scholarly journals Quantifying heterogeneity in SARS-CoV-2 transmission during the lockdown in India

2020 ◽  
Author(s):  
Nimalan Arinaminpathy ◽  
Jishnu Das ◽  
Tyler McCormick ◽  
Partha Mukhopadhyay ◽  
Neelanjan Sircar
Keyword(s):  
Disease Transmission ◽  
Index Case ◽  
Transmission Dynamics ◽  
Contact Tracing ◽  
Secondary Case ◽  
The Novel ◽  
Health Measure ◽  
Multiple Levels ◽  
Models Of Disease ◽  
And Control

The novel SARS-CoV-2 virus shows marked heterogeneity in its transmission. Here, we used data collected from contact tracing during the lockdown in Punjab, a major state in India, to quantify this heterogeneity, and to examine implications for transmission dynamics. We found evidence of heterogeneity acting at multiple levels: in the number of potentially infectious contacts per index case, and in the per-contact risk of infection. Incorporating these findings in simple mathematical models of disease transmission reveals that these heterogeneities act in combination to strongly influence transmission dynamics. Standard approaches, such as representing heterogeneity through secondary case distributions, could be biased by neglecting these underlying interactions between heterogeneities. We discuss implications for policy, and for more efficient contact tracing in resource-constrained settings such as India. Our results highlight how contact tracing, an important public health measure, can also provide important insights into epidemic spread and control.

scholarly journals Methicillin-Resistant Staphylococcus aureus Prevalence Among Healthcare Workers in Contact Tracings in a Dutch Hospital

2020 ◽  
Vol 41 (S1) ◽  
pp. s316-s317
Author(s):  
Veronica Weterings ◽  
Heidi Kievits ◽  
Miranda van Rijen ◽  
Jan Kluytmans
Keyword(s):  
Staphylococcus Aureus ◽  
The Netherlands ◽  
Healthcare Workers ◽  
Index Case ◽  
Contact Tracing ◽  
Secondary Case ◽  
National Guidelines ◽  
Carriage Rate ◽  
Methicillin Resistant ◽  
Mlva Type

Background: In The Netherlands, the national guidelines on Methicillin-Resistant Staphylococcus aureus (MRSA) prevention and control advocate screening of healthcare workers (HCWs) after unprotected exposure to MRSA carriers. Although this strategy is largely successful, contact tracing of staff is a time-consuming and costly component. We evaluated our contact tracing policy for HCWs over the years 2010–2018. Methods: A retrospective, observational study was performed in a Dutch teaching hospital. All HCWs who had unprotected contact with an MRSA carrier were included in contact tracing. When there had been a long period of unprotected admission prior to an MRSA finding, or when the index case was an HCW, the entire (nursing) team was tested. All samples of HCWs who were tested for MRSA carriage as part of contact tracing from 2010 until 2018 were included. A pooled nose, throat, and perineum swab was collected using the eSwab medium (Copan) and inoculated on chromID MRSA agar plates (bioMérieux) after enrichment in a broth. Molecular typing was performed using multiple-locus variable number of tandem repeat analysis (MLVA). Results: In total, we included 8,849 samples (range, 677–1,448 samples per year) from 287 contact tracings (range, 26–55 contact tracings per year). Overall, 32 HCWs were colonized with MRSA (0.36%; 95% CI, 0.26%–0.51%). None of them developed a clinical infection. Moreover, 8 HCWs (0.10%; 95% CI, 0.05%–0.19%) were colonized with the same MLVA type as the index case and were detected in 6 of 287 contact tracings (2%). In 4 of 8 of these cases, a positive HCW was the index for undertaking contact tracing. In 3 of 8 cases, it was clear that the HCW who was identified in the contact tracing was the source of the outbreak and was the cause of invasive MRSA infections in patients. Notably, a different MLVA type as the index case was found in 24 HCWs (0.27%; 95% CI, 0.18%–0.40%) of whom 7 of 24 HCWs (29.2%) were intermittent carriers. Conclusions: This study revealed a sustained low MRSA prevalence among samples in contact tracing of HCWs over 9 years. Furthermore, it shows that when MRSA contact tracing is performed according to the national guideline, only 1 of 1,000 samples results in a secondary case. This is similar to the population carriage rate of MRSA in The Netherlands. More frequently, an unrelated strain is found. These findings raise questions regarding the efficacy of the current strategy to perform contact tracing after unprotected exposure.Funding: NoneDisclosures: None

scholarly journals Exploring the role and mechanism of COVID-19 apps in fighting the current pandemic

