scholarly journals Transmission dynamics of the delta variant of SARS-CoV-2 infections in Daejeon, South Korea

2021 ◽  
Author(s):  
Hari Hwang ◽  
Jun-Sik Lim ◽  
Sun-Ah Song ◽  
Chiara Achangwa ◽  
Woobeom Sim ◽  
...  
Keyword(s):  
South Korea ◽  
Symptom Onset ◽  
Credible Interval ◽  
Transmission Dynamics ◽  
Contact Tracing ◽  
Nasopharyngeal Swab ◽  
Strict Adherence ◽  
Virus Shedding ◽  
Viral Shedding ◽  
Asymptomatic Patients

Abstract Background The delta variant of SARS-CoV-2 is now the predominant variant worldwide. However, its transmission dynamics remain unclear. Methods We analyzed all case patients in local clusters and temporal patterns of viral shedding using contact tracing data from 405 cases associated with the delta variant of SARS-CoV-2 between 22 June and 31 July 2021 in Daejeon, South Korea. Results Overall, half of the cases were aged under 19 years, and 20% were asymptomatic at the time of epidemiological investigation. We estimated the mean serial interval as 3.26 days (95% credible interval 2.92, 3.60), and 12% of the transmission occurred before symptom onset of the infector. We identified six clustered outbreaks, and all were associated with indoor facilities. In 23 household contacts, the secondary attack rate was 63% (52/82). We estimated that 15% (95% confidence interval, 13–18%) of cases seeded 80% of all local transmission. Analysis of the nasopharyngeal swab samples identified virus shedding from asymptomatic patients, and the highest viral load was observed two days after symptom onset. The temporal pattern of viral shedding did not differ between children and adults (P = 0.48). Conclusions Our findings suggest that the delta variant is highly transmissible in indoor settings and households. Rapid contact tracing, isolation of the asymptomatic contacts, and strict adherence to public health measures are needed to mitigate the community transmission of the delta variant.

scholarly journals Duration of Infectious Virus Shedding in Patients With Severe Coronavirus Disease 2019 Who Required Mechanical Ventilation

2021 ◽  
Author(s):  
Toshihito Nomura ◽  
Hiroki Kitagawa ◽  
Keitaro Omori ◽  
Norifumi Shigemoto ◽  
Masaki Kakimoto ◽  
...  
Keyword(s):  
Mechanical Ventilation ◽  
Symptom Onset ◽  
Infectious Virus ◽  
Quantitative Polymerase Chain Reaction ◽  
University Hospital ◽  
Nasopharyngeal Swab ◽  
Test Results ◽  
Virus Shedding ◽  
Viral Culture ◽  
Respiratory Management

Abstract Approximately 5% of patients with coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 develop severe COVID-19. Severe COVID-19 requires respiratory management with mechanical ventilation and an extended period of treatment. Prolonged infectious virus shedding is a concern in severe COVID-19 cases, but few reports have examined the duration of infectious virus shedding. Therefore, we investigated the duration of infectious virus shedding in patients transferred to Hiroshima University Hospital with severe COVID-19 requiring mechanical ventilation. Nasopharyngeal swab specimens were collected and analyzed using both viral culture and reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) tests between December 2020 and February 2021. Of the 23 patients tested, the proportions of those with positive test results at first specimen collection on RT-qPCR and viral culture tests were 95·7% and 30·4%, respectively. All six patients with positive viral culture test results who were followed-up tested negative 24 days after symptom onset but remained positive on RT-qPCR. The longest negative conversion time was observed in a dialysis patient on immunosuppressive drugs. This study indicated that patients with severe COVID-19 remain culture positive for ≥ 10 days after symptom onset. Additionally, immunosuppressed patients with severe COVID-19 could consider isolation for ≥ 20 days.

scholarly journals Pathogenicity of H5N8 High Pathogenicity Avian Influenza Virus in Chickens and Ducks from South Korea in 2020–2021

Viruses ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 1903
Author(s):  
Min-Ji Park ◽  
Ra Mi Cha ◽  
Soo-Jeong Kye ◽  
Yu-Na Lee ◽  
Na-Yeong Kim ◽  
...  
Keyword(s):  
Avian Influenza ◽  
South Korea ◽  
Clinical Symptoms ◽  
Transmission Rate ◽  
Lethal Dose ◽  
Winter Season ◽  
Virus Shedding ◽  
Viral Shedding ◽  
Death Time ◽  
High Pathogenicity

