Evaluating the effectiveness of lockdowns and restrictions during SARS-CoV-2 variant waves in the Canadian province of Nova Scotia

IntroductionAfter the initial onset of the SARS-CoV-2 pandemic, the government of Canada and provincial health authorities imposed restrictive policies to limit virus transmission and mitigate disease burden. In this study, the pandemic implications in the Canadian province of Nova Scotia (NS) were evaluated as a function of the movement of people and governmental restrictions during successive SARS-CoV-2 variant waves (i.e., Alpha through Omicron).MethodsPublicly available data obtained from community mobility reports (Google), the Bank of Canada Stringency Index, the “COVID-19 Tracker” service, including cases, hospitalizations, deaths, and vaccines, population mobility trends, and governmental response data were used to relate the effectiveness of policies in controlling movement and containing multiple waves of SARS-CoV-2.ResultsOur results indicate that the SARS-CoV-2 pandemic inflicted low burden in NS in the initial 2 years of the pandemic. In this period, we identified reduced mobility patterns in the population. We also observed a negative correlation between public transport (−0.78), workplace (−0.69), retail and recreation (−0.68) and governmental restrictions, indicating a tight governmental control of these movement patterns. During the initial 2 years, governmental restrictions were high and the movement of people low, characterizing a ‘seek-and-destroy’ approach. Following this phase, the highly transmissible Omicron (B.1.1.529) variant began circulating in NS at the end of the second year, leading to increased cases, hospitalizations, and deaths. During this Omicron period, unsustainable governmental restrictions and waning public adherence led to increased population mobility, despite increased transmissibility (26.41-fold increase) and lethality (9.62-fold increase) of the novel variant.DiscussionThese findings suggest that the low initial burden caused by the SARS-CoV-2 pandemic was likely a result of enhanced restrictions to contain the movement of people and consequently, the spread of the disease. Easing public health restrictions (as measured by a decline in the BOC index) during periods of high transmissibility of circulating COVID-19 variants contributed to community spread, despite high levels of immunization in NS

Ongoing mpox outbreak in Kamituga, South Kivu province, associated with monkeypox virus of a novel Clade I sub-lineage, Democratic Republic of the Congo, 2024

Since the beginning of 2023, the number of people with suspected monkeypox virus (MPXV) infection have sharply increased in the Democratic Republic of the Congo (DRC). We report near-to-complete MPXV genome sequences derived from six cases from the South Kivu province. Phylogenetic analyses reveal that the MPXV affecting the cases belongs to a novel Clade I sub-lineage. The outbreak strain genome lacks the target sequence of the probe and primers of a commonly used Clade I-specific real-time PCR.</p

A pooled testing strategy for identifying SARS-CoV-2 at low prevalence

Suppressing infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) will probably require the rapid identification and isolation of individuals infected with the virus on an ongoing basis. Reverse-transcription polymerase chain reaction (RT-PCR) tests are accurate but costly, which makes the regular testing of every individual expensive. These costs are a challenge for all countries around the world, but particularly for low-to-middle-income countries. Cost reductions can be achieved by pooling (or combining) subsamples and testing them in groups1-7. A balance must be struck between increasing the group size and retaining test sensitivity, as sample dilution increases the likelihood of false-negative test results for individuals with a low viral load in the sampled region at the time of the test8. Similarly, minimizing the number of tests to reduce costs must be balanced against minimizing the time that testing takes, to reduce the spread of the infection. Here we propose an algorithm for pooling subsamples based on the geometry of a hypercube that, at low prevalence, accurately identifies individuals infected with SARS-CoV-2 in a small number of tests and few rounds of testing. We discuss the optimal group size and explain why, given the highly infectious nature of the disease, largely parallel searches are preferred. We report proof-of-concept experiments in which a positive subsample was detected even when diluted 100-fold with negative subsamples (compared with 30-48-fold dilutions described in previous studies9-11). We quantify the loss of sensitivity due to dilution and discuss how it may be mitigated by the frequent re-testing of groups, for example. With the use of these methods, the cost of mass testing could be reduced by a large factor. At low prevalence, the costs decrease in rough proportion to the prevalence. Field trials of our approach are under way in Rwanda and South Africa. The use of group testing on a massive scale to monitor infection rates closely and continually in a population, along with the rapid and effective isolation of people with SARS-CoV-2 infections, provides a promising pathway towards the long-term control of coronavirus disease 2019 (COVID-19).info:eu-repo/semantics/publishe

