transmission chain
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2022 ◽  
Author(s):  
Shuo Sun ◽  
Mairead Shaw ◽  
Erica EM Moodie ◽  
Derek Ruths

We analyzed the effectiveness of the Canadian COVID Alert app on reducing COVID-19 infections and deaths due to the COVID-19 virus using two separate, but complementary approaches, were taken. First, we undertook a comparative study to assess how the adoption and usage of the COVID Alert app compared to those of similar apps deployed in other regions. Next, we used data from the COVID Alert server and a range of plausible parameter values to estimate the numbers of infections and deaths averted in Canada using a model that combines information on number of notifications, secondary attack rate, expected fraction of transmissions that could be prevented, quarantine effectiveness, and expected size of the full transmission chain in the absence of exposure notification. The comparative analysis revealed that the COVID Alert app had among the lowest adoption levels among apps that reported usage. Our model indicates that use of the COVID Alert app averted between 6,284 and 10,894 infections across the six Canadian provinces where app usage was highest during the March - July 2021 period. This range is equivalent to 1.6%-2.9% of the total recorded infections across Canada in that time. Using province-specific case fatality rates, 57-101 deaths were averted during the same period. The number of cases and deaths averted was greatest in Ontario, whereas the proportion of cases and death averted was greatest in Newfoundland and Labrador. App impact measures were reported so rarely and so inconsistently by other countries that the relative assessment of impact is inconclusive. While the nationwide rates are low, provinces with widespread adoption of the app showed high ratios of averted cases and deaths (upper bound was greater than 60% of averted cases). Our findings suggest that the COVID Alert app, when adopted at sufficient levels, can be an effective public health tool for combatting a pandemic such as COVID-19.


Author(s):  
Oscar Pérez-Hernández ◽  
Francisco Sautua ◽  
Santiago Domínguez-Monge ◽  
Carlos Cecilio Góngora-Canul ◽  
Marcelo Carmona

<p>Since the start of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing the coronavirus disease 2019 (COVID-19) pandemic, the concepts of serial and generation intervals have been used as key epidemiological measures to understand the transmission dynamics of the disease. We carefully examined and repurposed these concepts to the understanding of the transmission chain and dynamics of two major citrus diseases: tristeza virus (caused by Citrus tristeza virus, CTV) and Huanglongbing (caused by <em>Candidatus</em> Liberibacter asiaticus). Following the fundamental definition of the concepts, the review delineates the transmission chain in the SARS-CoV-2 and that of CTV and CLas, pointing out their major similarities and differences. Then, it discusses estimation of the serial and generation intervals and their distributions for both plant diseases. Identification of infector-infectee tree pairs in a transmission chain within orchards is proposed through use of disease incidence data from intensive mapping, spatial pattern analysis, conditional probability, and simulation approaches. Like in SARS-CoV-2 dynamics, pre-symptomatic transmission in these two plant pathosystems is of epidemiological significance. Hence, estimation of the serial and generation interval can lay the foundations to understanding of early disease transmission dynamics, thus the implementation of vector control measures or eradication of infected trees. We hope this review motivates discussions on estimation and usage of these concepts to enhance understanding of the epidemiology of both of the herein examined citrus diseases.</p>


2021 ◽  
Author(s):  
Ilya Plyusnin ◽  
Phuoc Thien Truong Nguyen ◽  
Tarja Sironen ◽  
Olli Vapalahti ◽  
Teemu Smura ◽  
...  

Summary: SARS-CoV-2 is the highly transmissible etiologic agent of coronavirus disease 2019 (COVID-19) and has become a global scientific and public health challenge since December 2019. Several new variants of SARS-CoV-2 have emerged globally raising concern about prevention and treatment of COVID-19. Early detection and in depth analysis of the emerging variants allowing pre-emptive alert and mitigation efforts are thus of paramount importance. Here we present ClusTRace, a novel bioinformatic pipeline for a fast and scalable analysis of sequence clusters or clades in large viral phylogenies. ClusTRace offers several high level functionalities including outlier filtering, aligning, phylogenetic tree reconstruction, cluster or clade extraction, variant calling, visualization and reporting. ClusTRace was developed as an aid for COVID-19 transmission chain tracing in Finland and the main emphasis has been on fast and unsupervised screening of phylogenies for markers of super-spreading events and other features of concern, such as high rates of cluster growth and/or accumulation of novel mutations. Availability: All code is freely available from https://bitbucket.org/plyusnin/clustrace/


