Human virome in nasopharynx and tracheal secretion samples

BACKGROUND In Brazil the implementation of the Sentinel Surveillance System of Influenza began in 2000. Central public health laboratories use reverse transcription-quantitative polymerase chain reaction (RT-qPCR) for diagnosis of respiratory viruses, but this protocol identifies only specific targets, resulted in inconclusive diagnosis for many samples. Thus, high-throughput sequencing (HTS) would be complementary method in the identification of pathogens in inconclusive samples for RT-qPCR or other specific detection protocols. OBJECTIVES This study aimed to detect unidentified viruses using HTS approach in negative samples of nasopharynx/tracheal secretions by the standard RT-qPCR collected in the Federal District, Brazil. METHODS Nucleic acids were extracted from samples collected in winter period of 2016 and subjected to HTS. The results were confirmed by the multiplex PR21 RT-qPCR, which identifies 21 respiratory pathogens. FINDINGS The main viruses identified by HTS were of families Herpesviridae, Coronaviridae, Parvoviridae and Picornaviridae, with the emphasis on rhinoviruses. The presence of respiratory viruses in the samples was confirmed by the PR21 multiplex RT-qPCR. Coronavirus, enterovirus, bocavirus and rhinovirus were found by multiplex RT-qPCR as well as by HTS analyses. MAIN CONCLUSIONS Wide virus diversity was found by different methodologies and high frequency of rhinovirus occurrence was confirmed in population in winter, showing its relevance for public health.

[Comparative study on 1D [VP1] region of foot and mouth disease virus [type A strain] among different isolates: Khorasan Razavi isolate and other Iranian and neighboring countries isolates]

Foot-and-mouth disease [FMD] is one of the most important virus disease in farm animals. Types O, A and Asial FMD virus have been endemic in Iran. In this study, samples from suspected livestock were analyzed by RT-PCR experiment. The number of 702 nucleotides determined at 1D- 2B region of type A strain isolated from Khorasan Razavi province sequenced and compared with that of other reported isolates type A from Iran and neighboring countries. The results show that field isolated type A has about 89% similarity with other reported isolates type A from Iran and neighboring countries. Furthermore, this virus shows the most similarity with A/IRN/1/87[Samuel. Phylogenitic analysis revealed that virus was closely related to A22-Iraq/99 and A/IRN/iso/105 that rest in the same lineage. The data showed high similarity between type A viruses involved in the Khorasan Razavi province and A/IRN/87v [vaccine strain]; so that it can be concluded that the vaccine can produce prophylactic antibody against this virus