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Sci Rep ; 12(1): 1857, 2022 02 03.
Article in English | MEDLINE | ID: covidwho-1671608


Amid COVID-19, many institutions deployed vast resources to test their members regularly for safe reopening. This self-focused approach, however, not only overlooks surrounding communities but also remains blind to community transmission that could breach the institution. To test the relative merits of a more altruistic strategy, we built an epidemiological model that assesses the differential impact on case counts when institutions instead allocate a proportion of their tests to members' close contacts in the larger community. We found that testing outside the institution benefits the institution in all plausible circumstances, with the optimal proportion of tests to use externally landing at 45% under baseline model parameters. Our results were robust to local prevalence, secondary attack rate, testing capacity, and contact reporting level, yielding a range of optimal community testing proportions from 18 to 58%. The model performed best under the assumption that community contacts are known to the institution; however, it still demonstrated a significant benefit even without complete knowledge of the contact network.

COVID-19 Testing/methods , COVID-19/diagnosis , COVID-19/prevention & control , COVID-19/epidemiology , COVID-19/transmission , Contact Tracing/methods , Female , Humans , Male , Prevalence , Public Health
Viruses ; 13(8)2021 08 13.
Article in English | MEDLINE | ID: covidwho-1376992


While investigating a signal of adaptive evolution in humans at the gene LARGE, we encountered an intriguing finding by Dr. Stefan Kunz that the gene plays a critical role in Lassa virus binding and entry. This led us to pursue field work to test our hypothesis that natural selection acting on LARGE-detected in the Yoruba population of Nigeria-conferred resistance to Lassa Fever in some West African populations. As we delved further, we conjectured that the "emerging" nature of recently discovered diseases like Lassa fever is related to a newfound capacity for detection, rather than a novel viral presence, and that humans have in fact been exposed to the viruses that cause such diseases for much longer than previously suspected. Dr. Stefan Kunz's critical efforts not only laid the groundwork for this discovery, but also inspired and catalyzed a series of events that birthed Sentinel, an ambitious and large-scale pandemic prevention effort in West Africa. Sentinel aims to detect and characterize deadly pathogens before they spread across the globe, through implementation of its three fundamental pillars: Detect, Connect, and Empower. More specifically, Sentinel is designed to detect known and novel infections rapidly, connect and share information in real time to identify emerging threats, and empower the public health community to improve pandemic preparedness and response anywhere in the world. We are proud to dedicate this work to Stefan Kunz, and eagerly invite new collaborators, experts, and others to join us in our efforts.

Disaster Planning , Lassa Fever/epidemiology , Lassa virus/physiology , Africa, Western/epidemiology , Disaster Planning/methods , Humans , Lassa Fever/genetics , Lassa Fever/prevention & control , Lassa Fever/virology , Lassa virus/genetics , N-Acetylglucosaminyltransferases/genetics , N-Acetylglucosaminyltransferases/immunology , Nigeria/epidemiology , Pandemics , Polymorphism, Genetic , Receptors, Virus/genetics , Receptors, Virus/immunology
J Clin Pathol ; 74(8): 496-503, 2021 Aug.
Article in English | MEDLINE | ID: covidwho-1247388


Developing and deploying new diagnostic tests are difficult, but the need to do so in response to a rapidly emerging pandemic such as COVID-19 is crucially important. During a pandemic, laboratories play a key role in helping healthcare providers and public health authorities detect active infection, a task most commonly achieved using nucleic acid-based assays. While the landscape of diagnostics is rapidly evolving, PCR remains the gold-standard of nucleic acid-based diagnostic assays, in part due to its reliability, flexibility and wide deployment. To address a critical local shortage of testing capacity persisting during the COVID-19 outbreak, our hospital set up a molecular-based laboratory developed test (LDT) to accurately and safely diagnose SARS-CoV-2. We describe here the process of developing an emergency-use LDT, in the hope that our experience will be useful to other laboratories in future outbreaks and will help to lower barriers to establishing fast and accurate diagnostic testing in crisis conditions.

COVID-19 Nucleic Acid Testing , COVID-19/diagnosis , Emergency Service, Hospital , Laboratories, Hospital , Real-Time Polymerase Chain Reaction , SARS-CoV-2/genetics , COVID-19/virology , Humans , Predictive Value of Tests , Reproducibility of Results