scholarly journals Estimating the transmissibility of SARS-CoV-2 VOC 202012/01 in Japan using travel history information

2022 ◽  
Vol 19 (3) ◽  
pp. 2750-2761
Author(s):  
Taishi Kayano ◽  
◽  
Hiroshi Nishiura
Keyword(s):  
Generation Time ◽  
Early Stage ◽  
Time Estimation ◽  
Right Censoring ◽  
Contact Tracing ◽  
Baseline Scenario ◽  
Primary Case ◽  
Travel History ◽  
Short Period ◽  
History Information

<abstract> <p>Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has rapidly spread across the globe. The variant of concern (VOC) 202012/01 (B.1.1.7, also known as the alpha variant) bearing the N501Y mutation emerged in late 2020. VOC 202012/01 was more transmissible than existing SARS-CoV-2 variants and swiftly became dominant in many regions. More than 150 cases of VOC 202012/01 were reported in Japan by 26 February 2021. During the very early stage of introduction, only a subset arose from domestic transmission. If the reproduction number <italic>R</italic> (i.e., the average number of secondary transmission events caused by a single primary case) is greater than 1, the corresponding proportion should converge to 1 in a short period of time, and thus it is critical to understand the transmissibility of VOC 202012/01 based on travel history information. The present study aimed to estimate <italic>R</italic> of VOC 202012/01 using overseas travel history information. A mathematical model was developed to capture the relationship between travel history and <italic>R</italic>. We obtained travel history data for each confirmed case of VOC 202012/01 infection from 26 December 2020 to 26 February 2021. Maximum likelihood estimation was used to estimate <italic>R</italic>, accounting for right censoring during real-time estimation. In the baseline scenario, <italic>R</italic> was estimated at 2.11 (95% confidence interval: 1.63, 2.94). By 26 February 2021, an average of nine generations had elapsed since the first imported case. If the generation time of VOC 202012/01 was assumed to be longer, <italic>R</italic> was increased, consistent with estimates of <italic>R</italic> from case data. The estimated <italic>R</italic> of VOC 202012/01 in Japan exceeded 1 on 26 February 2021, suggesting that domestic transmission events caused a major epidemic. Moreover, because our estimate of <italic>R</italic> was dependent on generation time and ascertainment biases, continuous monitoring of contact tracing data is crucial to decipher the mechanisms of increased VOC 202012/01 transmissibility.</p> </abstract>

scholarly journals Phylogenomics reveals viral sources, transmission, and potential superinfection in early-stage COVID-19 patients in Ontario, Canada

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Calvin P. Sjaarda ◽  
Nazneen Rustom ◽  
Gerald A. Evans ◽  
David Huang ◽  
Santiago Perez-Patrigeon ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Disease Surveillance ◽  
Early Stage ◽  
Emerging Diseases ◽  
Contact Tracing ◽  
Travel History ◽  
Infectious Disease Surveillance ◽  
Viral Genomes ◽  
Heterozygous Variant ◽  
Sequencing Platforms

AbstractThe emergence and rapid global spread of SARS-CoV-2 demonstrates the importance of infectious disease surveillance, particularly during the early stages. Viral genomes can provide key insights into transmission chains and pathogenicity. Nasopharyngeal swabs were obtained from thirty-two of the first SARS-CoV-2 positive cases (March 18–30) in Kingston Ontario, Canada. Viral genomes were sequenced using Ion Torrent (n = 24) and MinION (n = 27) sequencing platforms. SARS-CoV-2 genomes carried forty-six polymorphic sites including two missense and three synonymous variants in the spike protein gene. The D614G point mutation was the predominate viral strain in our cohort (92.6%). A heterozygous variant (C9994A) was detected by both sequencing platforms but filtered by the ARTIC network bioinformatic pipeline suggesting that heterozygous variants may be underreported in the SARS-CoV-2 literature. Phylogenetic analysis with 87,738 genomes in the GISAID database identified global origins and transmission events including multiple, international introductions as well as community spread. Reported travel history validated viral introduction and transmission inferred by phylogenetic analysis. Molecular epidemiology and evolutionary phylogenetics may complement contact tracing and help reconstruct transmission chains of emerging diseases. Earlier detection and screening in this way could improve the effectiveness of regional public health interventions to limit future pandemics.