During the 2020–2021 winter season, an outbreak of clade 2.3.4.4b H5N8 high pathogenicity avian influenza (HPAI) virus occurred in South Korea. Here, we evaluated the pathogenicity and transmissibility of A/mandarin duck/Korea/H242/2020 (H5N8) (H242/20(H5N8)) first isolated from this outbreak in specific pathogen-free (SPF) chickens and commercial ducks in comparison with those of A/duck/Korea/HD1/2017(H5N6) (HD1/17(H5N6)) from a previous HPAI outbreak in 2017–2018. In chickens, the 50% chicken lethal dose and mean death time of H242/20(H5N8) group were 104.5 EID50 and 4.3 days, respectively, which indicate less virulent than those of HD1/17(H5N6) (103.6 EID50 and 2.2 days). Whereas, chickens inoculated with H242/20(H5N8) survived longer and had a higher titer of viral shedding than those inoculated with HD1/17(H5N6), which may increase the risk of viral contamination on farms. All ducks infected with either HPAI virus survived without clinical symptoms. In addition, they exhibited a longer virus shedding period and a higher transmission rate, indicating that ducks may play an important role as a silent carrier of both HPAI viruses. These results suggest that the pathogenic characteristics of HPAI viruses in chickens and ducks need to be considered to effectively control HPAI outbreaks in the field.

scholarly journals Prospective comparison of saliva and nasopharyngeal swab sampling for mass screening for COVID-19

2020 ◽  
Author(s):  
◽  
mathieu nacher ◽  
magalie demar
Keyword(s):  
Mass Screening ◽  
Saliva Sample ◽  
Field Testing ◽  
Contact Tracing ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Prospective Comparison ◽  
Asymptomatic Patients ◽  
Patient Groups ◽  
Trained Staff

Current testing for COVID-19 relies on quantitative reverse-transcriptase polymerase chain reaction from a nasopharyngeal swab specimen. Saliva samples have advantages regarding ease and painlessness of collection, which does not require trained staff and may allow self-sampling. We enrolled 776 persons at various field-testing sites and collected nasopharyngeal and pooled saliva samples. 162 had a positive COVID-19 RT-PCR, 61% were mildly symptomatic and 39% asymptomatic. The sensitivity of RT-PCR on saliva samples versus nasopharygeal swabs varied depending on the patient groups considered or on Ct thresholds. There were 10 (6.2%) patients with a positive saliva sample and a negative nasopharyngeal swab, all of whom had Ct values<25. For symptomatic patients for whom the interval between symptoms onset and sampling was <10 days sensitivity was 77% but when excluding persons with isolated Ngen positivity (54/162), sensitivity was 90%. In asymptomatic patients, the sensitivity was only 24%. When we looked at patients with Cts <30, sensitivity was 83% or 88.9% when considering 2 genes. The relatively good performance for patients with low Cts suggests that Saliva testing could be a useful and acceptable tool to identify infectious persons in mass screening contexts, a strategically important task for contact tracing and isolation in the community.

scholarly journals Estimating transmission dynamics and serial interval of the first wave of COVID-19 infections under different control measures: a statistical analysis in Tunisia from February 29 to May 5, 2020

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Khouloud Talmoudi ◽  
Mouna Safer ◽  
Hejer Letaief ◽  
Aicha Hchaichi ◽  
Chahida Harizi ◽  
...  
Keyword(s):  
Credible Interval ◽  
Emerging Diseases ◽  
Control Measures ◽  
Transmission Dynamics ◽  
Contact Tracing ◽  
Epidemic Threshold ◽  
Illness Onset ◽  
Intervention Measures ◽  
Temporal Reproduction ◽  
Serial Interval

