Diagnosing the novel SARS-CoV-2 by quantitative RT-PCR: variations and opportunities.

The world is currently facing a novel viral pandemic (SARS-CoV-2), and large-scale testing is central to decision-making for the design of effective policies and control strategies to minimize its impact on the global population. However, testing for the presence of the virus is a major bottleneck in tracking the spreading of the disease. Given its adaptability regarding the nucleotide sequence of target regions, RT-qPCR is a strong ally to reveal the rapid geographical spreading of novel viruses. We assessed PCR variations in the SARS-CoV-2 diagnosis taking into account public genome sequences and diagnosis kits used by different countries. We analyzed 226 SARS-CoV-2 genome sequences from samples collected by March 22, 2020. Our work utilizes a phylogenetic approach that reveals the early evolution of the virus sequence as it spreads around the globe and informs the design of RT-qPCR primers and probes. The quick expansion of testing capabilities of a country during a pandemic is largely impaired by the availability of adequately trained personnel on RNA isolation and PCR analysis, as well as the availability of hardware (thermocyclers). We propose that rapid capacity development can circumvent these bottlenecks by training medical and non-medical personnel with some laboratory experience, such as biology-related graduate students. Furthermore, the use of thermocyclers available in academic and commercial labs can be promptly calibrated and certified to properly conduct testing during a pandemic. A decentralized, fast-acting training and testing certification pipeline will better prepare us to manage future pandemics.

[Spatial analysis and determination of priority areas for malaria control in the State of Tocantins, from 2003 to 2008]. / Análise espacial e determinação de áreas prioritárias para o controle da malária, no Estado no Tocantins, 2003-2008.

INTRODUCTION: In Tocantins, the behavior of malaria differs between microregions, with predominance of imported cases. This study describes a spatial analysis on malaria in the state covering 2003 to 2008, which sought to identify the incidence of autochthonous and imported cases, and the origin of the latter, in the microregions. METHODS: This was a retrospective study using secondary data. The data source was the epidemiological surveillance information system for malaria (SIVEP-Malária), and the data were analyzed using the Epi Info version 3.5.1 and Bioestat version 5.0 statistical software. RESULTS: It was found that malaria was not homogeneously distributed in all municipalities. The area of highest priority comprised municipalities located in microregions in the west of the state, at the border of Pará, which also had the highest number of autochthonous cases. The association between the autochthonous and imported cases and the Plasmodium species showed a statistically significant difference (G = 54.25; p < 0.0001). Among the eight microregions, Miracema do Tocantins, Araguaína and Bico do Papagaio accounted for 75.8% of the cases and, among these, eleven municipalities stood out. Regarding provenance, the State of Pará showed widespread distribution with 85.5% of the total, followed by French Guiana with 7.4%. CONCLUSIONS: These results demonstrated the predominance of imported cases and the difference between municipalities and microregions, and showed the influence of neighboring states in determining the areas of greatest risk. These data are important, since they contribute towards guiding and directing public policies regarding this disease in Tocantins.