2021 ◽  
Author(s):  
Eline A. Ampt ◽  
Jasper van Ruijven ◽  
Mark P. Zwart ◽  
Jos M. Raaijmakers ◽  
Aad J. Termorshuizen ◽  
...  

2021 ◽  
Author(s):  
Sarah A. Nadeau ◽  
Timothy G. Vaughan ◽  
Christiane Beckmann ◽  
Ivan Topolsky ◽  
Chaoran Chen ◽  
...  

Genome sequences allow quantification of changes in case introductions from abroad and local transmission dynamics. We sequenced 11,357 SARS-CoV-2 genomes from Switzerland in 2020 - the 6th largest effort globally. Using these data, we estimated introductions and their persistence throughout 2020. By contrasting estimates with null models, we estimate at least 83% of introductions were adverted during Switzerland's border closures. Further, transmission chain persistence roughly doubled after the partial lockdown was lifted. Then, using a novel phylodynamic method, we suggest transmission in newly introduced outbreaks slowed 36 - 64% upon outbreak detection in summer 2020, but not in fall. This could indicate successful contact tracing over summer before overburdening in fall. The study highlights the added value of genome sequencing data for understanding transmission dynamics.


2021 ◽  
Vol 26 (44) ◽  
Author(s):  
Sebastian Duchene ◽  
Leo Featherstone ◽  
Birgitte Freiesleben de Blasio ◽  
Edward C Holmes ◽  
Jon Bohlin ◽  
...  

Background Many countries have attempted to mitigate and control COVID-19 through non-pharmaceutical interventions, particularly with the aim of reducing population movement and contact. However, it remains unclear how the different control strategies impacted the local phylodynamics of the causative SARS-CoV-2 virus. Aim We aimed to assess the duration of chains of virus transmission within individual countries and the extent to which countries exported viruses to their geographical neighbours. Methods We analysed complete SARS-CoV-2 genomes to infer the relative frequencies of virus importation and exportation, as well as virus transmission dynamics, in countries of northern Europe. We examined virus evolution and phylodynamics in Denmark, Finland, Iceland, Norway and Sweden during the first year of the COVID-19 pandemic. Results The Nordic countries differed markedly in the invasiveness of control strategies, which we found reflected in transmission chain dynamics. For example, Sweden, which compared with the other Nordic countries relied more on recommendation-based rather than legislation-based mitigation interventions, had transmission chains that were more numerous and tended to have more cases. This trend increased over the first 8 months of 2020. Together with Denmark, Sweden was a net exporter of SARS-CoV-2. Norway and Finland implemented legislation-based interventions; their transmission chain dynamics were in stark contrast to their neighbouring country Sweden. Conclusion Sweden constituted an epidemiological and evolutionary refugium that enabled the virus to maintain active transmission and spread to other geographical locations. Our analysis reveals the utility of genomic surveillance where monitoring of active transmission chains is a key metric.


2021 ◽  
Vol 3 (11) ◽  
Author(s):  
Richard M. Mariita ◽  
James W. Peterson

SARS-CoV-2 is mostly transmitted through close contact with infected people by infected aerosols and fomites. Ultraviolet subtype C (UVC) lamps and light-emitting diodes can be used to disrupt the transmission chain by disinfecting fomites, thus managing the disease outbreak progression. Here, we assess the ultraviolet wavelengths that are most effective in inactivation of SARS-CoV-2 on fomites. Variations in UVC wavelengths impact the dose required for disinfection of SARS-CoV-2 and alter how rapidly and effectively disruption of the virus transmission chain can be achieved. This study reveals that shorter wavelengths (254–268 nm) take a maximum of 6.25 mJ/cm2 over 5 s to obtain a target SARS-CoV-2 reduction of 99.9%. Longer wavelengths, like 280 nm, take longer irradiation time and higher dose to inactivate SARS-CoV-2. These observations emphasize that SARS-CoV-2 inactivation is wavelength-dependent.