2020 ◽  
Vol 0 ◽  
pp. 1-6
Author(s):  
Karthikeyan P. Iyengar ◽  
Rachit Jain ◽  
David Ananth Samy ◽  
Vijay Kumar Jain ◽  
Raju Vaishya ◽  
...  
Keyword(s):  
Data Privacy ◽  
Viral Transmission ◽  
Contact Tracing ◽  
The Novel ◽  
Test Track ◽  
The World ◽  
Novel Coronavirus ◽  
And Control ◽  
Second Wave ◽  
Transmission Test

As COVID-19 pandemic spread worldwide, policies have been developed to contain the disease and prevent viral transmission. One of the key strategies has been the principle of “‘test, track, and trace” to minimize spread of the virus. Numerous COVID-19 contact tracing applications have been rolled around the world to monitor and control the spread of the disease. We explore the characteristics of various COVID-19 applications and especially the Aarogya Setu COVID-19 app from India in its role in fighting the current pandemic. We assessed the current literature available to us using conventional search engines, including but not limited to PubMed, Google Scholar, and Research Gate in May 2020 till the time of submission of this article. The search criteria used MeSH keywords such as “COVID-19,” “pandemics,” “contact tracing,” and “mobile applications.” A variable uptake of different COVID-19 applications has been noted with increasing enrolment around the world. Security concerns about data privacy remain. The various COVID-19 applications will complement manual contact tracing system to assess and prevent viral transmission. Test, track, trace, and support policy will play a key role in avoidance of a “second wave” of the novel coronavirus severe acute respiratory syndrome coronavirus 2 outbreak.

scholarly journals Role of children in household transmission of COVID-19

2020 ◽  
pp. archdischild-2020-319910 ◽  
Author(s):  
Jieun Kim ◽  
Young June Choe ◽  
Jin Lee ◽  
Young Joon Park ◽  
Ok Park ◽  
...  
Keyword(s):  
Attack Rate ◽  
Index Case ◽  
Clinical Findings ◽  
International Travel ◽  
Contact Tracing ◽  
Secondary Case ◽  
Household Transmission ◽  
Household Members ◽  
Index Cases

ObjectiveTransmissibility of COVID-19 by children in the household is not clear. Herein, we describe children’s role in household transmission of COVID-19.Design and settingAll paediatric COVID-19 index cases and their household members reported from 20 January to 6 April 2020 in South Korea were reviewed. The secondary attack rate (SAR) from child index case to household secondary case was calculated. Epidemiological and clinical findings of child index case-household secondary case pair was assessed.ResultsA total of 107 paediatric COVID-19 index cases and 248 of their household members were identified. One pair of paediatric index-secondary household case was identified, giving a household SAR of 0.5% (95% CI 0.0% to 2.6%). The index case was self-quarantined at home after international travel, stayed in her room, but shared a meal table with the secondary case.ConclusionThe SAR from children to household members was low in the setting of social distancing, underscoring the importance of rigorous contact tracing and early isolation in limiting transmission within households.

scholarly journals Inferencing superspreading potential using zero-truncated negative binomial model: exemplification with COVID-19

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Shi Zhao ◽  
Mingwang Shen ◽  
Salihu S. Musa ◽  
Zihao Guo ◽  
Jinjun Ran ◽  
...  
Keyword(s):  
Disease Transmission ◽  
Negative Binomial ◽  
Management Strategies ◽  
Analytical Framework ◽  
Stochastic Simulations ◽  
Contact Tracing ◽  
Secondary Case ◽  
Large Numbers ◽  
Sporadic Cases ◽  
Index Cases