Bioscience data literacy at the interface of the environment, human and wildlife : one health-centred education, research and practice perspectives in Rwanda

Advances in information technology have led to the availability of state-of-the-art technologies which in turn have been enabling the generation of unprecedented amounts of complex, structured or unstructured data sets that are sometimes difficult to process using conventional techniques. In particular, handling these large scale data in terms of collection, and aggregation, synthesis and analysis, interpretation, reporting, sharing and archiving processes, and interpreting them into descriptive models and enable effective interpretation requires continued development of robust computational models, algorithms and interoperable analytical frameworks (Hampton et al. 2017). This also involves the vital availability of data management expertise and reflects an imperative need for data science professionals, especially in the context of generating the most informative data for use and drive evidence-based decisions. Considering this, Rwanda has been fueling its economic transformation agenda, and, while this solely depends on natural resources exploitation, the scenario has led to critically concerning anthropogenic threats and unprecedented environmental vulnerability. Acknowledging the urgency to achieve its development needs while at the same time safeguarding the environmental sustainability, Rwanda has been promoting technology-enabled systems and approaches for sustainable management of environment and natural resources. Learning from global initiatives, Rwanda's journey targets the effective use of technology-supported systems and data science expertise to effectively drive management and decision making needs in environmental management, health research systems and biodiversity conservation planning (Karame et al. 2017). Rwanda champions the adoption and effective use of technology towards delivering its vision of knowledge-based economy. A particular emphasis relates to streamlining the education, research and application of technology-supported systems and platforms and strengthening their effective use. From a practical One Health perspective, Rwanda has been bridging inter-sectoral gaps related to joint planning and resource sharing for informed decision processes. This One Health concept emphasizes the interconnection of the health of human, animals and ecosystems and involves the applications of multidisciplinary, coordinated, cross-sectoral collaborative efforts to attain optimal health for people, animals and the environment (Buttke et al. 2015). One Health constitutes a promising approach in the advancement of biosciences. For example, big data and ecological and digital epidemiology analysis has led to promising progress beyond the traditional transdisciplinary conservation medicine approach, and One Health is now driving solutions to major conservation and health challenges. This paper aims to explore the perspectives of solving challenges in handling heterogeneous data and sources of uncertainty, the progress and feasibility of adopting (or developing, adapting and customizing) open code- and data-sharing platforms, and integrating the application of flexible statistical models and cloud-computing, all within the confines of limited resources. Africa needs to engage in data science to build and sustain capacity and to effectively use acquired knowledge and skills. Further, Africa can strategically align and tailor existing technology data science platforms to the unique context of this continent. It is time to assess the boundaries, explore new horizons, and reach beyond the limits of current practice in order to enable researchers to get the most from generated data. We envision a long-term integrative and digital approach to handling and processing health, environment, and wildlife data to mark the beginning of our journey forward

Understanding knowledge, attitudes and practices on Ebola Virus Disease: a multi-site mixed methods survey on preparedness in Rwanda