Abstract Background Describing transmission dynamics of the outbreak and impact of intervention measures are critical to planning responses to future outbreaks and providing timely information to guide policy makers decision. We estimate serial interval (SI) and temporal reproduction number (Rt) of SARS-CoV-2 in Tunisia. Methods We collected data of investigations and contact tracing between March 1, 2020 and May 5, 2020 as well as illness onset data during the period February 29–May 5, 2020 from National Observatory of New and Emerging Diseases of Tunisia. Maximum likelihood (ML) approach is used to estimate dynamics of Rt. Results Four hundred ninety-one of infector-infectee pairs were involved, with 14.46% reported pre-symptomatic transmission. SI follows Gamma distribution with mean 5.30 days [95% Confidence Interval (CI) 4.66–5.95] and standard deviation 0.26 [95% CI 0.23–0.30]. Also, we estimated large changes in Rt in response to the combined lockdown interventions. The Rt moves from 3.18 [95% Credible Interval (CrI) 2.73–3.69] to 1.77 [95% CrI 1.49–2.08] with curfew prevention measure, and under the epidemic threshold (0.89 [95% CrI 0.84–0.94]) by national lockdown measure. Conclusions Overall, our findings highlight contribution of interventions to interrupt transmission of SARS-CoV-2 in Tunisia.

scholarly journals COVID-19 Test & Trace Success Determinants: Modeling On A Network

2020 ◽  
Author(s):  
Ofir Reich
Keyword(s):  
Symptom Onset ◽  
Turnaround Time ◽  
Contact Tracing ◽  
Test Time ◽  
Test Analysis ◽  
Agent Based ◽  
Mathematical Arguments ◽  
Asymptomatic Patients ◽  
Wide Range ◽  
Range Of Values

What determines the success of a COVID-19 Test & Trace policy? We use an SEIR agent-based model on a graph, with realistic epidemiological parameters. Simulating variations in certain parameters of Testing & Tracing, we find that important determinants of successful containment are: (i) the time from symptom onset until a patient is self-isolated and tested, and (ii) the share of contacts of a positive patient who are successfully traced. Comparatively less important is (iii) the time of test analysis and contact tracing. When the share of contacts successfully traced is higher, the Test & Trace Time rises somewhat in importance. These results are robust to a wide range of values for how infectious presymptomatic patients are, to the amount of asymptomatic patients, to the network degree distribution and to base epidemic growth rate. We also provide mathematical arguments for why these simulation results hold in more general settings. Since real world Test & Trace systems and policies could affect all three parameters, Symptom Onset to Test Time should be considered, alongside test turnaround time and contact tracing coverage, as a key determinant of Test & Trace success.

scholarly journals Estimating transmission dynamics and serial interval of the first wave of COVID-19 infections under different control measures: A statistical analysis in Tunisia from February 29 to May 5, 2020 

2020 ◽  
Author(s):  
Khouloud Talmoudi ◽  
Mouna Safer ◽  
Hejer Letaief ◽  
Aicha Hchaichi ◽  
Chahida Harizi ◽  
...  
Keyword(s):  
Credible Interval ◽  
Emerging Diseases ◽  
Control Measures ◽  
Transmission Dynamics ◽  
Contact Tracing ◽  
Epidemic Threshold ◽  
Illness Onset ◽  
Intervention Measures ◽  
Temporal Reproduction ◽  
Serial Interval

Abstract Background: Describing transmission dynamics of the outbreak and impact of intervention measures are critical to planning responses to future outbreaks and providing timely information to guide policy makers decision. We estimate serial interval (SI) and temporal reproduction number (Rt) of SARS-CoV-2 in Tunisia. Methods: We collected data of investigations and contact tracing between March 1, 2020 and May 5, 2020 as well as illness onset data during the period February 29-May 5, 2020 from National Observatory of New and Emerging Diseases of Tunisia. Maximum likelihood (ML) approach is used to estimate dynamics of Rt. Results: 491 of infector-infectee pairs were involved, with 14.46% reported pre-symptomatic transmission. SI follows Gamma distribution with mean 5.30 days [95% Confidence Interval (CI) 4.66-5.95] and standard deviation 0.26 [95% CI 0.23-0.30]. Also, we estimated large changes in Rt in response to the combined lockdown interventions. The Rt moves from 3.18 [95% Credible Interval (CrI) 2.73-3.69] to 1.77 [95% CrI 1.49-2.08] with curfew prevention measure, and under the epidemic threshold (0.89 [95% CrI 0.84-0.94]) by national lockdown measure.Conclusions: Overall, our findings highlight contribution of interventions to interrupt transmission of SARS-CoV-2 in Tunisia.

scholarly journals Evolving Transmission Network Dynamics of COVID-19 Cluster Infections in South Korea: a descriptive study

