Successful containment to date of SARS-CoV-2 transmission in the Northern Territory.
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ABSTRACT:
SUBMITTER: Douglas NM
PROVIDER: S-EPMC7984294 | biostudies-literature | 2021 Mar
REPOSITORIES: biostudies-literature
Publications
Successful containment to date of SARS-CoV-2 transmission in the Northern Territory.
Douglas Nicholas M NM Meumann Ella M EM Krause Vicki L VL Davies Jane J
The Medical journal of Australia 20201028 5
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Project description:BackgroundDespite substantial resources deployed to curb SARS-CoV-2 transmission, controlling the COVID-19 pandemic has been a major challenge. New variants of the virus are frequently emerging leading to new waves of infection and re-introduction of control measures. In this study, we assessed the effectiveness of containment strategies implemented in the early phase of the pandemic.MethodsReal-world data for COVID-19 cases was retrieved for the period Jan 1 to May 1, 2020 from a number of different sources, including PubMed, MEDLINE, Facebook, Epidemic Forecasting and Google Mobility Reports. We analyzed data for 18 countries/regions that deployed containment strategies such as travel restrictions, lockdowns, stay-at-home requests, school/public events closure, social distancing, and exposure history information management (digital contact tracing, DCT). Primary outcome measure was the change in the number of new cases over 30 days before and after deployment of a control measure. We also compared the effectiveness of centralized versus decentralized DCT. Time series data for COVID-19 were analyzed using Mann-Kendall (M-K) trend tests to investigate the impact of these measures on changes in the number of new cases. The rate of change in the number of new cases was compared using M-K z-values and Sen's slope.ResultsIn spite of the widespread implementation of conventional strategies such as lockdowns, travel restrictions, social distancing, school closures, and stay-at-home requests, analysis revealed that these measures could not prevent the spread of the virus. However, countries which adopted DCT with centralized data storage were more likely to contain the spread.ConclusionsCentralized DCT was more effective in containing the spread of COVID-19. Early implementation of centralized DCT should be considered in future outbreaks. However, challenges such as public acceptance, data security and privacy concerns will need to be addressed.
| S-EPMC9052634 | biostudies-literature
Project description:Following the detection of the first imported case of COVID-19 in the northern sector of Ghana, we molecularly characterized and phylogenetically analysed sequences, including three complete genome sequences, of severe acute respiratory syndrome coronavirus 2 obtained from nine patients in Ghana. We performed high-throughput sequencing on nine samples that were found to have a high concentration of viral RNA. We also assessed the potential impact that long-distance transport of samples to testing centres may have on sequencing results. Here, two samples that were similar in terms of viral RNA concentration but were transported from sites that are over 400 km apart were analyzed. All sequences were compared to previous sequences from Ghana and representative sequences from regions where our patients had previously travelled. Three complete genome sequences and another nearly complete genome sequence with 95.6% coverage were obtained. Sequences with coverage in excess of 80% were found to belong to three lineages, namely A, B.1 and B.2. Our sequences clustered in two different clades, with the majority falling within a clade composed of sequences from sub-Saharan Africa. Less RNA fragmentation was seen in sample KATH23, which was collected 9 km from the testing site, than in sample TTH6, which was collected and transported over a distance of 400 km to the testing site. The clustering of several sequences from sub-Saharan Africa suggests regional circulation of the viruses in the subregion. Importantly, there may be a need to decentralize testing sites and build more capacity across Africa to boost the sequencing output of the subregion.