Abstract Background The overall goal of this survey was to understand the knowledge, attitudes, and practices related to the Ebola Virus Disease (EVD) in Rwanda. Methods This mixed-method cross-sectional survey was conducted in five selected districts of Rwanda. Quantitative data were collected from 1,010 participants using Kobo Collect Software and the analysis was performed using SPSS and Python software. Qualitative data were specifically collected from 98 participants through Key Informant Interviews (KIIs) and Focus Group Discussion (FGDs). Interview transcripts were imported into NVIVO 8 for coding and subsequent analysis. Results As per our quantitative findings, we report that from the 1,010 respondents, 99.6% reported having previously heard of Ebola, 97.2% believed that vaccination is important in combatting the disease and 93.3% of individuals reported a willingness to receive vaccination should one become available. Around 54% of the respondents were correct in identifying that the disease is of a viral origin which originates from wild animals (42.1%). When asked if they believed that Rwanda is at risk of an EVD outbreak, 90% of the respondents believe that the country is at risk of an EVD outbreak, and the cofactors *gender* and *whether people dwell in Rubavu/Rusizi* were found to significantly impact their perception of threat. As per our qualitative findings, the respondents mentioned that both geographical proximity and relations with the Democratic Republic of Congo place Rwanda at risk of developing an internal outbreak. Although the respondents seemed to be aware of the Ebola prevention behaviours, it was noted that some of them will require significant time before reintegrating into the community an EVD survivor, as they will first need assurance that the patient has fully recovered. Therefore, the qualitative findings reinforce what we originally reported in the quantitative approach to this study. Conclusion Our results show that there was high EVD-related knowledge and awareness among the general population in Rwanda. However, for strong public health awareness, preparedness, and protection, a massive investment should always be made in education about EVD with a special focus on districts neighboring countries where the disease is consistently being reported

Third COVID-19 vaccine dose boosts antibody function in Rwandans with high HIV viral load

Summary: SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) causing COVID-19 (coronavirus disease 2019) poses a greater health risk to immunocompromized individuals including people living with HIV (PLWH). However, most studies on PLWH have been conducted in higher-income countries. We investigated the post-vaccination antibody responses of PLWH in Rwanda by collecting peripheral blood from participants after receiving a second or third COVID-19 vaccine. Virus-binding antibodies as well as antibody neutralization ability against all major SARS-CoV-2 variants of concern were analyzed. We found that people with high HIV viral loads and two COVID-19 vaccine doses had lower levels of binding antibodies that were less virus neutralizing and less cross-reactive compared to control groups. A third vaccination increased neutralizing antibody titers. Our data suggest that people with high HIV viral loads require a third dose of vaccine to neutralize SARS-CoV-2 virus and new variants as they emerge

Author Correction: A pooled testing strategy for identifying SARS-CoV-2 at low prevalence (Nature, (2021), 589, 7841, (276-280), 10.1038/s41586-020-2885-5)

In Fig. 2 of this Article, the Ct values for the orf1ab gene (shown in Fig. 2b) in samples B16121 and B16122 at 20×, 50× and 100× dilution were accidental duplications of those of the N gene (shown in Fig. 2a). The Ct values for orf1ab have been corrected in Fig. 2 of the original Article, and Fig. 1 of this Amendment shows the original and corrected Fig. 2b, for transparency. As B16121 and B16122 are both low-Ct samples, this change has no effect on our conclusion that typical samples are easily detected after 100-fold dilution. In Extended Data Table 2 of this Article, which presents the source data for Fig. 2, the orf1ab Ct values for sample B16121 were incorrectly given as 29, 29.74 and 30.54 for 20×, 50× and 100× dilution, respectively, instead of 31, 30.51 and 30.95, respectively. In addition, the orf1ab Ct values for sample B16122 were incorrectly given as 26.81, 27.75 and 29.07 for 20×, 50× and 100× dilution, respectively, instead of 28.5, 29.4 and 30.2, respectively. Extended Data Table 2 of the original Article has been corrected online. We thank T. Carey for drawing this error to our attention. The original Article has been corrected online. (Figure presented.).SCOPUS: er.jinfo:eu-repo/semantics/publishe

Ongoing mpox outbreak in Kamituga, South Kivu province, associated with monkeypox virus of a novel Clade I sub-lineage, Democratic Republic of the Congo, 2024

Since the beginning of 2023, the number of people with suspected monkeypox virus (MPXV) infection have sharply increased in the Democratic Republic of the Congo (DRC). We report near-to-complete MPXV genome sequences derived from six cases from the South Kivu province. Phylogenetic analyses reveal that the MPXV affecting the cases belongs to a novel Clade I sub-lineage. The outbreak strain genome lacks the target sequence of the probe and primers of a commonly used Clade I-specific real-time PCR