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Bio Protoc ; 11(9): e4005, 2021 May 05.
Article in English | MEDLINE | ID: covidwho-2326923


The COVID-19 pandemic requires mass screening to identify those infected for isolation and quarantine. Individually screening large populations for the novel pathogen, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is costly and requires a lot of resources. Sample pooling methods improve the efficiency of mass screening and consume less reagents by increasing the capacity of testing and reducing the number of experiments performed, and are therefore especially suitable for under-developed countries with limited resources. Here, we propose a simple, reliable pooling strategy for COVID-19 testing using clinical nasopharyngeal (NP) and/or oropharyngeal (OP) swabs. The strategy includes the pooling of 10 NP/OP swabs for extraction and subsequent testing via quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR), and may also be applied to the screening of other pathogens.

Antarctic Science ; 33(6):645-659, 2021.
Article in English | ProQuest Central | ID: covidwho-1621176


Human- and animal-impacted sites in Antarctica can be contaminated with heavy metals, as well as areas influenced by underlying geology and naturally occurring minerals. The present study examined the relationship between heavy metal presence and soil microalgal occurrence across a range of human-impacted and undisturbed locations on Signy Island. Microalgae were identified based on cultures that developed after inoculation into an enriched medium. Twenty-nine microalgae representing Cyanobacteria, Bacillariophyta, Chlorophyta and Tribophyta were identified. High levels of As, Ca, Cd, Cu and Zn were detected in Gourlay Peninsula and North Point, both locations hosting dense penguin rookeries. Samples from Berntsen Point, the location of most intense human activity both today and historically, contained high levels of Pb. The contamination factor and pollution load index confirmed that the former locations were polluted by Cd, Cu and Zn, with these being of marine biogenic origin. Variation in the microalgal community was significantly correlated with concentrations of Mn, Ca, Mg, Fe, Zn, Cd, Co, Cr and Cu. However, the overall proportion of the total variation contributed by all metals was low (16.11%). Other factors not measured in this study are likely to underlie the majority of the observed variation in microalgal community composition between sampling locations.

PLoS One ; 15(8): e0238417, 2020.
Article in English | MEDLINE | ID: covidwho-732990


The rapid global spread of the coronavirus disease (COVID-19) has inflicted significant health and socioeconomic burden on affected countries. As positive cases continued to rise in Malaysia, public health laboratories experienced an overwhelming demand for COVID-19 screening. The confirmation of positive cases of COVID-19 has solely been based on the detection of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) using real-time reverse transcription polymerase chain reaction (qRT-PCR). In efforts to increase the cost-effectiveness and efficiency of COVID-19 screening, we evaluated the feasibility of pooling clinical Nasopharyngeal/Oropharyngeal (NP/OP) swab specimens during nucleic acid extraction without a reduction in sensitivity of qRT-PCR. Pools of 10 specimens were extracted and subsequently tested by qRT-PCR according to the WHO-Charité protocol. We demonstrated that the sample pooling method showed no loss of sensitivity. The effectiveness of the pooled testing strategy was evaluated on both retrospective and prospective samples, and the results showed a similar detection sensitivity compared to testing individual sample alone. This study demonstrates the feasibility of using a pooled testing strategy to increase testing capacity and conserve resources, especially when there is a high demand for disease testing.

Coronavirus Infections/diagnosis , Mass Screening/methods , Pneumonia, Viral/diagnosis , Real-Time Polymerase Chain Reaction , Specimen Handling/methods , Betacoronavirus , COVID-19 , Humans , Malaysia , Nasopharynx/virology , Oropharynx/virology , Pandemics , SARS-CoV-2 , Sensitivity and Specificity