An Epidemiological Analysis of COVID-19 Confirmed Cases, Reported at National Institute of Health, Pakistan (Preprint)

2020 ◽  
Author(s):  
Ambreen Chaudhry
Keyword(s):  
Age Groups ◽  
Target Population ◽  
Control Measures ◽  
Contact Tracing ◽  
Bivariate Analysis ◽  
Travel History ◽  
Disease Epidemiology ◽  
Hygiene Practices ◽  
Multi Center Study ◽  
Epidemiological Characteristics

BACKGROUND Coronavirus disease (Covid-19) is a zoonotic disease of novel origin that posed a continuous threat to health worldwide after taking the shape of the pandemic. An understanding of disease epidemiology is supportive in timely preventive and control measures as well as contact tracing and curbing surveillance activities. OBJECTIVE The objective of our study was to determine the epidemiological characteristics of COVID-19 confirmed cases reported at the National Institute of Health Pakistan and elements of its spread in Pakistan. METHODS A retrospective record review was conducted at the National Institute of Health (NIH) Islamabad, Pakistan from January 25 to April 4, 2020. Univariate and bivariate analysis was done with 95% CI and p<0.05. RESULTS A total of 14,422 samples of suspected COVID-19 cases were received with a positivity rate of 9% (n=1348). Among all 70% (n=939) were male. The median age was 41years of age (range: 01-99Years). Among all, 19% were from 30-39 years old followed by 50-59 years old (17%). Children remained the least affected by 3% (n=35). Of the total reported cases, 55% (n=735) have reported the travel history within the last 14 days. Among these travelers’ international travelers were 23% (n=166) and domestic travelers were 77% (n=569). Travel history including both international and domestic remained significantly associated with the different age groups and Young adults remained more vulnerable to COVID-19 (P=0.03). Fever, SOB, and Cough remained the most significantly associated (P<0.05) in all age groups. CONCLUSIONS A higher incidence of COVID-19 among elderly men suggests robust quarantine measures for this target population. An escalating incidence of local transmission needs strict social distancing and hygiene practices to help flatten the curve. An extensive multi-center study is also recommended for a full understanding of disease dynamics.

scholarly journals One Week of CDAHFD Induces Steatohepatitis and Mitochondrial Dysfunction with Oxidative Stress in Liver

2021 ◽  
Vol 22 (11) ◽  
pp. 5851
Author(s):  
Takehito Sugasawa ◽  
Seiko Ono ◽  
Masato Yonamine ◽  
Shin-ichiro Fujita ◽  
Yuki Matsumoto ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Mitochondrial Dysfunction ◽  
High Fat Diet ◽  
Early Stage ◽  
Droplet Deposition ◽  
Nonalcoholic Fatty Liver ◽  
Stress Markers ◽  
Mitochondrial Dna Copy Number ◽  
Short Period ◽  
And Oxidative Stress

The prevalence of nonalcoholic fatty liver disease (NAFLD) has been rapidly increasing worldwide. A choline-deficient, L-amino acid-defined, high-fat diet (CDAHFD) has been used to create a mouse model of nonalcoholic steatohepatitis (NASH). There are some reports on the effects on mice of being fed a CDAHFD for long periods of 1 to 3 months. However, the effect of this diet over a short period is unknown. Therefore, we examined the effect of 1-week CDAHFD feeding on the mouse liver. Feeding a CDAHFD diet for only 1-week induced lipid droplet deposition in the liver with increasing activity of liver-derived enzymes in the plasma. On the other hand, it did not induce fibrosis or cirrhosis. Additionally, it was demonstrated that CDAHFD significantly impaired mitochondrial respiration with severe oxidative stress to the liver, which is associated with a decreasing mitochondrial DNA copy number and complex proteins. In the gene expression analysis of the liver, inflammatory and oxidative stress markers were significantly increased by CDAHFD. These results demonstrated that 1 week of feeding CDAHFD to mice induces steatohepatitis with mitochondrial dysfunction and severe oxidative stress, without fibrosis, which can partially mimic the early stage of NASH in humans.

