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Martínez-Hernández F, Gonzalez-Arenas NR, Cervantes JAO, Villalobos G, Olivo-Diaz A, Rendon-Franco E, Maravilla P, Valdovinos MR, Muñoz-Garcia CI. Identification of SARS-CoV-2 in urban rodents from Southern Mexico City at the beginning of the COVID-19 pandemic. Rev Inst Med Trop Sao Paulo 2024; 66:e8. [PMID: 38324874 PMCID: PMC10846537 DOI: 10.1590/s1678-9946202466008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/08/2023] [Indexed: 02/09/2024] Open
Abstract
Currently, there are some concerns about the situation and, in particular, about the future of the COVID-19 pandemic and the new emerging variants of SARS-CoV-2. Rodents are an example of synanthropic animals in urban environments that harbor important zoonoses. Although the molecular identification of SARS-CoV-2 in Rattus norvegicus from New York City had been reported, in other studies, urban wild rodents infected with this virus have not been found. This study aimed to molecularly identify the presence of SARS-CoV-2 in urban wild rodents from Mexico City, trapped along a water channel of a public park as part of a pest control program, at the beginning of the COVID-19 pandemic, during the fall and winter of 2020. Up to 33 Mus musculus and 52 R. norvegicus were captured and euthanized, large intestine samples with feces from the animals were obtained. RNAs were obtained and subjected to qRT-PCR for SARS-CoV-2 identification and threshold cycle (Ct) values were obtained. Four mice (12.1%) and three rats (5.8%) were positive, three rodents exhibited Ct<30. Our results on the frequency of SARS-CoV-2 in urban rats are in line with other previous reports. Thus, similar to other authors, we suggest that surveillance for the detection of SARS-CoV-2 in urban wild rodents, as sentinel animals, should be maintained.
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Affiliation(s)
| | | | - José Antonio Ocampo Cervantes
- Universidad Autónoma Metropolitana, Centro de Investigaciones Biológicas y Acuícolas de Cuemanco, Ciudad de México, Mexico
| | - Guiehdani Villalobos
- Universidad Autónoma Metropolitana, Departamento de Producción Agrícola y Animal, Ciudad de México, Mexico
| | | | - Emilio Rendon-Franco
- Universidad Autónoma Metropolitana, Departamento de Producción Agrícola y Animal, Ciudad de México, Mexico
| | - Pablo Maravilla
- Hospital General “Dr. Manuel Gea González”, Ciudad de México, Mexico
| | - Mirza Romero Valdovinos
- Hospital General “Dr. Manuel Gea González”, Departamento de Biología Molecular e Histocompatibilidad, Laboratorio de Patógenos Emergentes, Ciudad de México, Mexico
| | - Claudia Irais Muñoz-Garcia
- Universidad Autónoma Metropolitana, Departamento de Producción Agrícola y Animal, Ciudad de México, Mexico
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Martinez-Hernandez F, Sanchez-Aguillon F, Martinez-Ocaña J, Gonzalez-Arenas NR, Romero-Valdovinos M, Lopez-Escamilla E, Maravilla P, Villalobos G. Genetic Variability of the Internal Transcribed Spacer and Pyruvate:Ferredoxin Oxidoreductase Partial Gene of Trichomonas vaginalis from Female Patients. Microorganisms 2023; 11:2240. [PMID: 37764084 PMCID: PMC10537638 DOI: 10.3390/microorganisms11092240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/31/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
In the present study, we evaluated the genetic variability of the internal transcribed spacer (ITS) region and the pyruvate:ferredoxin oxidoreductase (pfor) A gene of Trichomonas vaginalis from female patients and its possible implications in the host-parasite relationship. Phylogenetic and genetics of populations analyses were performed by analyzing sequences of the ITS region and partial pfor A gene of clinical samples with T. vaginalis, as previously documented. Alignments of protein sequences and prediction of three-dimensional structure were also performed. Although no correlation between the main clinical characteristics of the samples and the results of phylogeny was found, a median-joining analysis of ITS haplotypes showed two main clusters. Also, pfor A, due to its phylogenetic divergence, could be used as a marker to confirm the genus and species of trichomonads. Alignment of protein sequences and prediction of three-dimensional structure showed that PFOR A had a highly conserved structure with two synonymous mutations in the PFOR domain, substituting a V for a G or a S for a P. Our results suggest that the role of genetic variability of PFOR and ITS may not be significant in the symptomatology of this pathogen; however, their utility as genus and species markers in trichomonads is promising.
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Affiliation(s)
- Fernando Martinez-Hernandez
- Departamento de Ecologia de Agentes Patogenos, Hospital General “Dr. Manuel Gea Gonzalez”, Mexico City 14080, Mexico; (F.M.-H.); (J.M.-O.); (N.R.G.-A.); (E.L.-E.)
| | - Fabiola Sanchez-Aguillon
- Laboratorio de Investigación del Departamento de Biologia Molecular e Histocompatibilidad, Hospital General “Dr. Manuel Gea Gonzalez”, Mexico City 14080, Mexico;
| | - Joel Martinez-Ocaña
- Departamento de Ecologia de Agentes Patogenos, Hospital General “Dr. Manuel Gea Gonzalez”, Mexico City 14080, Mexico; (F.M.-H.); (J.M.-O.); (N.R.G.-A.); (E.L.-E.)
| | - Nelly Raquel Gonzalez-Arenas
- Departamento de Ecologia de Agentes Patogenos, Hospital General “Dr. Manuel Gea Gonzalez”, Mexico City 14080, Mexico; (F.M.-H.); (J.M.-O.); (N.R.G.-A.); (E.L.-E.)
