scholarly journals Estimation of the incubation period of COVID-19 using viral load data

Epidemics ◽  
2021 ◽  
pp. 100454
Author(s):  
Keisuke Ejima ◽  
Kwang Su Kim ◽  
Christina Ludema ◽  
Ana I. Bento ◽  
Shoya Iwanami ◽  
...  
Keyword(s):  
Viral Load ◽  
Incubation Period ◽  
Viral Load Data

scholarly journals Estimation of the incubation period of COVID-19 using viral load data

2020 ◽  
Author(s):  
Keisuke Ejima ◽  
Kwang Su Kim ◽  
Christina Ludema ◽  
Ana I. Bento ◽  
Shoya Iwanami ◽  
...  
Keyword(s):  
Mathematical Model ◽  
Viral Load ◽  
Incubation Period ◽  
Symptom Onset ◽  
Viral Dynamics ◽  
Infection Event ◽  
Viral Load Data ◽  
Novel Method ◽  
Using Data ◽  
Over Time

AbstractThe incubation period, or the time from infection to symptom onset of COVID-19 has been usually estimated using data collected through interviews with cases and their contacts. However, this estimation is influenced by uncertainty in recalling effort of exposure time. We propose a novel method that uses viral load data collected over time since hospitalization, hindcasting the timing of infection with a mathematical model for viral dynamics. As an example, we used the reported viral load data from multiple countries (Singapore, China, Germany, France, and Korea) and estimated the incubation period. The median, 2.5, and 97.5 percentiles of the incubation period were 5.23 days (95% CI: 5.17, 5.25), 3.29 days (3.25, 3.37), and 8.22 days (8.02, 8.46), respectively, which are comparable to the values estimated in previous studies. Using viral load to estimate the incubation period might be a useful approach especially when impractical to directly observe the infection event.

Detecting SARS-CoV-2 by Realtime RT-PCR in clinical samples collected in the North of Vietnam

2021 ◽  
Vol 30 (9) ◽  
pp. 11-17
Author(s):  
Hoang Vu Mai Phuong ◽  
Ung Thi Hong Trang ◽  
Nguyen Vu Son ◽  
Le Thi Thanh ◽  
Nguyen Le Khanh Hang ◽  
...  
Keyword(s):  
Viral Load ◽  
Average Rate ◽  
Clinical Samples ◽  
Viet Nam ◽  
Rt Pcr ◽  
Ct Value ◽  
The North ◽  
Viral Load Data ◽  
The Mean ◽  
High Level

From January to August 2020, Northern Viet Nam faced a COVID-19 outbreak, up to September 2020, there were 1122 confrmed cases of SARS-CoV-2, of which 465 cases were imported from Europe, America and Asia, 657 cases were identifed domestically. A total of 30,686 samples were collected during the SARS-CoV-2 outbreak in Northern Viet Nam and examined by Real-time RT-PCR using primers and probe from Charite - Berlin protocol. This study showed the initial results of SARS-CoV-2 detection and RNA quantitative in positive samples. The positive rate was 0.8%, ranging from 0.4 to 3.5% according to collection sites. Out of 251 positive samples, the mean Ct value was 28 (IQR: 22.3-32; range 14 - 38). The positive samples had a Ct value below 30 was 68.5%, there was no signifcant difference between the Ct value of the group ≤ 30 and > 30. The mean of the RNA copies/µl was 8.4.107, (IQR: 2.29.106 - 1.83.109 RNA copies/µl, range: 1.95.103 – 4.95.1011). In the group of imported COVID-19 cases, the rate of virus at low level was 29%, an average was 56% and at high level was 15%. In the community groups, the viral load data showed that the average rate at low, intermediate and high level were 20%, 63% and 17% respectively. The proportion of high-level viral load may raise an alert to start the quarantine process to reduce the transmission of SARS-CoV-2

scholarly journals Optimal design for phase 2 studies of SARS-CoV-2 antiviral drugs

2021 ◽  
Author(s):  
James A Watson ◽  
Stephen Kissler ◽  
Nicholas PJ Day ◽  
Yonatan H. Grad ◽  
Nicholas J White
Keyword(s):  
Viral Load ◽  
Rapid Identification ◽  
Antiviral Drugs ◽  
Viral Clearance ◽  
Assay Sensitivity ◽  
Virus Clearance ◽  
Viral Load Data ◽  
Type 2 Errors ◽  
Type 2 Error