scholarly journals Symptom and Age Homophilies in SARS-CoV-2 Transmission Networks during the Early Phase of the Pandemic in Japan

Biology ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 499
Author(s):  
Ali Andalibi ◽  
Naoru Koizumi ◽  
Meng-Hao Li ◽  
Abu Bakkar Siddique
Keyword(s):  
Early Stage ◽  
Graph Model ◽  
Initial Response ◽  
Contact Tracing ◽  
Pcr Analysis ◽  
Exponential Random Graph Model ◽  
Transmission Networks ◽  
Random Graph Model ◽  
Healthcare Settings ◽  
Exponential Random Graph

Kanagawa and Hokkaido were affected by COVID-19 in the early stage of the pandemic. Japan’s initial response included contact tracing and PCR analysis on anyone who was suspected of having been exposed to SARS-CoV-2. In this retrospective study, we analyzed publicly available COVID-19 registry data from Kanagawa and Hokkaido (n = 4392). Exponential random graph model (ERGM) network analysis was performed to examine demographic and symptomological homophilies. Age, symptomatic, and asymptomatic status homophilies were seen in both prefectures. Symptom homophilies suggest that nuanced genetic differences in the virus may affect its epithelial cell type range and can result in the diversity of symptoms seen in individuals infected by SARS-CoV-2. Environmental variables such as temperature and humidity may also play a role in the overall pathogenesis of the virus. A higher level of asymptomatic transmission was observed in Kanagawa. Moreover, patients who contracted the virus through secondary or tertiary contacts were shown to be asymptomatic more frequently than those who contracted it from primary cases. Additionally, most of the transmissions stopped at the primary and secondary levels. As expected, significant viral transmission was seen in healthcare settings.

scholarly journals Subcritical Transmission in the Early Stage of COVID-19 in Korea

2021 ◽  
Vol 18 (3) ◽  
pp. 1265
Author(s):  
Yong Sul Won ◽  
Jong-Hoon Kim ◽  
Chi Young Ahn ◽  
Hyojung Lee
Keyword(s):  
Incubation Period ◽  
Early Stage ◽  
Probability Distributions ◽  
Likelihood Estimation ◽  
Contact Tracing ◽  
Statistical Characterization ◽  
Serial Interval ◽  
Imported Cases ◽  
The Mean ◽  
Reporting Delays

While the coronavirus disease 2019 (COVID-19) outbreak has been ongoing in Korea since January 2020, there were limited transmissions during the early stages of the outbreak. In the present study, we aimed to provide a statistical characterization of COVID-19 transmissions that led to this small outbreak. We collated the individual data of the first 28 confirmed cases reported from 20 January to 10 February 2020. We estimated key epidemiological parameters such as reporting delay (i.e., time from symptom onset to confirmation), incubation period, and serial interval by fitting probability distributions to the data based on the maximum likelihood estimation. We also estimated the basic reproduction number (R0) using the renewal equation, which allows for the transmissibility to differ between imported and locally transmitted cases. There were 16 imported and 12 locally transmitted cases, and secondary transmissions per case were higher for the imported cases than the locally transmitted cases (nine vs. three cases). The mean reporting delays were estimated to be 6.76 days (95% CI: 4.53, 9.28) and 2.57 days (95% CI: 1.57, 4.23) for imported and locally transmitted cases, respectively. The mean incubation period was estimated to be 5.53 days (95% CI: 3.98, 8.09) and was shorter than the mean serial interval of 6.45 days (95% CI: 4.32, 9.65). The R0 was estimated to be 0.40 (95% CI: 0.16, 0.99), accounting for the local and imported cases. The fewer secondary cases and shorter reporting delays for the locally transmitted cases suggest that contact tracing of imported cases was effective at reducing further transmissions, which helped to keep R0 below one and the overall transmissions small.

