scholarly journals Genomic investigation of atypical malaria cases in Kanel, northern Senegal

2020 ◽  
Author(s):  
Mouhamad Sy ◽  
Aida Sadikh Badiane ◽  
Katherine J. Siddle ◽  
Amy Gaye ◽  
Tolla Ndiaye ◽  
...  
Keyword(s):  
Control Program ◽  
Metagenomic Sequencing ◽  
Public Health Response ◽  
The Public ◽  
Malaria Control Program ◽  
Malaria Burden ◽  
Atypical Symptoms ◽  
Health Response ◽  
National Malaria Control Program ◽  
Different Strains

Abstract BackgroundDiagnosis of malaria cases in regions where the malaria burden has decreased significantly and prevalence is very low becomes more challenging, in part because of reduced clinical presumption of malaria. The appearance of a cluster of malaria cases with atypical symptoms in Mbounguiel, a village in northern Senegal where malaria transmission is low, in September 2018 exemplifies this scenario. The collaboration between the national malaria control program (NMCP) at the Senegal ministry of health and the laboratory of parasitology mycology at Cheikh Anta Diop University worked together to evaluate this cluster of malaria cases using molecular and serology tools.ResultsNine of the fifteen patients were evaluated, and all nine samples were found to be positive for P. falciparum only. The 24 SNP molecular barcode showed the predominance of polygenomic infections, with identifiable strains being different from one another. All patients tested positive for the P. falciparum antigens. No other pathogenic infection was detected by either the serological panel or metagenomic sequencing. ConclusionsThis work undertaken locally within Senegal as a collaboration between the NMCP and a research malaria laboratory at University of Cheikh Anta Diop (UCAD) revealed that a cluster of malaria cases were caused by different strains of P. falciparum. The public health response in real time demonstrates the value of local molecular and genomics capacity in affected countries disease control and elimination.

scholarly journals Genomic investigation of atypical malaria cases in Kanel, northern Senegal

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Mouhamad Sy ◽  
Aida Sadikh Badiane ◽  
Awa Bineta Deme ◽  
Amy Gaye ◽  
Tolla Ndiaye ◽  
...  
Keyword(s):  
National Malaria Control Programme ◽  
Control Programme ◽  
Malaria Control Programme ◽  
Metagenomic Sequencing ◽  
Nucleotide Polymorphisms ◽  
Public Health Response ◽  
Malaria Burden ◽  
Atypical Symptoms ◽  
Health Response ◽  
Different Strains

Abstract Background The diagnosis of malaria cases in regions where the malaria burden has decreased significantly and prevalence is very low is more challenging, in part because of reduced clinical presumption of malaria. The appearance of a cluster of malaria cases with atypical symptoms in Mbounguiel, a village in northern Senegal where malaria transmission is low, in September 2018 exemplifies this scenario. The collaboration between the National Malaria Control Programme (NMCP) at the Senegal Ministry of Health and the Laboratory of Parasitology and Mycology at Cheikh Anta Diop University worked together to evaluate this cluster of malaria cases using molecular and serological tools. Methods Malaria cases were diagnosed primarily by rapid diagnostic test (RDT), and confirmed by photo-induced electron transfer-polymerase chain reaction (PET-PCR). 24 single nucleotide polymorphisms (SNPs) barcoding was used for Plasmodium falciparum genotyping. Unbiased metagenomic sequencing and Luminex-based multi-pathogen antibody and antigen profiling were used to assess exposure to other pathogens. Results Nine patients, of 15 suspected cases, were evaluated, and all nine samples were found to be positive for P. falciparum only. The 24 SNPs molecular barcode showed the predominance of polygenomic infections, with identifiable strains being different from one another. All patients tested positive for the P. falciparum antigens. No other pathogenic infection was detected by either the serological panel or metagenomic sequencing. Conclusions This work, undertaken locally within Senegal as a collaboration between the NMCP and a research laboratory at University of Cheikh Anta Diop (UCAD) revealed that a cluster of malaria cases were caused by different strains of P. falciparum. The public health response in real time demonstrates the value of local molecular and genomics capacity in affected countries for disease control and elimination.

