scholarly journals Comparison of antigen- and RT-PCR-based testing strategies for detection of Sars-Cov-2 in two high-exposure settings

2021 ◽  
Author(s):  
Jay Love ◽  
Megan T Wimmer ◽  
Damon J A Toth ◽  
Arthi Chandran ◽  
Dilip Makhija ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Disease Transmission ◽  
Disease Burden ◽  
Economic Cost ◽  
High Sensitivity ◽  
Population Level ◽  
Rt Pcr ◽  
High Exposure ◽  
Viral Culture ◽  
Infectious Stage

Surveillance testing for infectious disease is an important tool to combat disease transmission at the population level. During the SARS-CoV-2 pandemic, RT-PCR tests have been considered the gold standard due to their high sensitivity and specificity. However, RT-PCR tests for SARS-CoV-2 have been shown to return positive results when administered to individuals who are past the infectious stage of the disease. Meanwhile, antigen-based tests are often treated as a less accurate substitute for RT-PCR, however, new evidence suggests they may better reflect infectiousness. Consequently, the two test types may each be most optimally deployed in different settings. Here, we present an epidemiological model with surveillance testing and coordinated isolation in two congregate living settings (a nursing home and a university dormitory system) that considers test metrics with respect to viral culture, a proxy for infectiousness. Simulations show that antigen-based surveillance testing coupled with isolation greatly reduces disease burden and carries a lower economic cost than RT-PCR-based strategies. Antigen and RT-PCR tests perform different functions toward the goal of reducing infectious disease burden and should be used accordingly.

scholarly journals Comparison of antigen- and RT-PCR-based testing strategies for detection of SARS-CoV-2 in two high-exposure settings

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0253407
Author(s):  
Jay Love ◽  
Megan T. Wimmer ◽  
Damon J. A. Toth ◽  
Arthi Chandran ◽  
Dilip Makhija ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Disease Transmission ◽  
Disease Burden ◽  
Economic Cost ◽  
High Sensitivity ◽  
Population Level ◽  
Rt Pcr ◽  
High Exposure ◽  
Viral Culture ◽  
Infectious Stage

Surveillance testing for infectious disease is an important tool to combat disease transmission at the population level. During the SARS-CoV-2 pandemic, RT-PCR tests have been considered the gold standard due to their high sensitivity and specificity. However, RT-PCR tests for SARS-CoV-2 have been shown to return positive results when performed to individuals who are past the infectious stage of the disease. Meanwhile, antigen-based tests are often treated as a less accurate substitute for RT-PCR, however, new evidence suggests they may better reflect infectiousness. Consequently, the two test types may each be most optimally deployed in different settings. Here, we present an epidemiological model with surveillance testing and coordinated isolation in two congregate living settings (a nursing home and a university dormitory system) that considers test metrics with respect to viral culture, a proxy for infectiousness. Simulations show that antigen-based surveillance testing coupled with isolation greatly reduces disease burden and carries a lower economic cost than RT-PCR-based strategies. Antigen and RT-PCR tests perform different functions toward the goal of reducing infectious disease burden and should be used accordingly.

scholarly journals Disease transmission and introgression can explain the long-lasting contact zone of modern humans and Neanderthals

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Gili Greenbaum ◽  
Wayne M. Getz ◽  
Noah A. Rosenberg ◽  
Marcus W. Feldman ◽  
Erella Hovers ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Immune System ◽  
Disease Transmission ◽  
Disease Burden ◽  
Species Interaction ◽  
Disease Dynamics ◽  
Modern Humans ◽  
Systems Models ◽  
Species Boundary ◽  
Infectious Disease Dynamics

Abstract Neanderthals and modern humans both occupied the Levant for tens of thousands of years prior to the spread of modern humans into the rest of Eurasia and their replacement of the Neanderthals. That the inter-species boundary remained geographically localized for so long is a puzzle, particularly in light of the rapidity of its subsequent movement. Here, we propose that infectious-disease dynamics can explain the localization and persistence of the inter-species boundary. We further propose, and support with dynamical-systems models, that introgression-based transmission of alleles related to the immune system would have gradually diminished this barrier to pervasive inter-species interaction, leading to the eventual release of the inter-species boundary from its geographic localization. Asymmetries between the species in the characteristics of their associated ‘pathogen packages’ could have generated feedback that allowed modern humans to overcome disease burden earlier than Neanderthals, giving them an advantage in their subsequent spread into Eurasia.

scholarly journals Using linked health data in international comparisons of infectious disease burden

