Publications by authors named "Joel Armando Vázquez-Pérez"

6 Publications

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Steady-state persistence of respiratory syncytial virus in a macrophage-like cell line and sequence analysis of the persistent viral genome.

Virus Res 2021 May 5;297:198367. Epub 2021 Mar 5.

Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, 04510, Mexico City, Mexico. Electronic address:

Long-term infection by human respiratory syncytial virus (hRSV) has been reported in immunocompromised patients. Cell lines are valuable in vitro model systems to study mechanisms associated with viral persistence. Persistent infections in cell cultures have been categorized at least as in "carrier-state", where there exist a low proportion of cells infected by a lytic virus, and as in "steady-state", where most of cells are infected, but in absence of cytophatic effect. Here, we showed that hRSV maintained a steady-state persistence in a macrophage-like cell line after 120 passages, since the viral genome was detected in all of the cells analyzed by fluorescence in situ hybridization, whereas only defective viruses were identified by sucrose gradients and titration assay. Interestingly, eight percent of cells harboring the hRSV genome revealed undetectable expression of the viral nucleoprotein N; however, when this cell population was sorted by flow cytometry and independently cultured, viral protein expression was induced at detectable levels since the first post-sorting passage, supporting that sorted cells harbored the viral genome. Sequencing of the persistent hRSV genome obtained from virus collected from cell-culture supernatants, allowed assembling of a complete genome that displayed 24 synonymous and 38 nonsynonymous substitutions in coding regions, whereas extragenic and intergenic regions displayed 12 substitutions, two insertions and one deletion. Previous reports characterizing mutations in extragenic regulatory sequences of hRSV, suggested that some mutations localized at the 3' leader region of our persistent virus might alter viral transcription and replication, as well as assembly of viral nucleocapsids. Besides, substitutions in P, F and G proteins might contribute to altered viral assembly, budding and membrane fusion, reducing the cytopathic effect and in consequence, contributing to host-cell survival. Full-length mutant genomes might be part of the repertoire of defective viral genomes formed during hRSV infections, contributing to the establishment and maintenance of virus persistence.
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http://dx.doi.org/10.1016/j.virusres.2021.198367DOI Listing
May 2021

Swine virome on rural backyard farms in Mexico: communities with different abundances of animal viruses and phages.

Arch Virol 2021 Feb 4;166(2):475-489. Epub 2021 Jan 4.

Laboratorio de Biotecnología en Salud Animal, Centro Nacional de Investigación Disciplinaria en Microbiología Animal (CENID-Microbiología), Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias (INIFAP), carretera federal México-Toluca km 15.5, colonia palo Alto, Cuajimalpa, P.C. 05110, Mexico City, Mexico.

Domestic swine have been introduced by humans into a wide diversity of environments and have been bred in different production systems. This has resulted in an increased risk for the occurrence and spread of diseases. Although viromes of swine in intensive farms have been described, little is known about the virus communities in backyard production systems around the world. The aim of this study was to describe the viral diversity of 23 healthy domestic swine maintained in rural backyards in Morelos, Mexico, through collection and analysis of nasal and rectal samples. Next-generation sequencing was used to identify viruses that are present in swine. Through homology search and bioinformatic analysis of reads and their assemblies, we found that rural backyard swine have a high degree of viral diversity, different from those reported in intensive production systems or under experimental conditions. There was a higher frequency of bacteriophages and lower diversity of animal viruses than reported previously. In addition, sapoviruses, bocaparvoviruses, and mamastroviruses that had not been reported previously in our country were identified. These findings were correlated with the health status of animals, their social interactions, and the breeding/rearing environment (which differed from intensive systems), providing baseline information about viral communities in backyard swine.
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http://dx.doi.org/10.1007/s00705-020-04894-yDOI Listing
February 2021

Genomic Analysis of Early SARS-CoV-2 Variants Introduced in Mexico.

J Virol 2020 08 31;94(18). Epub 2020 Aug 31.

Instituto de Diagnóstico y Referencia Epidemiológicos, Dirección General de Epidemiología, Mexico City, Mexico

The coronavirus disease 2019 (COVID-19) pandemic has affected most countries in the world. Studying the evolution and transmission patterns in different countries is crucial to enabling implementation of effective strategies for disease control and prevention. In this work, we present the full genome sequence for 17 SARS-CoV-2 isolates corresponding to the earliest sampled cases in Mexico. Global and local phylogenomics, coupled with mutational analysis, consistently revealed that these viral sequences are distributed within 2 known lineages, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage A/G, containing mostly sequences from North America, and lineage B/S, containing mainly sequences from Europe. Based on the exposure history of the cases and on the phylogenomic analysis, we characterized 14 independent introduction events. Additionally, three cases with no travel history were identified. We found evidence that two of these cases represented local transmission cases occurring in Mexico during mid-March 2020, denoting the earliest events described for the country. Within this local transmission cluster, we also identified an H49Y amino acid change in the Spike protein. This mutation represents a homoplasy occurring independently through time and space and may function as a molecular marker to follow any further spread of these viral variants throughout the country. Our results provide a general picture of the SARS-CoV-2 variants introduced at the beginning of the outbreak in Mexico, setting the foundation for future surveillance efforts. Understanding the introduction, spread, and establishment of SARS-CoV-2 within distinct human populations as well as the evolution of the pandemics is crucial to implement effective control strategies. In this work, we report that the initial virus strains introduced in Mexico came from Europe and the United States and that the virus was circulating locally in the country as early as mid-March. We also found evidence for early local transmission of strains with a H49Y mutation in the Spike protein, which could be further used as a molecular marker to follow viral spread within the country and the region.
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http://dx.doi.org/10.1128/JVI.01056-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7459550PMC
August 2020