2020 ◽  
Author(s):  
Yejin Kim ◽  
Xiaoqian Jiang
Keyword(s):  
Older Adults ◽  
Nursing Home ◽  
South Korea ◽  
Transmission Dynamics ◽  
Contact Tracing ◽  
Transmission Network ◽  
Middle Aged ◽  
Reproduction Numbers ◽  
Path Lengths ◽  
Middle Aged Adults

AbstractBackgroundExtensive contact tracing and testing in South Korea allows us to investigate the transmission dynamics of the COVID-19 into diverse local communities.ObjectiveUnderstand the critical aspects of transmission dynamics in a different age, sex, and clusters with various activities.MethodsWe conducted a retrospective observational study with 3,127 confirmed cases’ contact tracing data from the Center for Disease and Prevention (CDC) of South Korea. We investigated network property concerning infected persons’ demographics and different infection clusters.FindingsOverall, women had higher centrality scores than men after week four, when the confirmed cases rapidly increased. Older adults have higher centrality than young/middle-aged adults after week 9. In the infection clusters, young/middle-aged adults’ infection clusters (such as religious gatherings and gym facilities) have higher average path lengths and diameter than older adult’s nursing home infection clusters.InterpretationSome women had higher reproduction numbers and bridged successive transmission than men when the confirmed cases rapidly increased. Similarly, some older adults (who were not residents of nursing homes) had higher reproduction numbers and bridged successive transmission than young/middle-aged adults after the peak has passed. The young/middle-aged adults’ religious gatherings and group workout have caused long successive transmissions. In contrast, the older adults’ nursing homes were a small world where the transmissions within a few steps can reach out to many persons.FundingUT Startup award, UT STARs award, and Cancer Prevention Research in Texas, and National Institute of General Medical SciencesResearch in contextEvidence before this study:On May 1, 2020, PubMed query (“COVID-19” OR “SARS-nCoV-2” OR “novel coronavirus” OR “nCoV”) AND (“transmission network” OR “transmission dynamics” OR “transmission pattern” OR “centrality”) AND (“cluster” OR “community”) yield eight peer-reviewed papers. These papers have provided an evolving epidemiology and transmission dynamics via estimated reproduction number. However, most of them have focused on the entire system in one location and there was no comparison between transmission dynamics of different clusters.Added value of this study:This study, to the best of our knowledge, is the first to compare the transmission dynamics of different cluster infections. We present the transmission dynamic with varying levels of granularity: entire country vs cluster infections as a longitudinal view. From the whole country-level analysis, we found that females have higher centrality (degree or betweenness) than males. From the cluster infection view, we found that young/middle-aged adults’ infection clusters (such as religious gatherings and gym facilities) have higher average path lengths and diameter than older adult’s nursing home infection clusters.Implications of all the available evidence:This study sheds light on different transmission dynamics concerning demographics (age and sex) and diverse behavior in cluster infections. These findings are essential for planning tailored policies to diverse communities. Our analysis code is publicly available to adapt to newly reported cases.

scholarly journals Effectiveness of Intervention Strategies on MERS-CoV Transmission Dynamics in South Korea, 2015: Simulations on the Network Based on the Real-World Contact Data

2021 ◽  
Vol 18 (7) ◽  
pp. 3530
Author(s):  
Yunhwan Kim ◽  
Hohyung Ryu ◽  
Sunmi Lee
Keyword(s):  
South Korea ◽  
Real World ◽  
Intervention Strategies ◽  
Transmission Dynamics ◽  
Contact Tracing ◽  
Agent Based ◽  
The Real ◽  
Scale Free ◽  
Contact Data

The MERS-CoV spread in South Korea in 2015 was not only the largest outbreak of MERS-CoV in the region other than the Middle East but also a historic epidemic in South Korea. Thus, investigation of the MERS-CoV transmission dynamics, especially by agent-based modeling, would be meaningful for devising intervention strategies for novel infectious diseases. In this study, an agent-based model on MERS-CoV transmission in South Korea in 2015 was built and analyzed. The prominent characteristic of this model was that it built the simulation environment based on the real-world contact tracing network, which can be characterized as being scale-free. In the simulations, we explored the effectiveness of three possible intervention scenarios; mass quarantine, isolation, and isolation combined with acquaintance quarantine. The differences in MERS-CoV transmission dynamics by the number of links of the index case agent were examined. The simulation results indicate that isolation combined with acquaintance quarantine is more effective than others, and they also suggest the key role of super-spreaders in MERS-CoV transmission.