Abstract Background In infectious disease transmission dynamics, the high heterogeneity in individual infectiousness indicates that few index cases generate large numbers of secondary cases, which is commonly known as superspreading events. The heterogeneity in transmission can be measured by describing the distribution of the number of secondary cases as a negative binomial (NB) distribution with dispersion parameter, k. However, such inference framework usually neglects the under-ascertainment of sporadic cases, which are those without known epidemiological link and considered as independent clusters of size one, and this may potentially bias the estimates. Methods In this study, we adopt a zero-truncated likelihood-based framework to estimate k. We evaluate the estimation performance by using stochastic simulations, and compare it with the baseline non-truncated version. We exemplify the analytical framework with three contact tracing datasets of COVID-19. Results We demonstrate that the estimation bias exists when the under-ascertainment of index cases with 0 secondary case occurs, and the zero-truncated inference overcomes this problem and yields a less biased estimator of k. We find that the k of COVID-19 is inferred at 0.32 (95%CI: 0.15, 0.64), which appears slightly smaller than many previous estimates. We provide the simulation codes applying the inference framework in this study. Conclusions The zero-truncated framework is recommended for less biased transmission heterogeneity estimates. These findings highlight the importance of individual-specific case management strategies to mitigate COVID-19 pandemic by lowering the transmission risks of potential super-spreaders with priority.

scholarly journals Disease contact tracing in random and clustered networks

2005 ◽  
Vol 272 (1570) ◽  
pp. 1407-1414 ◽  
Author(s):  
Istvan Z Kiss ◽  
Darren M Green ◽  
Rowland R Kao
Keyword(s):  
Disease Transmission ◽  
Latency Period ◽  
Foot And Mouth Disease ◽  
Stochastic Simulations ◽  
Moment Closure ◽  
Contact Tracing ◽  
Dominant Factor ◽  
Epidemic Size ◽  
Precise Knowledge ◽  
Models Of Disease

The efficacy of contact tracing, be it between individuals (e.g. sexually transmitted diseases or severe acute respiratory syndrome) or between groups of individuals (e.g. foot-and-mouth disease; FMD), is difficult to evaluate without precise knowledge of the underlying contact structure; i.e. who is connected to whom? Motivated by the 2001 FMD epidemic in the UK, we determine, using stochastic simulations and deterministic ‘moment closure’ models of disease transmission on networks of premises (nodes), network and disease properties that are important for contact tracing efficiency. For random networks with a high average number of connections per node, little clustering of connections and short latency periods, contact tracing is typically ineffective. In this case, isolation of infected nodes is the dominant factor in determining disease epidemic size and duration. If the latency period is longer and the average number of connections per node small, or if the network is spatially clustered, then the contact tracing performs better and an overall reduction in the proportion of nodes that are removed during an epidemic is observed.

scholarly journals The secondary transmission pattern of COVID-19 based on contact tracing in Rwanda

2021 ◽  
Vol 6 (6) ◽  
pp. e004885
Author(s):  
Muhammed Semakula ◽  
FranÇois Niragire ◽  
Angela Umutoni ◽  
Sabin Nsanzimana ◽  
Vedaste Ndahindwa ◽  
...  
Keyword(s):  
Risk Factors ◽  
High Risk ◽  
Disease Transmission ◽  
Index Case ◽  
Conditional Logistic Regression ◽  
Contact Tracing ◽  
African Countries ◽  
Targeted Interventions ◽  
The Impact ◽  
Mapping Models

IntroductionCOVID-19 has shown an exceptionally high spread rate across and within countries worldwide. Understanding the dynamics of such an infectious disease transmission is critical for devising strategies to control its spread. In particular, Rwanda was one of the African countries that started COVID-19 preparedness early in January 2020, and a total lockdown was imposed when the country had only 18 COVID-19 confirmed cases known. Using intensive contact tracing, several infections were identified, with the majority of them being returning travellers and their close contacts. We used the contact tracing data in Rwanda for understanding the geographic patterns of COVID-19 to inform targeted interventions.MethodsWe estimated the attack rates and identified risk factors associated to COVID-19 spread. We used Bayesian disease mapping models to assess the spatial pattern of COVID-19 and to identify areas characterised by unusually high or low relative risk. In addition, we used multiple variable conditional logistic regression to assess the impact of the risk factors.ResultsThe results showed that COVID-19 cases in Rwanda are localised mainly in the central regions and in the southwest of Rwanda and that some clusters occurred in the northeast of Rwanda. Relationship to the index case, being male and coworkers are the important risk factors for COVID-19 transmission in Rwanda.ConclusionThe analysis of contact tracing data using spatial modelling allowed us to identify high-risk areas at subnational level in Rwanda. Estimating risk factors for infection with SARS-CoV-2 is vital in identifying the clusters in low spread of SARS-CoV-2 subnational level. It is imperative to understand the interactions between the index case and contacts to identify superspreaders, risk factors and high-risk places. The findings recommend that self-isolation at home in Rwanda should be reviewed to limit secondary cases from the same households and spatiotemporal analysis should be introduced in routine monitoring of COVID-19 in Rwanda for policy making decision on real time.

