Diagnostic performance of a colorimetric RT -LAMP for the identification of SARS-CoV-2: A multicenter prospective clinical evaluation in sub-Saharan Africa.

BACKGROUND: Management and control of the COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus SARS-CoV-2 is critically dependent on quick and reliable identification of the virus in clinical specimens. Detection of viral RNA by a colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a simple, reliable and cost-effective assay, deployable in resource-limited settings (RLS). Our objective was to evaluate the intrinsic and extrinsic performances of RT-LAMP in RLS. METHODS: This is a multicenter prospective observational study of diagnostic accuracy, conducted from October 2020 to February 2021 in four African Countries: Cameroon, Ethiopia, Kenya and Nigeria; and in Italy. We enroled 1657 individuals who were either COVID-19 suspect cases, or asymptomatic and presented for screening. RNA extracted from pharyngeal swabs was tested in parallel by a colorimetric RT-LAMP and by a standard real time polymerase chain reaction (RT-PCR). FINDINGS: The sensitivity and specificity of index RT LAMP compared to standard RT-PCR on 1657 prospective specimens from infected individuals was determined. For a subset of 1292 specimens, which underwent exactly the same procedures in different countries, we obtained very high specificity (98%) and positive predictive value (PPV = 99%), while the sensitivity was 87%, with a negative predictive value NPV = 70%, Stratification of RT-PCR data showed superior sensitivity achieved with an RT-PCR cycle threshold (Ct) below 35 (97%), which decreased to 60% above 35. INTERPRETATION: In this field trial, RT-LAMP appears to be a reliable assay, comparable to RT-PCR, particularly with medium-high viral loads (Ct < 35). Hence, RT-LAMP can be deployed in RLS for timely management and prevention of COVID-19, without compromising the quality of output.

Multidisciplinary approach towards training of the next generation of forensic DNA analysts in Africa; a Kenyan perspective.

The uptake of forensic DNA testing technologies in Africa has been slow despite the revolutionary technology being discovered and adopted 3 decades ago. African governments and partners have invested in construction and equipping of forensic laboratories in Africa but the benefits are yet to be realised as the laboratories are still faced with the challenge of shortage of adequately trained personnel. This paper describes an innovative multidisciplinary training approach that was developed and used to train officers from the Directorate of Criminal Investigations Kenya. We report on the structure, implementation and effectiveness of the training. It is expected that with the increased number of trained forensic DNA analysts, there will be an improvement in quality of forensic DNA evidence presented in courts and a reduction in backlog in the forensic biology laboratories in Kenya.

A Comparison of Kenyan Biomphalaria pfeifferi and B. Sudanica as Vectors for Schistosoma mansoni, Including a Discussion of the Need to Better Understand the Effects of Snail Breeding Systems on Transmission.

In Kenya, schistosomes infect an estimated 6 million people with >30 million people at risk of infection. We compared compatibility with, and ability to support and perpetuate, Schistosoma mansoni of Biomphalaria pfeifferi and Biomphalaria sudanica, 2 prominent freshwater snail species involved in schistosomiasis transmission in Kenya. Field-derived B. pfeifferi (from a stream in Mwea, central Kenya) and B. sudanica (from Nawa, Lake Victoria, in western Kenya) were exposed to S. mansoni miracidia isolated from fecal samples of naturally infected humans from Mwea or Nawa. Juvenile (<6 mm shell diameter), young adult (6-9 mm), and adult snails (>9 mm) were each exposed to a single miracidium. Schistosoma mansoni developed faster and consistently had higher infection rates (39.6-80.7%) in B. pfeifferi than in B. sudanica (2.4-21.5%), regardless of the source of S. mansoni or the size of the snails used. Schistosoma mansoni from Nawa produced higher infection rates in both B. pfeifferi and B. sudanica than did S. mansoni from Mwea. Mean daily cercariae production was greater for B. pfeifferi exposed to sympatric than allopatric S. mansoni (583-1,686 vs. 392-1,232), and mean daily cercariae production among B. sudanica were consistently low (50-590) with no significant differences between sympatric or allopatric combinations. Both non-miracidia-exposed and miracidia-exposed B. pfeifferi had higher mortality rates than for B. sudanica, but mean survival time of shedding snails (9.3-13.7 wk) did not differ significantly between the 2 species. A small proportion (1.5%) of the cercariae shedding B. pfeifferi survived up to 40 wk post-exposure. Biomphalaria pfeifferi was more likely to become infected and to shed more cercariae than B. sudanica, suggesting that the risk per individual snail of perpetuating transmission in Kenyan streams or lacustrine habitats may differ considerably. High infection rates exhibited by the preferential self-fertilizing B. pfeifferi relative to the out-crossing B. sudanica point to the need to investigate further the role of host breeding systems in influencing transmission of schistosomiasis by snail hosts.