2018 ◽  
Vol 3 (4) ◽  
Author(s):  
Rachel Reeves
Keyword(s):  
Infectious Disease ◽  
Respiratory Syncytial Virus ◽  
Infectious Diseases ◽  
Disease Burden ◽  
International Comparisons ◽  
Population Level ◽  
Health Data ◽  
Routinely Collected Data ◽  
Syncytial Virus ◽  
International Comparative

Linking population-level health databases – such as those on hospital admissions, GP consultations, prescriptions, maternal and perinatal data, and laboratory data – provides great opportunities to explore the epidemiology and burden of infectious diseases. Furthermore, comparing the epidemiology and burden of infectious diseases on an international scale is crucial in designing and implementing national and global prevention and control measures. However, substantial differences between countries in national health systems (including thresholds for hospital admission), as well as varying availability and quality of routinely collected data, can pose challenges when using linked population-level health databases to compare estimates of infectious disease burden between countries. This session aims to highlight and discuss the opportunities and challenges of international comparisons of infectious disease burden using linked population-level health data. This session will facilitate discussion of the methodological, ethical and resource challenges when using linked health data to produce internationally comparable estimates of the burden of infectious diseases. We will use as an example the ongoing work of the REspiratory Syncytial virus Consortium in Europe (RESCEU) – a large-scale collaborative project producing evidence to inform policymaking and regulatory decisions on novel respiratory syncytial virus (RSV) vaccines and therapeutics. The RESCEU project involves at least seven European countries each using linked routinely collected health data to produce national estimates of the health and economic burden of RSV, by age and risk group, for comparison. The results will highlight target populations for future vaccines and therapeutics, and provide a baseline estimate of the pre-vaccine era burden of disease that can be used to measure future vaccine impact. We will share the challenges faced in the RESCEU project with regards to using linked health data in international comparative work. We will then discuss, with relevance to other ongoing or future projects, how these challenges may be overcome. This session will generate ideas for procedures and tools for international comparative work using routinely collected data to investigate infectious diseases. This session will provide the opportunity to network with other researchers working in this area. We aim to facilitate the generation and dissemination of ideas for current and future projects, and therefore this session is likely to identify areas for potential future international collaborative work.

scholarly journals Behavioural ecology and infectious disease: implications for conservation of biodiversity

2019 ◽  
Vol 374 (1781) ◽  
pp. 20180054 ◽  
Author(s):  
James Herrera ◽  
Charles L. Nunn
Keyword(s):  
Infectious Disease ◽  
Disease Transmission ◽  
Disease Ecology ◽  
Scale Up ◽  
Species Conservation ◽  
Population Level ◽  
Behavioural Ecology ◽  
Parasite Transmission ◽  
Transmission Potential ◽  
Increased Risk

Behaviour underpins interactions among conspecifics and between species, with consequences for the transmission of disease-causing parasites. Because many parasites lead to declines in population size and increased risk of extinction for threatened species, understanding the link between host behaviour and disease transmission is particularly important for conservation management. Here, we consider the intersection of behaviour, ecology and parasite transmission, broadly encompassing micro- and macroparasites. We focus on behaviours that have direct impacts on transmission, as well as the behaviours that result from infection. Given the important role of parasites in host survival and reproduction, the effects of behaviour on parasitism can scale up to population-level processes, thus affecting species conservation. Understanding how conservation and infectious disease control strategies actually affect transmission potential can therefore often only be understood through a behavioural lens. We highlight how behavioural perspectives of disease ecology apply to conservation by reviewing the different ways that behavioural ecology influences parasite transmission and conservation goals. This article is part of the theme issue ‘Linking behaviour to dynamics of populations and communities: application of novel approaches in behavioural ecology to conservation’.

scholarly journals Modeling the Transmission of Respiratory Infectious Diseases in Mass Transportation Systems

2020 ◽  
Author(s):  
Christian Alvin H. Buhat ◽  
Destiny SM. Lutero ◽  
Yancee H. Olave ◽  
Monica C. Torres ◽  
Jomar F. Rabajante
Keyword(s):  
Infectious Disease ◽  
Disease Transmission ◽  
Disease Outbreaks ◽  
Optimal Strategies ◽  
Transportation Systems ◽  
Public Utility ◽  
Mass Transportation ◽  
Transit System ◽  
High Exposure ◽  
Social Distancing