scholarly journals Estimation of the Transmission Risk of the 2019-nCoV and Its Implication for Public Health Interventions

2020 ◽  
Vol 9 (2) ◽  
pp. 462 ◽  
Author(s):  
Biao Tang ◽  
Xia Wang ◽  
Qian Li ◽  
Nicola Luigi Bragazzi ◽  
Sanyi Tang ◽  
...  
Keyword(s):  
Reproduction Number ◽  
Transmission Risk ◽  
Sensitivity Analyses ◽  
Contact Tracing ◽  
The Novel ◽  
Intervention Measures ◽  
Novel Coronavirus ◽  
Restrictive Measures ◽  
And Control ◽  
Travel Restriction

Since the emergence of the first cases in Wuhan, China, the novel coronavirus (2019-nCoV) infection has been quickly spreading out to other provinces and neighboring countries. Estimation of the basic reproduction number by means of mathematical modeling can be helpful for determining the potential and severity of an outbreak and providing critical information for identifying the type of disease interventions and intensity. A deterministic compartmental model was devised based on the clinical progression of the disease, epidemiological status of the individuals, and intervention measures. The estimations based on likelihood and model analysis show that the control reproduction number may be as high as 6.47 (95% CI 5.71–7.23). Sensitivity analyses show that interventions, such as intensive contact tracing followed by quarantine and isolation, can effectively reduce the control reproduction number and transmission risk, with the effect of travel restriction adopted by Wuhan on 2019-nCoV infection in Beijing being almost equivalent to increasing quarantine by a 100 thousand baseline value. It is essential to assess how the expensive, resource-intensive measures implemented by the Chinese authorities can contribute to the prevention and control of the 2019-nCoV infection, and how long they should be maintained. Under the most restrictive measures, the outbreak is expected to peak within two weeks (since 23 January 2020) with a significant low peak value. With travel restriction (no imported exposed individuals to Beijing), the number of infected individuals in seven days will decrease by 91.14% in Beijing, compared with the scenario of no travel restriction.

scholarly journals Secondary transmission of SARS-CoV-2 in educational settings in Northern Italy from September 2020 to April 2021: a population-based study

2021 ◽  
Author(s):  
Olivera Djuric ◽  
Elisabetta Larosa ◽  
Mariateresa Cassinadri ◽  
Silvia Cilloni ◽  
Eufemia Bisaccia ◽  
...  
Keyword(s):  
Attack Rate ◽  
Index Case ◽  
School Setting ◽  
Population Based ◽  
Contact Tracing ◽  
Secondary Case ◽  
Secondary Transmission ◽  
Source Of Infection ◽  
Alpha Variant ◽  
Type Of School

Background: We aimed to quantify the risk of transmission of SARS-CoV-2 in the school setting by type of school, characteristics of the index case and calendar period in the Reggio Emilia province (RE), Italy, from school reopening in September 2020 until the beginning of April 2021. The secondary aim was to estimate the promptness of contact tracing. Methods: A population-based analysis of surveillance data of all COVID-19 cases occurring in RE, Italy, from September 1, 2020, to April 4th, 2021, for which a school contact and/or exposure was suspected. Indicator of the delay in contact tracing was computed as the time elapsed since positivity of the index case and the date on which the swab for classmates was scheduled (or most were scheduled). Results: Overall, 30,426 and 13,571 contacts among classmates and teachers/staff, respectively, were identified and received recommendation for testing; 43,414 (98.7%) performed the test. Secondary transmission occurred in about 40% of the investigated classes, and the overall secondary case attack rate was 4%, slightly higher when the index case was a teacher, but with almost no differences by type of school and stable during the study period. Promptness of contact tracing increased during the study period, reducing the time from index case identification and testing of contacts from 7 to 3 days, as well the ability to identify possible source of infection in the index case (from 42% in September/October, to 22% in November, to 50% in December-April). Conclusions: Despite the spread of the Alpha variant during the study period in RE, the secondary case attack rate remained stable from school reopening in September 2020 until the beginning of April 2021.