| S-EPMC7959303 | biostudies-literature
Project description:BackgroundThe spatiotemporal profiling of molecular transmission clusters (MTCs) using viral genomic data can effectively identify transmission networks in order to inform public health actions targeting SARS-CoV-2 spread.MethodsWe used whole genome SARS-CoV-2 sequences derived from ten European regions belonging to eight countries to perform phylogenetic and phylodynamic analysis. We developed dedicated bioinformatics pipelines to identify regional MTCs and to assess demographic factors potentially associated with their formation.ResultsThe total number and the scale of MTCs varied from small household clusters identified in all regions, to a super-spreading event found in Uusimaa-FI. Specific age groups were more likely to belong to MTCs in different regions. The clustered sequences referring to the age groups 50-100 years old (y.o.) were increased in all regions two weeks after the establishment of the lockdown, while those referring to the age group 0-19 y.o. decreased only in those regions where schools' closure was combined with a lockdown.ConclusionsThe spatiotemporal profiling of the SARS-CoV-2 MTCs can be a useful tool to monitor the effectiveness of the interventions and to reveal cryptic transmissions that have not been identified through contact tracing.
| S-EPMC8001481 | biostudies-literature
Project description:Hereby, we report a confirmed case of intrauterine SARS-CoV-2 transmission with rapid placental dysfunction and fetal distress.
| PRJEB40434 | ENA
Project description:BackgroundThe first community transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant of concern (VOC) in Guangzhou, China occurred between May and June 2021. Herein, we describe the epidemiological characteristics of this outbreak and evaluate the implemented containment measures against this outbreak.Methodology/principal findingsGuangzhou Center for Disease Control and Prevention provided the data on SARS-CoV-2 infections reported between 21 May and 24 June 2021. We estimated the incubation period distribution by fitting a gamma distribution to the data, while the serial interval distribution was estimated by fitting a normal distribution. The instantaneous effective reproductive number (Rt) was estimated to reflect the transmissibility of SARS-CoV-2. Clinical severity was compared for cases with different vaccination statuses using an ordinal regression model after controlling for age. Of the reported local cases, 7/153 (4.6%) were asymptomatic. The median incubation period was 6.02 (95% confidence interval [CI]: 5.42-6.71) days and the means of serial intervals decreased from 5.19 (95% CI: 4.29-6.11) to 3.78 (95% CI: 2.74-4.81) days. The incubation period increased with age (P<0.001). A hierarchical prevention and control strategy against COVID-19 was implemented in Guangzhou, with Rt decreasing from 6.83 (95% credible interval [CrI]: 3.98-10.44) for the 7-day time window ending on 27 May 2021 to below 1 for the time window ending on 8 June and thereafter. Individuals with partial or full vaccination schedules with BBIBP-CorV or CoronaVac accounted for 15.3% of the COVID-19 cases. Clinical symptoms were milder in partially or fully vaccinated cases than in unvaccinated cases (odds ratio [OR] = 0.26 [95% CI: 0.07-0.94]).Conclusions/significanceThe hierarchical prevention and control strategy against COVID-19 in Guangzhou was timely and effective. Authorised inactivated vaccines are likely to contribute to reducing the probability of developing severe disease. Our findings have important implications for the containment of COVID-19.
| S-EPMC8730460 | biostudies-literature
Project description:The antiviral immune response to SARS-CoV-2 infection can limit viral spread and prevent development of pneumonic COVID-19. However, the protective immunological response associated with successful viral containment in the upper airways remain unclear. Here, we combine a multiomics approach with longitudinal sampling to reveal temporally resolved protective immune signatures in non-pneumonic and ambulatory SARS-CoV-2 infected patients and associate specific immune trajectories with upper airway viral containment. We see a distinct systemic rather than local immune state associated with viral containment, characterized by interferon stimulated gene (ISG) upregulation across circulating immune cell subsets in non-pneumonic SARS-CoV2 infection. We report reduced cytotoxic potential of Natural Killer (NK) and T cells, and an immune-modulatory monocyte phenotype with protective immunity in COVID-19. Together, we show protective immune trajectories in SARS-CoV2 infection, which have important implications for patient prognosis and the development of immunomodulatory therapies.