AbstractMass transportation is one of the areas that are badly hit by respiratory infectious disease outbreaks due to moderate to high exposure risk to pathogens brought about by the interaction among commuters. Here, we formulate agent-based models that simulate the spread of a respiratory infectious disease in a train wagon in the Manila Light Rail Transit System, and in a 49-seater public utility bus. We consider preventive measures such as implementation of social distancing, and limitation of interaction or movement among the commuters to investigate how these measures will inhibit disease transmission. We also consider the effect of protective gears and practices, crowd density, and prevalence of disease in the community on the possible number of newly-infected individuals. Our simulations show that (i) individuals must have protection with more than 90% effectiveness to inhibit transmission of the disease; (ii) social or physical distancing by more than 1m distance reduces the risk of being infected; (iii) minimizing movement or interaction with other passengers reduces the risk of transmission by 50%; (iv) passenger capacity should be less than 10-50% of the maximum seating capacity to reduce the number of infections depending on the level of imposed social distancing and passenger interaction; (v) vehicles with greater number of occupied seating capacity generate higher number of infections but vehicles with smaller dimensions have faster disease transmissions; and (vi) ideal set-up for a 24-seater train wagon (49-seater bus) is to allow a maximum of 12 (24) passengers, with little to no interaction among passengers, with social distancing of more than 1m distance apart, and each person has a protection with 90% effectiveness as much as possible. These results can aid policy makers in determining optimal strategies to minimize infections while maintaining transportation services during pandemics or disease outbreaks.

scholarly journals Quantifying arbovirus disease and transmission risk at the municipality level in the Dominican Republic: the inception of Rm

2020 ◽  
Author(s):  
Rhys Kingston ◽  
Isobel Routledge ◽  
Samir Bhatt ◽  
Leigh R Bowman
Keyword(s):  
Dominican Republic ◽  
Disease Transmission ◽  
Disease Surveillance ◽  
Disease Burden ◽  
Economic Cost ◽  
Transmission Risk ◽  
San Jose ◽  
Transmission Chain ◽  
Reproduction Numbers ◽  
Dengue Epidemic

AbstractArboviruses remain a significant cause of morbidity, mortality and economic cost across the global human population. Epidemics of arboviral disease, such as Zika and dengue, also cause significant disruption to health services at local and national levels. This study examined 2014-16 Zika and dengue epidemic data at the sub-national level to characterise transmission across the Dominican Republic.For each municipality, spatio-temporal mapping was used to characterise disease burden, while data were age and sex standardised to quantify burden distributions among the population. In separate analyses, time-ordered data were combined with the underlying disease migration interval distribution to produce a network of likely transmission chain events, displayed using transmission chain likelihood matrices. Finally, municipal-specific reproduction numbers (Rm) were established using a Wallinga-Teunis matrix.Dengue and Zika epidemics peaked during weeks 39-52 of 2015 and weeks 14-27 of 2016 respectively. At the provincial level, dengue attack rates were high in Hermanas Mirabal and San José de Ocoa (58.1 and 49.2 cases per 10,000 population respectively), compared with the Zika burden, which was highest in Independencia and San José de Ocoa (21.2 and 13.4 cases per 10,000 population respectively). Across municipalities, high disease burden was observed in Cotui (622 dengue cases per 10,000 population) and Jimani (32 Zika cases per 10,000 population). Municipal infector-infectee transmission likelihood matrices identified six 0% likelihood transmission events throughout the dengue epidemic and one 0% likelihood transmission event during the Zika epidemic. Municipality reproduction numbers (Rm) were consistently higher, and persisted for a greater duration during the Zika epidemic (Rm = 1.0), than during the dengue epidemic (Rm = <1.0).This research highlights the importance of disease surveillance in land-border municipalities as an early warning for infectious disease transmission. It also demonstrates that a high number of importation events are required to sustain transmission in endemic settings, and vice versa for newly emerged diseases. The inception of a novel epidemiological metric, Rm, reports transmission risk using standardised spatial units, and can be used to identify high transmission risk municipalities to better focus public health interventions for dengue, Zika, and other infectious diseases.Author SummaryArboviruses remain a significant cause of morbidity, mortality and economic cost. Between the years 2014-16, two large arbovirus outbreaks occurred in the Dominican Republic. The first was a wave of dengue cases, followed by a large Zika epidemic. Using various mathematical modelling and geospatial approaches, a number of analyses were undertaken to both characterise the pattern of disease transmission and identify high-burden municipalities. Throughout the process, a novel metric was developed: the Rm. This parameter was used to identify the transmission potential of any given municipality to surrounding municipalities, where >1.0 is high transmission risk, and <1.0 is low transmission risk. This is useful as it provides a standardised approach to determine where public health resources might be focussed to better impact ongoing disease transmission. Additionally, analyses demonstrated the importance of increased disease surveillance in municipalities that share land borders with neighbouring countries, and how relatively few disease importation events can spark and sustain an epidemic.