Alveolar microbiota profile in patients with human pulmonary tuberculosis and interstitial pneumonia.

Microb Pathog 2020 Feb 9;139:103851. Epub 2019 Nov 9.

Departamento de Investigación en Microbiología, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico. Electronic address:

Background: The presence of the human lung microbiota has been demonstrated in patients with different lung diseases, mainly in sputum samples. However, for study of the alveolar microbiota, a bronchoalveolar lavage (BAL) sample represents the lower respiratory tract (LRT) environment. It is currently unknown whether there is a specific alveolar microbiota profile in human lung diseases, such as pulmonary tuberculosis (TB) and interstitial pneumonia (IP).

Methods: BAL samples from six active TB patients, six IP patients and ten healthy volunteers were used for DNA extraction followed by amplification of the complete bacterial 16S ribosomal RNA gene (16S rDNA). The 16S rDNA was sequenced with a MiSeq Desktop Sequencer, and the data were analysed by QIIME software for taxonomic assignment.

Results: The alveolar microbiota in TB and IP patients and healthy volunteers was characterized by six dominant phyla, Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Fusobacteria and Cyanobacteria. A significant reduction in the abundance of Firmicutes was observed in IP patients. In TB and IP patients, the diversity of the alveolar microbiota was diminished, characterized by a significant reduction in the abundance of the Streptococcus genus and associated with increased Mycobacterium abundance in TB patients and diminished Acinetobacter abundance in IP patients with respect to their abundances in healthy volunteers. However, an important difference was observed between TB and IP patients: the Fusobacterium abundance was significantly reduced in TB patients. Exclusive genera that were less abundant in patients than in healthy volunteers were characterized for each study group.

Conclusions: This study shows that the alveolar microbiota profile in BAL samples from TB and IP patients, representing infectious and non-infectious lung diseases, respectively, is characterized by decreased diversity.
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http://dx.doi.org/10.1016/j.micpath.2019.103851DOI Listing
February 2020

Amino acid changes in HA and determinants of pathogenicity associated with influenza virus A H1N1pdm09 during the winter seasons 2015-2016 and 2016-2017 in Mexico.

Virus Res 2019 10 21;272:197731. Epub 2019 Aug 21.

Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City, Mexico.

Biennial H1N1pdm09 influenza A virus (IAV) epidemics have been associated with major severity of respiratory disease in Mexico. Atypically and in contrast with what happened in USA, Canada and Europe during 2017, an increase of infections due to the H1N1pdm09 pandemic virus instead of H3N2 was observed. In order to determine the viral contribution to severe acute respiratory disease, we characterized the pathogenicity determinants of IAV in Mexico during the 2015-2016 and 2016-2017 seasons. The RNA segments of 20 IAV samples were sequenced by NGS platform and phylogenetic analysis was conducted. The analysis of the hemagglutinin (HA) sequences established that all virus samples, except one, belong to clade (6B.1). The IAVs presented the substitution S162 N, which introduces a new glycosylation site in the hemagglutinin. We also found the D222 G substitution, which has been associated with a higher tropism towards the lower respiratory tract, and a non-reported insertion of one Ile in NS1 (Ile113). The IAVs from 2016 to 2017 in Mexico belong to the new clade 6B.1. The new glycosylation site in HA (S162 N) is a major change that may affect the efficacy of the current vaccine. We detected in several patients pathogenicity determinants associated with the severity of the respiratory disease.
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http://dx.doi.org/10.1016/j.virusres.2019.197731DOI Listing
October 2019

[Cellular restriction factors that inhibit human immunodeficiency virus replication: new strategies in antiretroviral therapy].

Rev Invest Clin 2014 Jul-Aug;66(4):359-68

Human immunodeficiency virus requires receptors and cellular factors in target cells in order to complete a successful replication. Conversely, host cells express different proteins like TRIM5a, Tetherin BST-2, as well as cytidine deaminase proteins (APOBEC3) to suppress viral replication. These proteins, known as cellular restriction factors, provide an initial defense against infection as components of the innate immune response. The best characterized restriction factor is the cytidine deaminase APOBEC3G that has been shown to have an important role in HIV pathogenesis. Here, we review the current knowledge of host restriction factors, focusing on APOBEC3G, and possible therapeutic strategies against HIV infection.
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March 2015