"Steady-state" competence for bacterial transformation

1968 ◽  
Vol 14 (3) ◽  
pp. 290-292
Author(s):  
Herbert H. Eichhorn ◽  
Shigeyo Arikawa ◽  
Stephen Zamenhof
Keyword(s):  
Bacillus Subtilis ◽  
Steady State ◽  
Continuous Culture ◽  
Generation Time ◽  
Bacterial Transformation ◽  
Short Period ◽  
Minimal Media ◽  
Harmful Effects ◽  
Specific Phase

The cells of Bacillus subtilis, grown in minimal media, are known to become competent for transformation for a short period at a specific phase of ceil growth. In the present work the cells (strain 168 ind−) were grown in continuous culture (chemostat; glucose limiting, generation time 4 h, 37 °C). Aliquots were removed at 20- to 24-h intervals and immediately tested for competence. The viability (41 h) was 97%. The initial very low competence increased up to 200-fold within the 24 h and remained at this high, slowly decreasing level for at least 168 h. It is concluded that a long-lasting competence may develop and persist in the cells in continuous culture ("steady-state"), without demonstrable harmful effects to the population.

The complication of cyber manhunt: How cyber manhunt further complicated the ethical conflict between breaching the confidentiality and endangering the society in face of the COVID-19 pandemic (Preprint)

2021 ◽  
Author(s):  
Yen-Chang Chen ◽  
Yen-Yuan Chen
Keyword(s):  
Public Health ◽  
Large Scale ◽  
Health Workers ◽  
Early Stage ◽  
Personal Information ◽  
Public Health Intervention ◽  
Contact Tracing ◽  
Online Activity ◽  
Contact Investigation ◽  
The Impact

UNSTRUCTURED While health care and public health workers are working on measures to mitigate the COVID-19 pandemic, there is an unprecedentedly large number of people spending much more time indoors, and relying heavily on the Internet as their lifeline. What has been overlooked is the influence of the increasing online activities on public health issues. In this article, we pointed out how a large-scale online activity called cyber manhunt may threaten to offset the efficacy of contact tracing investigation, a public health intervention considered highly effective in limiting further transmission in the early stage of a highly contagious disease outbreak such as the COVID-19 pandemic. In the first section, we presented a case to show how personal information obtained from contact investigation and disclosed in part on the media provoked a vehement cyber manhunt. We then discussed the possible reasons why netizens collaborate to reveal anonymized personal information about contact investigation, and specify, from the perspective of public health and public health ethics, four problems of cyber manhunt, including the lack of legitimate public health goals, the concerns about privacy breach, the impact of misinformation, and social inequality. Based on our analysis, we concluded that more moral weight may be given to protecting one's confidentiality, especially in an era with the rapid advance of digital and information technologies.

Carbon metabolism snapshot by ddPCR during the early step of Candida albicans phagocytosis by macrophages

2020 ◽  
Vol 78 (1) ◽  
Author(s):  
Romain Laurian ◽  
Cécile Jacot-des-Combes ◽  
Fabiola Bastian ◽  
Karine Dementhon ◽  
Pascale Cotton
Keyword(s):  
Carbon Metabolism ◽  
Early Stage ◽  
Yeast Cells ◽  
Transcription Level ◽  
Digital Droplet Pcr ◽  
Metabolic Genes ◽  
Glucose Transport System ◽  
Short Period ◽  
Droplet Pcr ◽  
Alternative Sources

