ABSTRACT
ResumeO_ST_ABSObjectiveC_ST_ABSThe goal of this study is to determine the presence of SARS-CoV-2 in food surfaces and public space surfaces in 3 districts of Lima, Peru. Material and methodsCross-sectional descriptive study, carried out in the districts of San Juan de Lurigancho, San Martin de Porres and Villa el Salvador. Surfaces that were exposed to the greatest user manipulation were selected, samples were swabbed for 4 weeks and transported to the laboratory to determine the presence of the virus. Results1095 inert surface samples and 960 food surface samples were evaluated for the identification of SARS-CoV-2 by the RT-PCR molecular test, whereby only one sample from an ATM (Automated Teller Machine) was positive. ConclusionsMost of the inert and food surfaces evaluated did not show the presence of SARS-CoV-2 during the time of sample collection. Despite the negative results, the frequency of disinfection measures should be maintained and increased, especially on inert high-contact surfaces, and hygiene measures on food should be continue.
ABSTRACT
Molecular diagnosis of SARS-CoV-2 in developing countries is still a big challenge. The reference standard, RT-qPCR, recommended by WHO, is not widely available, difficulting early identification of cases. Furthermore, the transport logistic between the sample collection point and the laboratory facilities can alter the samples, producing false negative results. RT-LAMP is a cheaper, simpler molecular technique that can be an interesting alternative to be offered in hospital laboratories. We present the evaluation of a RT-LAMP for diagnosis of SARS-CoV-2 in two steps: the laboratory standardization and the clinical validation, comparing it with the standard RT-qPCR. In the standardization phase, limit of detection and robustness values were obtained using RNA from a Peruvian SARS-CoV-2 strain. It presented 100% agreement between triplicates (RT-LAMP agreement with all RT-qPCR reactions that presented Ct [≤] 30) and robustness (RT-LAMP successful reactions with 80% reaction volume and 50% primer concentration). 384 nasal and pharyngeal swabs collected from symptomatic patients and stored in the INS biobank were tested and we obtained 98.75%, 87.41%, 97.65% and 92.96% for specificity, sensitivity, positive predictive value and negative predictive values respectively. Then, 383 samples from symptomatic patients with less than 15 days of disease, were tested both with the RT-LAMP and with the RT-qPCR, obtaining e 98.8%, 88.1%, 97.7% y 93.3% of specificity, sensitivity, positive predictive value and negative predictive values respectively. The laboratory standardization and the clinical validation presented the same value by Kappa-Cohen index (0.88) indicating an almost perfect agreement between RT-LAMP and RT-qPCR for molecular detection of SARS-CoV-2. We conclude that this RT-LAMP protocol presented high diagnostic performance values and can be an effective alternative for COVID-19 molecular diagnosis in hospitals, contributing to early diagnosis and reducing the spread of virus transmission in the Peruvian population.