scholarly journals Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak

Science ◽  
2019 ◽  
Vol 363 (6422) ◽  
pp. 74-77 ◽  
Author(s):  
L. E. Kafetzopoulou ◽  
S. T. Pullan ◽  
P. Lemey ◽  
M. A. Suchard ◽  
D. U. Ehichioya ◽  
...  
Keyword(s):  
Transmission Rate ◽  
Lassa Fever ◽  
World Health ◽  
Metagenomic Sequencing ◽  
Public Health Response ◽  
The Public ◽  
Real Time Analysis ◽  
Health Response ◽  
Health Organization ◽  
First Time

The 2018 Nigerian Lassa fever season saw the largest ever recorded upsurge of cases, raising concerns over the emergence of a strain with increased transmission rate. To understand the molecular epidemiology of this upsurge, we performed, for the first time at the epicenter of an unfolding outbreak, metagenomic nanopore sequencing directly from patient samples, an approach dictated by the highly variable genome of the target pathogen. Genomic data and phylogenetic reconstructions were communicated immediately to Nigerian authorities and the World Health Organization to inform the public health response. Real-time analysis of 36 genomes and subsequent confirmation using all 120 samples sequenced in the country of origin revealed extensive diversity and phylogenetic intermingling with strains from previous years, suggesting independent zoonotic transmission events and thus allaying concerns of an emergent strain or extensive human-to-human transmission.

scholarly journals Estimation of the Actual Incidence of Coronavirus Disease (COVID-19) in Emergent Hotspots: The Example of Hokkaido, Japan during February–March 2020

2021 ◽  
Vol 10 (11) ◽  
pp. 2392
Author(s):  
Andrei R. Akhmetzhanov ◽  
Kenji Mizumoto ◽  
Sung-Mok Jung ◽  
Natalie M. Linton ◽  
Ryosuke Omori ◽  
...  
Keyword(s):  
Cumulative Incidence ◽  
Surveillance System ◽  
Negative Binomial ◽  
Actual Number ◽  
Public Health Response ◽  
The Public ◽  
Health Response ◽  
Using Data ◽  
Insight Into ◽  
Actual Incidence

Following the first report of the coronavirus disease 2019 (COVID-19) in Sapporo city, Hokkaido Prefecture, Japan, on 14 February 2020, a surge of cases was observed in Hokkaido during February and March. As of 6 March, 90 cases were diagnosed in Hokkaido. Unfortunately, many infected persons may not have been recognized due to having mild or no symptoms during the initial months of the outbreak. We therefore aimed to predict the actual number of COVID-19 cases in (i) Hokkaido Prefecture and (ii) Sapporo city using data on cases diagnosed outside these areas. Two statistical frameworks involving a balance equation and an extrapolated linear regression model with a negative binomial link were used for deriving both estimates, respectively. The estimated cumulative incidence in Hokkaido as of 27 February was 2,297 cases (95% confidence interval (CI): 382–7091) based on data on travelers outbound from Hokkaido. The cumulative incidence in Sapporo city as of 28 February was estimated at 2233 cases (95% CI: 0–4893) based on the count of confirmed cases within Hokkaido. Both approaches resulted in similar estimates, indicating a higher incidence of infections in Hokkaido than were detected by the surveillance system. This quantification of the gap between detected and estimated cases helped to inform the public health response at the beginning of the pandemic and provided insight into the possible scope of undetected transmission for future assessments.

scholarly journals United States response to the COVID-19 pandemic, January–November 2020

2021 ◽  
pp. 1-14
Author(s):  
Mathew Alexander ◽  
Lynn Unruh ◽  
Andriy Koval ◽  
William Belanger
Keyword(s):  
United States ◽  
The United States ◽  
Contact Tracing ◽  
Public Health Response ◽  
The Public ◽  
The Past ◽  
Health Response ◽  
Physical Infrastructure ◽  
Key Policy ◽  
United States Healthcare

Abstract As of November 2020, the United States leads the world in confirmed coronavirus disease 2019 (COVID-19) cases and deaths. Over the past 10 months, the United States has experienced three peaks in new cases, with the most recent spike in November setting new records. Inaction and the lack of a scientifically informed, unified response have contributed to the sustained spread of COVID-19 in the United States. This paper describes major events and findings from the domestic response to COVID-19 from January to November 2020, including on preventing transmission, COVID-19 testing and contact tracing, ensuring sufficient physical infrastructure and healthcare workforce, paying for services, and governance. We further reflect on the public health response to-date and analyse the link between key policy decisions (e.g. closing, reopening) and COVID-19 cases in three states that are representative of the broader regions that have experienced spikes in cases. Finally, as we approach the winter months and undergo a change in national leadership, we highlight some considerations for the ongoing COVID-19 response and the broader United States healthcare system. These findings describe why the United States has failed to contain COVID-19 effectively to-date and can serve as a reference in the continued response to COVID-19 and future pandemics.

