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Objectives: The aim of this study was to investigate the feasibility of saliva sampling as a non-invasive and safer tool to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and to compare its reproducibility and sensitivity with nasopharyngeal swab samples (NPS). The use of sample pools was also investigated. Methods: A total of 2107 paired samples were collected from asymptomatic healthcare and office workers in Mexico City. Sixty of these samples were also analyzed in two other independent laboratories for concordance analysis. Sample processing and analysis of virus genetic material were performed according to standard protocols described elsewhere. A pooling analysis was performed by analyzing the saliva pool and the individual pool components. Results: The concordance between NPS and saliva results was 95.2% (kappa 0.727, p = 0.0001) and 97.9% without considering inconclusive results (kappa 0.852, p = 0.0001). Saliva had a lower number of inconclusive results than NPS (0.9% vs 1.9%). Furthermore, saliva showed a significantly higher concentration of both total RNA and viral copies than NPS. Comparison of our results with those of the other two laboratories showed 100% and 97% concordance. Saliva samples are stable without the use of any preservative, and a positive SARS-CoV-2 sample can be detected 5, 10, and 15 days after collection when the sample is stored at 4 °C. Conclusions: The study results indicate that saliva is as effective as NPS for the identification of SARS-CoV-2-infected asymptomatic patients. Sample pooling facilitates the analysis of a larger number of samples, with the benefit of cost reduction.

OBJECTIVE: To compare three methods: Biochemical tests, high-performance liquid chromatography (HPLC) and polymerase chain reaction-restriction fragments length polymorphism (PCR-RFLP), for the identification of mycobacteria, and to perform a cost-benefit analysis to define an optimum identification algorithm. MATERIAL AND METHODS: One-hundred-and-seven mycobacteria isolates were identified by the three methods at Instituto de Diagnóstico y Referencia Epidemiológicos, between February of 1999 and January of 2000 and the results were compared with those of a reference laboratory using the Q-Cochran statistical test. RESULTS: PCR-RFLP was the most rapid and specific procedure but also the most expensive; biochemical tests excelled for identification of Mycobacterium tuberculosis, but were lengthy and expensive for other mycobacteria; HPLC ranked in the middle for price, speed and specificity. CONCLUSIONS: Considering the expected proportion of M. tuberculosis, the following algorithm was proposed: Initially, biochemical tests should be performed; if the results indicate a non-tuberculous mycobacteria, the isolate should be analyzed with HPLC; if results are unclear, the isolate should be analyzed using PCR-RFLP. Isolates showing a previously undescribed PCR-RFLP pattern should be characterized by DNA sequencing.OBJETIVO: Comparar tres métodos: pruebas bioquímicas, cromatografía líquida de alta resolución (HPLC, por sus siglas en inglés) y reacción en cadena de la polimerasa-polimorfismo del tamaño de fragmentos de restricción (PCR-RFLP) para identificar micobacterias a nivel especie, analizando costo-beneficio y proponiendo un algoritmo de identificación. MATERIAL Y MÉTODOS: Entre febrero de 1999 y enero de 2000, en los laboratorios del Instituto de Diagnóstico y Referencia Epidemiológicos se tipificaron 107 aislados de micobacterias y los resultados se compararon con los obtenidos en un laboratorio de referencia utilizando la prueba estadística Q de Cochran. RESULTADOS: Se encontró que el PCR-RFLP fue el método más específico y rápido pero también el más caro. Las pruebas bioquímicas fueron confiables para la identificación de Mycobacterium tuberculosis, pero lentas e inespecíficas para otras micobacterias. El HPLC estuvo en un nivel medio tomando en cuenta costo, tiempo y especificidad. CONCLUSIONES: Considerando la proporción esperada de M. tuberculosis, se propone el siguiente algoritmo: si las pruebas bioquímicas indican una micobacteria no tuberculosa, el aislado será analizado por HPLC; si la identificación no es clara, el aislado será analizado usando PCR-RFLP. Si el aislado no pertenece a un patrón descrito, se identificará por secuenciación de ADN.

During May 2009–April 2010, we analyzed 692 samples of pandemic (H1N1) 2009 virus from patients in Mexico. We detected the H275Y substitution of the neuraminidase gene in a specimen from an infant with pandemic (H1N1) 2009 who was treated with oseltamivir. This virus was susceptible to zanamivir and resistant to adamantanes and oseltamivir.