scholarly journals Performance of SARS-CoV-2 antigen testing in symptomatic and asymptomatic adults: a single-center evaluation

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Stephanie L. Mitchell ◽  
Steven Orris ◽  
Tanner Freeman ◽  
Megan C. Freeman ◽  
Michelle Adam ◽  
...  
Keyword(s):  
Symptom Onset ◽  
Point Of Care ◽  
False Negative ◽  
Poor Performance ◽  
Nasopharyngeal Swab ◽  
Lower Sensitivity ◽  
Negative Results ◽  
Asymptomatic Patients ◽  
False Negative Results ◽  
Antigen Testing

Abstract Background Antigen testing offers rapid and inexpensive testing for SARS-CoV-2 but concerns regarding performance, especially sensitivity, remain. Limited data exists for use of antigen testing in asymptomatic patients; thus, performance and reliability of antigen testing remains unclear. Methods 148 symptomatic and 144 asymptomatic adults were included. A nasal swab was collected for testing by Quidel Sofia SARS IFA (Sofia) as point of care. A nasopharyngeal swab was also collected and transported to the laboratory for testing by Cepheid Xpert Xpress SARS-CoV-2/Flu/RSV RT-PCR (Cepheid). Results Overall, Sofia had good agreement with Cepheid (> 95%) in adults, however was less sensitive. Sofia had a sensitivity of 87.8% and 33.3% for symptomatic and asymptomatic patients, respectively. Among symptomatic patients, testing > 5 days post symptom onset resulted in lower sensitivity (82%) when compared with testing within 5 days of symptom onset (90%). Of the four Sofia false-negative results in the asymptomatic cohort, 50% went on to develop COVID-19 disease within 5 days of testing. Specificity in both symptomatic and asymptomatic cohorts was 100%. Conclusions Sofia has acceptable performance in symptomatic adults when tested < 5 days of symptom onset. Caution should be taken when testing patients with ≥ 5 days of symptoms. The combination of low prevalence and reduced sensitivity results in relatively poor performance of in asymptomatic patients. NAAT-based diagnostic assays should be considered in when antigen testing is unreliable, particularly in symptomatic patients with > 5 days of symptom onset and asymptomatic patients.

scholarly journals Prospective Comparison of Saliva and Nasopharyngeal Swab Sampling for Mass Screening for COVID-19

2021 ◽  
Vol 8 ◽  
Author(s):  
Mathieu Nacher ◽  
Mayka Mergeay-Fabre ◽  
Denis Blanchet ◽  
Orelie Benoit ◽  
Tristan Pozl ◽  
...  
Keyword(s):  
Mass Screening ◽  
Saliva Sample ◽  
Field Testing ◽  
Contact Tracing ◽  
N Gene ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Prospective Comparison ◽  
Asymptomatic Patients ◽  
Patient Groups

Current testing for COVID-19 relies on reverse-transcriptase polymerase chain reaction from a nasopharyngeal swab specimen. Saliva samples have advantages regarding ease and painlessness of collection, which does not require trained staff and may allow self-sampling. We enrolled 776 persons at various field-testing sites and collected nasopharyngeal and pooled saliva samples. One hundred sixty two had a positive COVID-19 RT-PCR, 61% were mildly symptomatic and 39% asymptomatic. The sensitivity of RT-PCR on saliva samples vs. nasopharygeal swabs varied depending on the patient groups considered or on Ct thresholds. There were 10 (6.2%) patients with a positive saliva sample and a negative nasopharyngeal swab, all of whom had Ct values &lt;25 for three genes. For symptomatic patients for whom the interval between symptoms onset and sampling was &lt;10 days sensitivity was 77% but when excluding persons with isolated N gene positivity (54/162), sensitivity was 90%. In asymptomatic patients, the sensitivity was only 24%. When we looked at patients with Cts &lt;30, sensitivity was 83 or 88.9% when considering two genes. The relatively good performance for patients with low Cts suggests that Saliva testing could be a useful and acceptable tool to identify infectious persons in mass screening contexts, a strategically important task for contact tracing and isolation in the community.

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