2022-01-17 | GSE193708 | GEO
Project description:SARS-CoV-2 enters host cells through its viral spike protein binding to angiotensin-converting enzyme 2 (ACE2) receptors on the host cells. Here, we show that functionalized nanoparticles, termed "Nanotraps," completely inhibited SARS-CoV-2 infection by blocking the interaction between the spike protein of SARS-CoV-2 and the ACE2 of host cells. The liposomal-based Nanotrap surfaces were functionalized with either recombinant ACE2 proteins or anti-SARS-CoV-2 neutralizing antibodies and phagocytosis-specific phosphatidylserines. The Nanotraps effectively captured SARS-CoV-2 and completely blocked SARS-CoV-2 infection to ACE2-expressing human cell lines and primary lung cells; the phosphatidylserine triggered subsequent phagocytosis of the virus-bound, biodegradable Nanotraps by macrophages, leading to the clearance of pseudotyped and authentic virus in vitro. Furthermore, the Nanotraps demonstrated an excellent biosafety profile in vitro and in vivo. Finally, the Nanotraps inhibited pseudotyped SARS-CoV-2 infection in live human lungs in an ex vivo lung perfusion system. In summary, Nanotraps represent a new nanomedicine for the inhibition of SARS-CoV-2 infection.
| S-EPMC8062026 | biostudies-literature
Project description:ObjectivesAir temperature has been considered a modifiable and contributable variable in COVID-19 transmission. Implementation of non-pharmaceutical interventions (NPIs) has also made an impact on COVID-19 transmission, changing the transmission pattern to intrahousehold transmission under stringent containment measures. Therefore, it is necessary to re-estimate the influence of air temperature on COVID-19 transmission while excluding the influence of NPIs.Design, setting and participantsThis study is a data-based comprehensive modelling analysis. A stochastic epidemiological model, the ScEIQR model (contactable susceptible-exposed-infected-quarantined-removed), was established to evaluate the influence of air temperature and containment measures on the intrahousehold spread of COVID-19. Epidemic data on COVID-19, including daily confirmed cases, number of close contacts, etc, were collected from the National Health Commission of China.Outcome measuresThe model was fitted using the Metropolis-Hastings algorithm with a cost function based on the least squares method. The LOESS (locally weighted scatterplot smoothing) regression function was used to assess the relationship between air temperature and rate of COVID-19 transmission within the ScEIQR model.ResultsThe ScEIQR model indicated that the optimal temperature for spread of COVID-19 peaked at 10℃ (50℉), ranging from 5℃ to 14℃ (41℉-57.2℉). In the fitted model, the fitted intrahousehold transmission rate (β') of COVID-19 was 10.22 (IQR 8.47-12.35) across mainland China. The association between air temperature and β' of COVID-19 suggests that COVID-19 might be seasonal. Our model also validated the effectiveness of NPIs, demonstrating that diminishing contactable susceptibility (Sc) and avoiding delay in diagnosis and hospitalisation (η) were more effective than contact tracing (κ and ρ).ConclusionsWe constructed a novel epidemic model to estimate the effect of air temperature on COVID-19 transmission beyond implementation of NPIs, which can inform public health strategy and predict the transmission of COVID-19.