There is no agreed methodology for pharmacometric assessment of candidate antiviral drugs in COVID-19. The most widely used measure of virological response in clinical trials so far is the time to viral clearance assessed by qPCR of viral nucleic acid in eluates from serial nasopharyngeal swabs. We posited that the rate of viral clearance would have better discriminatory value. Using a pharmacodynamic model fit to individual SARS-CoV-2 virus clearance data from 46 uncomplicated COVID-19 infections in a cohort of prospectively followed adults, we simulated qPCR viral load data to compare type 2 errors when using time to clearance and rate of clearance under varying antiviral effects, sample sizes, sampling frequencies and durations of follow-up. The rate of viral clearance is a uniformly superior endpoint as compared to time to clearance with respect to type 2 error, and it is not dependent on initial viral load or assay sensitivity. For greatest efficiency pharmacometric assessments should be conducted in early illness and daily qPCR samples should be taken over 7 to 10 days in each patient studied. Adaptive randomisation and early stopping for success permits more rapid identification of active interventions.

scholarly journals Vaccinated and unvaccinated individuals have similar viral loads in communities with a high prevalence of the SARS-CoV-2 delta variant

2021 ◽  
Author(s):  
Kasen K Riemersma ◽  
Brittany E Grogan ◽  
Amanda Kita-Yarbro ◽  
Gunnar E Jeppson ◽  
David H O'Connor ◽  
...  
Keyword(s):  
Viral Load ◽  
Vaccine Coverage ◽  
High Volume ◽  
The United States ◽  
Quantitative Information ◽  
Self Report ◽  
Local Health ◽  
Viral Loads ◽  
Viral Load Data ◽  
Single Standard

SARS-CoV-2 variant B.1.617.2 (delta) is associated with higher viral loads [1] and increased transmissibility relative to other variants, as well as partial escape from polyclonal and monoclonal antibodies [2]. The emergence of the delta variant has been associated with increasing case counts and test-positivity rates, indicative of rapid community spread. Since early July 2021, SARS-CoV-2 cases in the United States have increased coincident with delta SARS-CoV-2 becoming the predominant lineage nationwide [3]. Understanding how and why the virus is spreading in settings where there is high vaccine coverage has important public health implications. It is particularly important to assess whether vaccinated individuals who become infected can transmit SARS-CoV-2 to others. In Wisconsin, a large local contract laboratory provides SARS-CoV-2 testing for multiple local health departments, providing a single standard source of data using the same assay to measure virus burdens in test-positive cases. This includes providing high-volume testing in Dane County, a county with extremely high vaccine coverage. These PCR-based tests provide semi-quantitative information about the viral load, or amount of SARS-CoV-2 RNA, in respiratory specimens. Here we use this viral load data to compare the amount of SARS-CoV-2 present in test-positive specimens from people who self-report their vaccine status and date of final immunization, during a period in which the delta variant became the predominant circulating variant in Wisconsin. We find no difference in viral loads when comparing unvaccinated individuals to those who have vaccine "breakthrough" infections. Furthermore, individuals with vaccine breakthrough infections frequently test positive with viral loads consistent with the ability to shed infectious viruses. Our results, while preliminary, suggest that if vaccinated individuals become infected with the delta variant, they may be sources of SARS-CoV-2 transmission to others.

scholarly journals Modelling SARS-CoV-2 Dynamics: Implications for Therapy

2020 ◽  
Author(s):  
Kwang Su Kim ◽  
Keisuke Ejima ◽  
Yusuke Ito ◽  
Shoya Iwanami ◽  
Hirofumi Ohashi ◽  
...  
Keyword(s):  
Viral Load ◽  
De Novo ◽  
Virus Production ◽  
Severe Case ◽  
Tracheal Aspirate ◽  
Viral Dynamics ◽  
Antiviral Therapies ◽  
Infection Dynamics ◽  
Viral Load Data ◽  
Novel Coronavirus

The scientific community is focussed on developing antiviral therapies to mitigate the impacts of the ongoing novel coronavirus disease (COVID-19) outbreak. This will be facilitated by improved understanding of viral dynamics within infected hosts. Here, using a mathematical model in combination with published viral load data collected from the same specimen (throat / nasal swabs or nasopharyngeal / sputum / tracheal aspirate), we compare within-host dynamics for patients infected in the current outbreak with analogous dynamics for MERS-CoV and SARS-CoV infections. Our quantitative analyses revealed that SARS-CoV-2 infection dynamics are more severe than those for mild cases of MERS-CoV, but are similar to severe cases, and that the viral dynamics of SARS-CoV infection are similar to those of MERS-CoV in mild cases but not in severe case. Consequently, SARS-CoV-2 generates infection dynamics that are more severe than SARS-CoV. Furthermore, we used our viral dynamics model to predict the effectiveness of unlicensed drugs that have different methods of action. The effectiveness was measured by AUC of viral load. Our results indicated that therapies that block de novo infections or virus production are most likely to be effective if initiated before the peak viral load (which occurs around three days after symptom onset on average), but therapies that promote cytotoxicity are likely to have only limited effects. Our unique mathematical approach provides insights into the pathogenesis of SARS-CoV-2 in humans, which are useful for development of antiviral therapies.

