, Nickson Murunga, Clement Lewa, Martin Mutunga, Godfrey Bigogo, Nancy Otieno, Bryan Nyawanda, Clayton Onyango, D. James Nokes, Charles N. Agoti, Patrick K. Munywoki
Rhinoviruses (RVs) are one of the most commonly detected viruses in people with acute respiratory illness (ARI). Despite their significant disease burden, RV epidemiology at national levels is underexplored. The circulation patterns of RV types throughout a population and the role of virus genotype in this distribution are ill-defined. We generated 803 VP4/VP2 gene sequences from rhinovirus-positive
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Obesity is associated with increased pediatric dengue virus infection and disease: A 9-year cohort study in Managua, Nicaragua medRxiv. Infect. Dis. Pub Date : 2024-04-03 Reinaldo Mercado-Hernandez, Rachel Myers, Fausto Bustos Carillo, José Victor Zambrana, Brenda López, Nery Sanchez, Aubree Gordon, Angel Balmaseda, Guillermina Kuan, Eva Harris
Background Obesity is on the rise globally in adults and children, including in tropical areas where diseases such as dengue have a substantial burden, particularly in children. Obesity impacts the risk of severe dengue disease; however, the impact on dengue virus (DENV) infection and dengue cases remains an open question.
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Field comparison of STANDARD™ Q Filariasis Antigen Test (QFAT) with Bioline Filariasis Test Strip (FTS) for the detection of Lymphatic Filariasis in Samoa, 2023 medRxiv. Infect. Dis. Pub Date : 2024-04-03 Jessica L Scott, Helen J Mayfield, Jane Sinclair, Beatris Mario Martin, Maddison Howlett, Ramona Muttucumaru, Kimberly Y Won, Robert Thomsen, Satupaitea Viali, Rossana Tofaeono-Pifeleti, Patricia M Graves, Colleen L Lau
Background To monitor the progress of lymphatic filariasis (LF) elimination programmes, field surveys to assess filarial antigen (Ag) prevalence require access to reliable, user-friendly rapid diagnostic tests. We aimed to evaluate the performance of the new Q Filariasis Antigen Test (QFAT) with the currently recommended Filariasis Test Strip (FTS) for detecting the Ag of Wuchereria bancrofti, the
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Persistent Mycobacterium tuberculosis bioaerosol release in a tuberculosis-endemic setting medRxiv. Infect. Dis. Pub Date : 2024-04-03 Ryan Dinkele, Sophia Gessner, Benjamin Patterson, Andrea McKerry, Zeenat Hoosen, Andiswa Vazi, Ronnett Seldon, Anastasia Koch, Digby F. Warner, Robin Wood
Pioneering studies linking symptomatic disease and cough-mediated release of Mycobacterium tuberculosis (Mtb) established the infectious origin of tuberculosis (TB), simultaneously informing the pervasive notion that pathology is a prerequisite for Mtb transmission. Our prior work has challenged this assumption: by sampling TB clinic attendees, we detected equivalent release of Mtb-containing bioaerosols
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Human adenovirus outbreak at a university campus monitored by wastewater and clinical surveillance medRxiv. Infect. Dis. Pub Date : 2024-03-28 Steven C. Holland, Matthew F. Smith, LaRinda A. Holland, Rabia Maqsood, James C. Hu, Vel Murugan, Erin M. Driver, Rolf U. Halden, Efrem S. Lim
Areas of dense population congregation are prone to experience respiratory virus outbreaks. We monitored wastewater and clinic patients for the presence of respiratory viruses on a large, public university campus. Campus sewer systems were monitored in 16 locations for the presence of viruses using next generation sequencing over 22 weeks in 2023. During this period, we detected a surge in human adenovirus
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The 10-year health impact, economic impact, and return on investment of the South African molecular diagnostics programme for HIV, Tuberculosis and SARS-CoV-2 medRxiv. Infect. Dis. Pub Date : 2024-03-28 Brooke E Nichols, Alexandra de Nooy, Naseem Cassim, Lucia Hans, Manuel Pedro da Silva, Kamy Chetty, Kyra H Grantz, Alvin X. Han, Andrew N Phillips, Lise Jamieson, Lesley E Scott, Wendy S Stevens
To ensure there is adequate investment into diagnostics, an understanding of the magnitude of impact and return on investment is necessary. We therefore sought to understand the health and economic impacts of the molecular diagnostic programme in South Africa, to deepen the under-standing on the broad value of diagnostics and guide future healthcare investments. We calcu-lated the 10-year (where data
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Subtracting the background: Reducing cell-free DNA's confounding effects on Mycobacterium tuberculosis quantitation and the sputum microbiome medRxiv. Infect. Dis. Pub Date : 2024-03-28 Charissa C Naidoo, Rouxjeane Venter, Francesc Codony, Gemma Agusti, Natasha Kitchin, Selisha Naidoo, Hilary Monaco, Hridesh Mishra, Yonghua Li, Jose Clemente, Robin Warren, Leopoldo N Segal, Grant Theron