2021 ◽  
Vol 23 (1) ◽  
Author(s):  
Uma Shankar Saha ◽  
Minakshi Gupta ◽  
Minakshi Mishra ◽  
Rajan Chaudhry ◽  
Sudhir Rai

Rapidly increasing COVID-19 or SARS-CoV-2 in whole world caused a tremendous pressure on existing diagnostic setup to give accurate diagnosis on time by gold standard RT-PCR technique forcing scientist to think beyond RT-PCR which ultimately ended with invent of Rapid antigen test which can give about 100% specific and rapid result but may miss many case due to low sensitivity. So we wanted to evaluate the Rapid antigen test against RT-PCR for its diagnostic accuracy. We followed standard procedure for sample collection, Rapid antigen test and RT-PCR test. In about one and half month span we collected 554 antigen negative samples in our hospital. About 13% sample (74/554) turned out as positive by RT-PCR test. About 40 % (30/74) positive samples had low Ct value (<25) indicating higher viral load present in those patients. Above findings indicate that only antigen test will miss a significant portion of positive cases with higher viral load which may complicate the pandemic by unknowingly spreading the virus within the society. So we should try to improve our infrastructure to carry out more RTPCR test so we can detect more cases to identify and isolate them from others to prevent or slowdown the transmission chain.


2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Luciano Rodrigo Lopes ◽  
Giancarlo de Mattos Cardillo ◽  
Natália Carvalho de Lucca Pina ◽  
Antonio Carlos da Silva Junior ◽  
Silvana Kertzer Kasinski ◽  
...  

AbstractSevere acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 are thought to transmit to humans via wild mammals, especially bats. However, evidence for direct bat-to-human transmission is lacking. Involvement of intermediate hosts is considered a reason for SARS-CoV-2 transmission to humans and emergence of outbreak. Large biodiversity is found in tropical territories, such as Brazil. On the similar line, this study aimed to predict potential coronavirus hosts among Brazilian wild mammals based on angiotensin-converting enzyme 2 (ACE2) sequences using evolutionary bioinformatics. Cougar, maned wolf, and bush dogs were predicted as potential hosts for coronavirus. These indigenous carnivores are philogenetically closer to the known SARS-CoV/SARS-CoV-2 hosts and presented low ACE2 divergence. A new coronavirus transmission chain was developed in which white-tailed deer, a susceptible SARS-CoV-2 host, have the central position. Cougar play an important role because of its low divergent ACE2 level in deer and humans. The discovery of these potential coronavirus hosts will be useful for epidemiological surveillance and discovery of interventions that can contribute to break the transmission chain.


PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0256901
Author(s):  
James W. A. Strachan ◽  
Arianna Curioni ◽  
Merryn D. Constable ◽  
Günther Knoblich ◽  
Mathieu Charbonneau

The ability to transmit information between individuals through social learning is a foundational component of cultural evolution. However, how this transmission occurs is still debated. On the one hand, the copying account draws parallels with biological mechanisms for genetic inheritance, arguing that learners copy what they observe and novel variations occur through random copying errors. On the other hand, the reconstruction account claims that, rather than directly copying behaviour, learners reconstruct the information that they believe to be most relevant on the basis of pragmatic inference, environmental and contextual cues. Distinguishing these two accounts empirically is difficult based on data from typical transmission chain studies because the predictions they generate frequently overlap. In this study we present a methodological approach that generates different predictions of these accounts by manipulating the task context between model and learner in a transmission episode. We then report an empirical proof-of-concept that applies this approach. The results show that, when a model introduces context-dependent embedded signals to their actions that are not intended to be transmitted, it is possible to empirically distinguish between competing predictions made by these two accounts. Our approach can therefore serve to understand the underlying cognitive mechanisms at play in cultural transmission and can make important contributions to the debate between preservative and reconstructive schools of thought.


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