| S-EPMC8995577 | biostudies-literature
Project description:BackgroundDespite their clear lesser vulnerability to COVID-19, the extent by which children are susceptible to getting infected by SARS-CoV-2 and their capacity to transmit the infection to other people remains inadequately characterized. We aimed to evaluate the role of school reopening and the preventive strategies in place at schools in terms of overall risk for children and community transmission, by comparing transmission rates in children as detected by a COVID-19 surveillance platform in place in Catalonian Schools to the incidence at the community level.Methods and findingsInfections detected in Catalan schools during the entire first trimester of classes (September-December 2020) were analysed and compared with the ongoing community transmission and with the modelled predicted number of infections. There were 30.486 infections (2.12%) documented among the circa 1.5M pupils, with cases detected in 54.0% and 97.5% of the primary and secondary centres, respectively. During the entire first term, the proportion of "bubble groups" (stable groups of children doing activities together) that were forced to undergo confinement ranged between 1 and 5%, with scarce evidence of substantial intraschool transmission in the form of chains of infections, and with ~75% of all detected infections not leading to secondary cases. Mathematical models were also used to evaluate the effect of different parameters related to the defined preventive strategies (size of the bubble group, number of days of confinement required by contacts of an index case). The effective reproduction number inside the bubble groups in schools (R*), defined as the average number of schoolmates infected by each primary case within the bubble, was calculated, yielding a value of 0.35 for primary schools and 0.55 for secondary schools, and compared with the outcomes of the mathematical model, implying decreased transmissibility for children in the context of the applied measures. Relative homogenized monthly cumulative incidence ([Formula: see text]) was assessed to compare the epidemiological dynamics among different age groups and this analysis suggested the limited impact of infections in school-aged children in the context of the overall community incidence.ConclusionsDuring the fall of 2020, SARS-CoV-2 infections and COVID-19 cases detected in Catalan schools closely mirrored the underlying community transmission from the neighbourhoods where they were set and maintaining schools open appeared to be safe irrespective of underlying community transmission. Preventive measures in place in those schools appeared to be working for the early detection and rapid containment of transmission and should be maintained for the adequate and safe functioning of normal academic and face-to-face school activities.
| S-EPMC8849486 | biostudies-literature
Project description:AbstractThe severe acute respiratory syndrome coronavirus 2 has caused a worldwide pandemic. Control measures differ among countries and have a varying degree of effectiveness, which requires assessment. To evaluate the effectiveness of public health interventions of the coronavirus disease 2019 (COVID-19) in Guangzhou by 3 periods according to interventions: January 7 to 22 (no intervention), January 23 to February 23 (implemented intensive interventions), and February 24 to May 17 (the normalization mode of COVID-19 prevention and control).We collected the information of 745 COVID-19 patients and their close contacts as well as control measures in Guangzhou from January 7 to May 17, 2020. We estimated the epidemiological characteristics, disease spectrum of COVID-19 cases, key time-to-event intervals, and effective reproduction number over the 3 periods. The basic reproduction number of severe acute respiratory syndrome coronavirus 2 was also calculated over period 1.Approximately 45.8%, 49.8%, and 4.4% of cases from close contacts were asymptomatic, symptomatic, and severe, respectively. The median incubation period was 5.3 days (the percentiles of 2.5-97.5, 1.5-18.4 days) and the median serial interval fitted with gamma distribution was 5.1 days (the percentiles of 2.5-97.5, 0.8-15.9 days). The estimated median of onset-to-quarantined time in Period 1 to 3 were 7.5, 3.4, and 2.9 days (the percentiles of 2.5-97.5, 2.1-14.2, 3.9-14.7, and 6.0-20.0 days) respectively and the median of onset-to-confirmation time in period 1 to 3 were 8.9, 4.9 and 2.4 days (the percentiles of 2.5-97.5, 2.6-16.6, 0.9-14.6, and 0.5-11.8 days). In period 1, the reproduction number was 0.9 (95% confidence interval, 0.5-1.4) and fluctuated below 1.0 before January 22 except for January 14. The effective reproduction number gradually decreased in the period 2 with the lowest point of 0.1 on February 20, then increased again since March 27 and reach a spike of 1.8 on April 12. The number decreased to below 1.0 after April 17 and decreased further to <0.2 after May 7 in the period 3.Under prospective dynamic observation, close contacts turned into infected cases could provide a spectrum of COVID-19 cases from real-world settings. The lockdown of Wuhan and closed-loop management of people arriving Guangzhou were effective in halting the spread of the COVID-19 cases to Guangzhou. The spread of COVID-19 was successfully controlled in Guangzhou by social distancing, wearing a face mask, handwashing, disinfection in key places, mass testing, extensive contact tracing, and strict quarantine of close contacts.
| S-EPMC9191374 | biostudies-literature