scholarly journals COVID-19 outbreak investigation and response in a penitentiary setting: the experience of a prison in Italy, February to April 2020

2021 ◽  
Vol 26 (38) ◽  
Author(s):  
Ruggero Giuliani ◽  
Cristina Cairone ◽  
Lara Tavoschi ◽  
Laura Ciaffi ◽  
Teresa Sebastiani ◽  
...  
Keyword(s):  
Prevention And Control ◽  
Index Case ◽  
Task Force ◽  
Routine Data ◽  
Control Measures ◽  
Contact Tracing ◽  
Case Identification ◽  
Cultural Affinity ◽  
Prevention And Control Measures ◽  
And Control

Prisons are high-risk settings for COVID-19 and present specific challenges for prevention and control. We describe a COVID-19 outbreak in a large prison in Milan between 20 February and 30 April 2020. We performed a retrospective analysis of routine data collected during the COVID-19 emergency in prison. We analysed the spatial distribution of cases and calculated global and specific attack rates (AR). We assessed prevention and control measures. By 30 April 2020, 57 confirmed COVID-19 cases and 66 clinically probable cases were recorded among a population of 1,480. Global AR was 8.3%. The index case was a custodial officer. Two clusters were detected among custodial staff and healthcare workers. On 31 March, a confirmed case was identified among detained individuals. COVID-19 spread by physical proximity or among subgroups with cultural affinity, resulting in a cluster of 22 confirmed cases. Following index case identification, specific measures were taken including creation of a multidisciplinary task-force, increasing diagnostic capacity, contact tracing and dedicated isolation areas. Expanded use of personal protective equipment, environmental disinfection and health promotion activities were also implemented. Outbreaks of COVID-19 in prison require heightened attention and stringent comprehensive measures.

A coadunation of biological and mathematical perspectives on the pandemic COVID-19: A Review

Coronaviruses ◽  
2021 ◽  
Vol 02 ◽  
Author(s):  
Sahar Qazi ◽  
Kayenat Sheikh ◽  
Mo Faheem ◽  
Arshad Khan ◽  
Khalid Raza
Keyword(s):  
Phylogenetic Analysis ◽  
Aspartic Acid ◽  
Disease Transmission ◽  
The Novel ◽  
Amino Acid Residues ◽  
Replication Process ◽  
Diagnosis And Prognosis ◽  
Models Of Disease ◽  
Novel Coronavirus ◽  
Preliminary Phylogenetic Analysis

Background: Coronavirus disease 2019 (COVID-19) outbreak has created an emergency globally, and social distancing and isolation is the only solution to prevent its spread. Several countries have announced full lockdown to tackle this pandemic. The coronavirus family is inclusive of pathogens of both – animal species and humans, encapsulating the isolated severe acute respiratory syndrome coronavirus (SARS-CoV). Researchers round the globe have been dexterously working to decode this lethal virus. Many mathematical frameworks have also been depicted which have helped to understand the dynamics of the COVID-19. Methods: This systematic review highlights the virus genomic composition, preliminary phylogenetic analysis, pathogenesis, symptomatology, diagnosis, and prognosis along with mathematical models of disease transmission and dynamics. Results: Our preliminary phylogenetic analysis of the novel coronavirus sequence discerns that although shares its lineage with SARS, BAT-CoV, Beta-BAT-SARS,however, this protein is highly dissimilar to its ancestors. The widely prominent amino acid residues found in the protein are alanine (ALA), aspartic acid (ASP), phenylalanine (PHE), leucine (LEU), aspartic acid (ASP), threonine (THR), valine (VAL), tyrosine (TYR) and asparagine (ASN) that are responsible for its replication process. Conclusion: Research on coronaviruses continues towards developing a strong understanding of the rapidly evolving viral replication and its transmission between individuals.

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