ABSTRACT During Candida macrophage interactions, phagocytosed yeast cells feed in order to grow, develop hyphae and escape. Through numerous proteomic and transcriptomic studies, two metabolic phases have been described. A shift to a starvation mode is generally identified as early as one-hour post phagocytosis, followed by a glycolytic growth mode after C. albicans escaped from the macrophage. Healthy macrophages contain low amounts of glucose. To determine if this carbon source was sensed and metabolized by the pathogen, we explored the transcription level of a delimited set of key genes expressed in C. albicans cells during phagocytosis by macrophages, at an early stage of the interaction. This analysis was performed using a technical digital droplet PCR approach to quantify reliably the expression of carbon metabolic genes after 30 min of phagocytosis. Our data confirm the technique of digital droplet PCR for the detection of C. albicans transcripts using cells recovered after a short period of phagocytosis. At this stage, carbon metabolism is clearly oriented towards the use of alternative sources. However, the activation of high-affinity glucose transport system suggests that the low amount of glucose initially present in the macrophages is detected by the pathogen.

scholarly journals Quantifying the impact of early-stage contact tracing on controlling Ebola diffusion

2018 ◽  
Vol 15 (5) ◽  
pp. 1165-1180 ◽  
Author(s):  
Narges Montazeri Shahtori ◽  
◽  
Tanvir Ferdousi ◽  
Caterina Scoglio ◽  
Faryad Darabi Sahneh
Keyword(s):  
Early Stage ◽  
Contact Tracing ◽  
The Impact

scholarly journals Estimation of the test to test distribution as a proxy for generation interval distribution for the Omicron variant in England

2022 ◽  
Author(s):  
Sam Abbott ◽  
Katharine Sherratt ◽  
Moritz Gerstung ◽  
Sebastian Funk
Keyword(s):  
South Africa ◽  
Standard Deviation ◽  
Generation Time ◽  
Time Distribution ◽  
Immune Escape ◽  
Credible Interval ◽  
Contact Tracing ◽  
Time Varying ◽  
Daily Growth ◽  
Gene Target

Background Early estimates from South Africa indicated that the Omicron COVID-19 variant may be both more transmissible and have greater immune escape than the previously dominant Delta variant. The rapid turnover of the latest epidemic wave in South Africa as well as initial evidence from contact tracing and household infection studies has prompted speculation that the generation time of the Omicron variant may be shorter in comparable settings than the generation time of the Delta variant. Methods We estimated daily growth rates for the Omicron and Delta variants in each UKHSA region from the 23rd of November to the 23rd of December 2021 using surveillance case counts by date of specimen and S-gene target failure status with an autoregressive model that allowed for time-varying differences in the transmission advantage of the Delta variant where the evidence supported this. By assuming a gamma distributed generation distribution we then estimated the generation time distribution and transmission advantage of the Omicron variant that would be required to explain this time varying advantage. We repeated this estimation process using two different prior estimates for the generation time of the Delta variant first based on household transmission and then based on its intrinsic generation time. Results Visualising our growth rate estimates provided initial evidence for a difference in generation time distributions. Assuming a generation time distribution for Delta with a mean of 2.5-4 days (90% credible interval) and a standard deviation of 1.9-3 days we estimated a shorter generation time distribution for Omicron with a mean of 1.5-3.2 days and a standard deviation of 1.3-4.6 days. This implied a transmission advantage for Omicron in this setting of 160%-210% compared to Delta. We found similar relative results using an estimate of the intrinsic generation time for Delta though all estimates increased in magnitude due to the longer assumed generation time. Conclusions We found that a reduction in the generation time of Omicron compared to Delta was able to explain the observed variation over time in the transmission advantage of the Omicron variant. However, this analysis cannot rule out the role of other factors such as differences in the populations the variants were mixing in, differences in immune escape between variants or bias due to using the test to test distribution as a proxy for the generation time distribution.

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