scholarly journals Toward a critical race analysis of the COVID-19 crisis in US carceral institutions

2021 ◽  
pp. 026101832110014
Author(s):  
Paddy Farr
Keyword(s):  
Critical Race Theory ◽  
Racial Justice ◽  
Critical Race ◽  
Public Health Response ◽  
The Public ◽  
Detention Centers ◽  
Health Response ◽  
Increased Risk ◽  
History Of ◽  
Race Analysis

People in carceral institutions are at increased risk for COVID-19 infection. Applying critical race theory to the problem of COVID-19 provides tools to analyze the risk of infection and evaluate the public health response within the imprisoned, jailed, and detained population. On the surface, this is due to factors related to a lack of hygiene products, an inability to physically distance, a low quality and inaccessible health care, and poor health. However, at root, the increased risk for infection is directly linked to the legacy of slavery and colonization within the history of US prisons, jails, and detention centers. As a solution to the crisis of COVID-19 and prevention of future pandemics within prisons, jails and detention centers, a critical race orientation provides reason and direction for mass decarceration and racial justice.

scholarly journals Effect of COVID-19 on childhood Mycoplasma pneumoniae infection in Chengdu, China

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ying Zhang ◽  
Yijie Huang ◽  
Tao Ai ◽  
Jun Luo ◽  
Hanmin Liu
Keyword(s):  
Public Health ◽  
Mycoplasma Pneumoniae ◽  
Close Contact ◽  
Serum Antibody ◽  
Pathogen Transmission ◽  
Western China ◽  
Public Health Response ◽  
The Public ◽  
Health Response ◽  
The Impact

Abstract Background Following the outbreak of the COVID-19 pandemic, a change in the incidence and transmission of respiratory pathogens was observed. Here, we retrospectively analyzed the impact of COVID-19 on the epidemiologic characteristics of Mycoplasma pneumoniae infection among children in Chengdu, one of the largest cities of western China. Method M. pneumoniae infection was diagnosed in 33,345 pediatric patients with respiratory symptoms at the Chengdu Women’s & Children’s Central Hospital between January 2017 and December 2020, based on a serum antibody titer of ≥1:160 measured by the passive agglutination assay. Differences in infection rates were examined by sex, age, and temporal distribution. Results Two epidemic outbreaks occurred between October-December 2017 and April-December 2019, and two infection peaks were detected in the second and fourth quarters of 2017, 2018, and 2019. Due to the public health response to COVID-19, the number of positive M. pneumoniae cases significantly decreased in the second quarter of 2020. The number of M. pneumoniae infection among children aged 3–6 years was higher than that in other age groups. Conclusions Preschool children are more susceptible to M. pneumoniae infection and close contact appears to be the predominant factor favoring pathogen transmission. The public health response to COVID-19 can effectively control the transmission of M. pneumoniae.

scholarly journals The Australian industrial system in the era of COVID-19

2021 ◽  
pp. 002218562110128
Author(s):  
Michele O’Neil
Keyword(s):  
Industrial Relations ◽  
National Level ◽  
Recovery Phase ◽  
Public Health Response ◽  
The Public ◽  
Paid Leave ◽  
Union Movement ◽  
Health Response ◽  
Decentralised Systems ◽  
Australian Economy

COVID-19 caused sudden and serious damage to the Australian economy. The effects have been spread unevenly, and highlighted the shortcomings of over-reliance on insecure forms of work. The lack of any form of paid leave for casual and other insecure workers undermined the public health response, and was emblematic of the broader consequences of insecurity. Despite its limitations, Australia’s industrial relations system responded to the challenges of the pandemic in a way that less regulated and ‘decentralised’ systems would not have been able to. This article argues that the union movement was critical to Australia’s successful response, and that the award system proved to be an adaptable mechanism to deliver change at a national level while ensuring that the representative voice of workers was heard, and basic industrial protections were not jettisoned. Industry bargaining would have also been a beneficial tool to deal with economy-wide issues of this kind. The article urges that the lessons of the pandemic be learned as we move to a recovery phase and that we ensure there are more secure jobs, better bargaining rights and improvements to basic protections to ensure that workers’ rights are not eroded.

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