Adapting Disease Prevention Protocols for Human Spaceflight During COVID-19

2021 ◽  
Vol 92 (7) ◽  
pp. 597-602
Author(s):  
Eric Petersen ◽  
James M. Pattarini ◽  
Robert A. Mulcahy ◽  
Samuel B. Beger ◽  
Matthew R. Mitchell ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Disease Prevention ◽  
Infectious Diseases ◽  
Disease Transmission ◽  
Descriptive Analysis ◽  
Commercial Application ◽  
Flight Crew ◽  
Rt Pcr ◽  
Infectious Disease Transmission ◽  
Human Spaceflight

BACKGROUND: The National Aeronautics and Space Administration (NASA) Flight Crew Health Stabilization Program (HSP) was historically implemented to minimize infectious disease transmission to astronauts in the immediate prelaunch period. The first ever commercial application and adaptation of the NASA HSP was implemented during the Crew Demo-2 mission in the time of the Coronavirus disease 2019 (COVID-19) pandemic. This article details and discusses the first commercial implementation and adaptation of the HSP prior to the Crew Demo-2 launch.METHODS: This is a retrospective descriptive analysis of the application of NASA disease prevention protocols for human spaceflight during the COVID-19 pandemic. In the context of the pandemic, extra precautions added to the HSP included daily symptom surveys completed by Primary Contacts of the crew, COVID-19 RT-PCR testing, and improved quarantine protocols.RESULTS: Of the 91 SpaceX Primary Contacts who completed a total of 2720 daily symptom surveys prior to launch, 22 individuals (24.2) and 198 surveys (7.3) returned positive for potential symptoms of COVID-19. Two individuals were removed due to symptoms indistinguishable from COVID-19. Through this survey, systematic quarantine, and PCR testing, the Crew Demo-2 mission was successful with no known infectious diseases transmitted.CONCLUSIONS: Overall, the commercial implementation of the NASA Health Stabilization Program by SpaceX with adjustments required during the COVID-19 pandemic was a success, with protocols allowing identification and removal of potentially infectious persons from the program. The principles of the HSP may provide an adequate infectious disease playbook for commercial spaceflight operations going forward.Petersen E, Pattarini JM, Mulcahy RA, Beger SB, Mitchell MR, Hu YD, Middleton KN, Frazier W, Mormann B, Esparza H, Asadi A, Musk ER, Alter G, Nilles E, Menon AS. Adapting disease prevention protocols for human spaceflight during COVID-19. Aerosp Med Hum Perform. 2021; 92(7):597602.

Travel Connectivity and Infectious Disease Transmission Risks in Oceania

2020 ◽  
Author(s):  
Angela Maria Cadavid Restrepo ◽  
Luis Furuya-Kanamori ◽  
Helen Mayfield ◽  
Eric J. Nilles ◽  
Colleen L. Lau
Keyword(s):  
Infectious Disease ◽  
Disease Transmission ◽  
Infectious Disease Transmission

scholarly journals Prolonged SARS-CoV-2-RNA Detection from Nasopharyngeal Swabs in an Oncologic Patient: What Impact on Cancer Treatment?

2021 ◽  
Vol 28 (1) ◽  
pp. 847-852
Author(s):  
Anna Ferrari ◽  
Marco Trevenzoli ◽  
Lolita Sasset ◽  
Elisabetta Di Liso ◽  
Toni Tavian ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Cancer Treatment ◽  
Cancer Patients ◽  
Clinical Symptoms ◽  
Palliative Radiotherapy ◽  
Rt Pcr ◽  
Cancer Treatments ◽  
Global Challenge ◽  
Viral Culture ◽  
Pcr Assays

The pandemic of SARS-CoV-2 is a serious global challenge affecting millions of people worldwide. Cancer patients are at risk for infection exposure and serious complications. A prompt diagnosis of SARS-CoV-2 infection is crucial for the timely adoption of isolation measures and the appropriate management of cancer treatments. In lung cancer patients the symptoms of infection 19 may resemble those exhibited by the underlying oncologic condition, possibly leading to diagnostic overlap and delays. Moreover, cancer patients might display a prolonged positivity of nasopharyngeal RT-PCR assays for SARS-CoV-2, causing long interruptions or delay of cancer treatments. However, the association between the positivity of RT-PCR assays and the patient’s infectivity remains uncertain. We describe the case of a patient with non-small cell lung cancer, and a severe ab extrinseco compression of the trachea, whose palliative radiotherapy was delayed because of the prolonged positivity of nasopharyngeal swabs for SARS-CoV-2. The patient did not show clinical symptoms suggestive of active infection, but the persistent positivity of RT-PCR assays imposed the continuation of isolation measures and the delay of radiotherapy for over two months. Finally, the negative result of SARS-CoV-2 viral culture allowed us to verify the absence of viral activity and to rule out the infectivity of the patient, who could finally continue her cancer treatment.

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