scholarly journals Factors Associated With Virological Suppression of HIV Viral Load in Patients on Antiretroviral Therapy in Conakry, Guinea

2021 ◽  
Author(s):  
Alimou camara ◽  
Penda Maladho Diallo ◽  
Mamadou Bobo Diallo ◽  
Talla Nioké ◽  
Adama Cissé ◽  
...  
Keyword(s):  
Viral Load ◽  
Antiretroviral Therapy ◽  
Detection Threshold ◽  
Virological Suppression ◽  
Hiv Positive ◽  
People Living With Hiv ◽  
Viral Load Suppression ◽  
Viral Load Data ◽  
Living With Hiv ◽  
Hiv Aids

Abstract BackgroundThe viral load has become an indispensable tool in evaluating antiretroviral therapy (ART) in people living with HIV / AIDS. This study aimed to assess virological suppression among in people living with HIV / AIDS on antiretroviral therapy in Guinea.MethodsThis was a descriptive cross-sectional study of more than three years that involved adult HIV-positive patients treated in different sites in Conakry. A total of 9815 viral load data were collected. The viral load was quantified by the Generic Biocentric technique and the detection threshold set at 350 copies/ml. Statistical analyses were performed by R software version R4.0.3..ResultsA total of 9815 viral load data collected at the national public health laboratory were analysed. The sample was dominated by women (72%), with an average age of 29 [29, 39]. Of these, 6,706 (68%) of HIV-positive people on ART had viral load suppression. The univaried analysis showed that women were 22% more likely to have VL suppression (p-value <0.001) moreover, the chance for all HIV-positive people on treatment to achieve viral load suppression was related to the length of treatment.Conclusionthe results of this study show viral load suppression greater than 68%. The length of antiretroviral therapy, female gender, and advancing age of PLHIV were all favourable to VL suppression.

scholarly journals A Systematic Review of the Incubation Period of SARS-CoV-2: The Effects of Age, Biological Sex, and Location on Incubation Period

2020 ◽  
Author(s):  
Caitlin Daley ◽  
Megan Fydenkevez ◽  
Shari Ackerman-Morris
Keyword(s):  
Systematic Review ◽  
Viral Load ◽  
Incubation Period ◽  
Inverse Relationship ◽  
Severe Disease ◽  
Hubei Province ◽  
Period Length ◽  
Biological Sex ◽  
Quantitative Studies ◽  
Severity Of The Disease

ABSTRACTA systematic review of the incubation period of COVID-19 was compiled and analyzed from 21 quantitative studies. We investigated the incubation period of COVID-19 with regard to age, biological sex, location, and severity of the disease. Based on the data extracted, we report an overall mean and median incubation period for SARS-CoV-2 of 5.894 days and 5.598 days, respectively. The incubation period did not statistically vary for biological sex or age, but some studies suggest a longer incubation period in the young and elderly. Cases of COVID-19 in Wuhan and Hubei Province of China may have a shorter incubation period for COVID-19 but the shorter incubation period may be due to an increase in viral load. In studying coronavirus strains such as SARS and MERS, researchers have discovered an inverse relationship between incubation period length and virus severity. Taking into consideration that SARS-CoV-2 is part of the beta-coronavirus family, as well as the study mentioned above, we suggest that people who experience more severe disease due to SARS-CoV-2 may have a shorter incubation period.

scholarly journals Inferring Timing of Infection Using Within-host SARS-CoV-2 Infection Dynamics Model: Are “Imported Cases” Truly Imported?

2020 ◽  
Author(s):  
Keisuke Ejima ◽  
Kwang Su Kim ◽  
Yusuke Ito ◽  
Shoya Iwanami ◽  
Hirofumi Ohashi ◽  
...  
Keyword(s):  
Viral Load ◽  
Symptom Onset ◽  
Travel History ◽  
Secondary Transmission ◽  
Additional Information ◽  
Novel Approach ◽  
Infection Dynamics ◽  
Imported Cases ◽  
Viral Load Data ◽  
Public Health Strategies

AbstractIn countries/communities at risk of future outbreaks of COVID-19, ascertaining whether cases are imported or the result of local secondary transmission is important for government to shape appropriate public health strategies. In this study, we propose a novel approach to identify the timing of infection, whereby we developed a within-host model to capture viral load dynamics post-symptom onset. We submit our approach allow us to differentiate imported cases from local secondary cases. To illustrate our method, we use the initial reported cases in Singapore, where the first reported 18 cases were considered imported, as these individuals had recent travel history to Wuhan, China, which is a hotspot of COVID-19 outbreak. With additional information regarding day of entrance in Singapore, we were able to infer whether these were infected locally or prior to arriving in Singapore. Of all the cases, we identified 6 as likely evidence of ongoing secondary transmission within Singapore. In an early phase of outbreaks, collecting viral load data over time from cases from symptom onset is highly recommended.

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