Evaluation of sample pooling for screening of SARS CoV-2.

BACKGROUND: The coronavirus disease 2019 (COVID-19) pandemic has revealed the global public health importance of robust diagnostic testing. To overcome the challenge of nucleic acid (NA) extraction and testing kit availability, an efficient method is urgently needed. OBJECTIVES: To establish an efficient, time and resource-saving and cost-effective methods, and to propose an ad hoc pooling approach for mass screening of SARS-CoV-2. METHODS: We evaluated pooling approach on both direct clinical and NA samples. The standard reverse transcriptase polymerase chain reaction (RT-PCR) test of the SARS CoV-2 was employed targeting the nucleocapsid (N) and open reading frame (ORF1ab) genomic region of the virus. The experimental pools were created using SARS CoV-2 positive clinical samples and extracted RNA spiked with up to 9 negative samples. For the direct clinical samples viral NA was extracted from each pool to a final extraction volume of 200µL, and subsequently both samples tested using the SARS CoV-2 RT-PCR assay. RESULTS: We found that a single positive sample can be amplified and detected in pools of up to 7 samples depending on the cycle threshold (Ct) value of the original sample, corresponding to high, and low SARS CoV-2 viral copies per reaction. However, to minimize false negativity of the assay with pooling strategies and with unknown false negativity rate of the assay under validation, we recommend pooling of 4/5 in 1 using the standard protocols of the assay, reagents and equipment. The predictive algorithm indicated a pooling ratio of 5 in 1 was expected to retain accuracy of the test irrespective of the Ct value samples spiked, and result in a 137% increase in testing efficiency. CONCLUSIONS: The approaches showed its concept in easily customized and resource-saving manner and would allow expanding of current screening capacities and enable the expansion of detection in the community. We recommend clinical sample pooling of 4 or 5 in 1. However, we don't advise pooling of clinical samples when disease prevalence is greater than 7%; particularly when sample size is large.

Prevalence, Risk Factors, and Spectrum of Fungi in Patients with Onychomycosis in Addis Ababa, Ethiopia: A Prospective Study.

BACKGROUND: Onychomycosis is a common refractory infection deleteriously affecting quality of life via social stigma and upsetting day-to-day activities. OBJECTIVE: To study the prevalence of onychomycosis, spectrum of fungal etiological agents, and associated risk factors. METHODS: A prospective nonrandomized study on the prevalence of onychomycosis was carried out from September 2017 to April 2018 at a dermatology center in Addis Ababa. Nail scrapings were collected from 303 patients clinically identified with nail disorders of fungal origin by dermatologists. Fungal etiological agents were identified microscopically and by culture method following standard procedures. RESULTS: The prevalence of onychomycosis was 60.4%. Fungi neither were detected nor showed visible fungal growth in 39.6% of the cases. Females were more likely to present dystrophic nails than men. Patients in the middle age group were more affected. The isolation rates of dermatophytes, yeasts, and nondermatophyte molds were 44.7%, 33.3%, and 32.3%, respectively. Trichophyton rubrum, Scytalidium dimidiatum, and Candida albicans were the dominant species of dermatophytes, nondermatophyte molds, and yeasts, respectively. There was no statistically significant association between onychomycosis and risk factors. CONCLUSIONS: The prevalence rate of onychomycosis in the present study was high. The isolation rate of nondermatophyte molds was comparable with that of dermatophytes. Further studies on the prevalence of onychomycosis, fungal etiological agents, and changes in species distribution of the etiological agents of nail infection in Ethiopia are important.