Characterising DNA in specimens from people with tuberculosis (TB), a major cause of death, is critical for evaluating diagnostics and the microbiome, yet extracellular DNA, more frequent in people on chemotherapy, confounds results. We evaluated whether nucleic acid dyes [propidium monoazide (PMA), PEMAX] and DNaseI could reduce this. PCR [16S Mycobacterium tuberculosis complex (Mtb) qPCR, Xpert MTB/RIF]
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COHORT PROFILE: IMMUNE RESPONSES TO SARS-COV-2 VACCINATION AND INFECTION IN A LONGITUDINAL SAMPLING AMIDST THE COVID-19 PANDEMIC (LONGTONG-SARS2) IN MALAYSIA medRxiv. Infect. Dis. Pub Date : 2024-03-28 Naim Che-Kamaruddin, Jefree Johari, Hasmawati Yahaya, Huy C Nguyen, Andrew G. Letizia, Robert D. Hontz, Sazaly AbuBakar
Purpose: This prospective, longitudinal study aims to evaluate the durability and functionality of SARS-CoV-2 Ancestral strain (Wuhan-Hu-1)-specific immune responses induced by COVID-19 vaccination and natural infection over a 12-month period. This article reviews the study protocol, design, methodology, ongoing data collection, analysis procedures, and demographic characteristics of the cohort enrolled
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Validation of an unbiased metagenomic detection assay for RNA viruses in viral transport media and plasma medRxiv. Infect. Dis. Pub Date : 2024-03-27 Anthony D Kappell, Kathleen Q. Schulte, Elizabeth A Scheuermann, Matthew B Scholz, Nicolette C Keplinger, Amanda N Scholes, Taylor A Wolt, Viviana M June, Cole J Schulte, Leah W Allen, Krista L Ternus, F Curtis Hewitt
Unbiased long read sequencing holds enormous potential for the detection of pathogen sequences in clinical samples. However, the untargeted nature of these methods precludes conventional PCR approaches, and the metagenomic content of each sample increases the challenge of bioinformatic analysis. Here, we evaluate a previously described novel workflow for unbiased RNA virus sequence identification in
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Unbiased metagenomic detection of RNA viruses for rapid identification of viral pathogens in clinical samples medRxiv. Infect. Dis. Pub Date : 2024-03-27 Anthony D. Kappell, Amanda N Scholes, Matthew B. Scholz, Nicolette C. Keplinger, Leah W. Allen, Matthew C Murray, Krista L Ternus, F. Curtis Hewitt
Unbiased long read sequencing approaches for clinical metagenomic sample analysis holds enormous potential for pathogen detection, including improved detection of unknown, novel or emerging viruses. However, the rapid rate of development in nanopore sequencing and library preparation methods complicates the process of selecting a standardized method for unbiased RNA virus detection. Here, we evaluate
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Laboratory Comparison of Rapid Antigen Diagnostic Tests for Lymphatic Filariasis: STANDARDTM Q Filariasis Antigen Test (QFAT) and Bioline Filariasis Test Strip (FTS) medRxiv. Infect. Dis. Pub Date : 2024-03-27 Patricia M Graves, Jessica L Scott, Alvaro Berg Soto, Antin YN Widi, Maxine Whittaker, Derek Lee, Colleen L Lau, Kimberly Y Won
Background: Accurate and user-friendly rapid diagnostic tests (RDT) are needed to assess prevalence of Wuchereria bancrofti antigen in the Global Programme to Eliminate Lymphatic Filariasis (GPELF). We evaluated performance under laboratory conditions of the new Q Filariasis Antigen Test (QFAT) against the Filariasis Test Strip (FTS) for detecting antigen of Wuchereria bancrofti, a causative agent
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First Phase 1b, single-center, age de-escalation trial of the P. falciparum blood-stage malaria vaccine candidate RH5.1/Matrix-M™: a delayed boost regimen induces high levels of functional antibodies in 5-17 month old Tanzanian infants medRxiv. Infect. Dis. Pub Date : 2024-03-26 Sarah E Silk, Wilmina F Kalinga, Jo Salkeld, Ivanny M Mtaka, Saumu Ahmed, Florence Milando, Ababacar Diouf, Caroline K Bundi, Neema Balige, Omar Hassan, Catherine G Mkindi, Stella Rwezaula, Thabit Athumani, Sarah Mswata, Nasoro S Lilolime, Beatus Simon, Hania Msami, Mohamed Mohamed, Damiano M David, Latipha Mohammed, Gloria Nyaulingo, Bakari Mwalimu, Omary Juma, Tunu G Mwamlima, Ibrahim A Sasamalo
Background RH5.1 is a soluble protein vaccine candidate for blood-stage Plasmodium falciparum malaria, previously trialed in healthy UK adults in combination with AS01B adjuvant. Here, RH5.1 was formulated with Matrix-M™ adjuvant to assess safety and immunogenicity in a malaria-endemic adult and pediatric population for the first time. Methods We conducted a Phase 1b, single-center, dose-escalation