| | - Mirza Romero-Valdovinos
- Laboratorio de Patogenos Emergentes, Departamento de Biologia Molecular e Histocompatibilidad, Hospital General “Dr. Manuel Gea Gonzalez”, Mexico City 14080, Mexico;
| | - Eduardo Lopez-Escamilla
- Departamento de Ecologia de Agentes Patogenos, Hospital General “Dr. Manuel Gea Gonzalez”, Mexico City 14080, Mexico; (F.M.-H.); (J.M.-O.); (N.R.G.-A.); (E.L.-E.)
| | - Pablo Maravilla
- Departamento de Ecologia de Agentes Patogenos, Hospital General “Dr. Manuel Gea Gonzalez”, Mexico City 14080, Mexico; (F.M.-H.); (J.M.-O.); (N.R.G.-A.); (E.L.-E.)
| | - Guiehdani Villalobos
- Departamento de Ecologia de Agentes Patogenos, Hospital General “Dr. Manuel Gea Gonzalez”, Mexico City 14080, Mexico; (F.M.-H.); (J.M.-O.); (N.R.G.-A.); (E.L.-E.)
- Laboratorio de Biologia Molecular del Departamento de Produccion Agricola y Animal, Universidad Autonoma Metropolitana, Mexico City 04960, Mexico
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Villalobos G, Sanchez-Aguillon F, Carmona-Maldonado MV, Gonzalez-Arenas NR, Lopez-Escamilla E, Hernandez-Castro R, Romero-Valdovinos M, Martinez-Flores WA, Ramirez-Hinojosa JP, Maravilla P, Martinez-Hernandez F. Unexpected Presence of Blastocystis Subtype 1-3 DNA in Human Vaginal and Sperm Samples Coinfected with Trichomonas vaginalis. Korean J Parasitol 2022; 60:195-200. [PMID: 35772738 PMCID: PMC9256282 DOI: 10.3347/kjp.2022.60.3.195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/12/2022] [Indexed: 11/23/2022]
Abstract
There have been few reports on extra-enteric infections by <i>Blastocystis</i> STs and none have been molecularly identified in samples from human reproductive organs. We report for the first time the identification of 3 different subtypes of <i>Blastocystis</i> (ST1-3) in vaginal and sperm samples, from patients infected with <i>Trichomonas vaginalis</i>. <i>Blastocystis</i> STs were identified by PCR-sequencing and by phylogenetic inferences using 28 vaginal swab samples and 7 sperm samples from patients trichomoniasis. <i>Blastocystis</i> STs were identified in 6 of 28 vaginal swabs (21.4%) and in 3 of 7 sperm samples (42.8%). In both biological samples, STs 1-3 were found; one vaginal sample showed subtype co-infection with ST1 and ST3. High genetic variation was observed in the sequences obtained and no specific clustering in the phylogenetic trees was detected. Most of the haplotypes identified were placed far from the main dispersal centers. Our finding suggested that incorrect cleaning of the genital area or a contamination by combination of anal and vaginal intercourse.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Pablo Maravilla
- Hospital General “Dr. Manuel Gea Gonzalez”, Mexico City 14080,
Mexico
- Corresponding authors (; )
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Ramirez-Hinojosa JP, Rodriguez-Sanchez Y, Romero-Gonzalez AK, Chavez-Gutierrez M, Gonzalez-Arenas NR, Ibarra-Arce A, Arroyo-Escalante S, Zavaleta-Villa B, Leon-Juarez M, Cruz-Holguin VJ, Espinosa de Los Monteros-Perez LE, Olivo-Diaz A, Hernandez-Castro R, Suarez-Roa L, Prado-Calleros H, Sierra-Martinez O, Avila-Ramirez G, Flisser A, Maravilla P, Romero-Valdovinos M. Association between cycle threshold (C t ) values and clinical and laboratory data in inpatients with COVID-19 and asymptomatic health workers. J Med Virol 2021; 93:5969-5976. [PMID: 34196423 PMCID: PMC8427125 DOI: 10.1002/jmv.27170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 06/28/2021] [Indexed: 12/18/2022]
Abstract
In‐house assays for the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) by quantitative reverse‐transcription polymerase chain reaction (qRT‐PCR), are feasible alternatives, particularly in developing countries. Cycle threshold (Ct) values obtained by qRT‐PCR were compared with clinical and laboratory data from saliva of inpatients with COVID‐19 and asymptomatic health workers (AHW) were studied. Saliva specimens from 58 inpatients confirmed by qRT‐PCR for SARS‐CoV‐2 using nasopharyngeal specimens, and 105 AHW were studied by qRT‐PCR using three sets of primers for the N (N1, N2, and N3) gene of SARS‐CoV‐2, according to the CDC Diagnostic Panel protocol, showing a positivity of 88% for inpatients and 8% for AHW. Bivariate analysis revealed an association between Ct < 38.0 values for N2 and mechanical ventilation assistance among patients (p = .013). In addition, values of aspartate‐transaminase, lactate dehydrogenase, and ferritin showed significant correlations with Ct values of N1 and N3 genes in inpatients. Therefore, our results show that Ct values correlate with some relevant clinical data for inpatients with COVID‐19.
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Affiliation(s)
| | | | | | | | | | - Aurora Ibarra-Arce
- División de Parasitología, Hospital General "Dr. Manuel Gea Gonzalez", Mexico City, Mexico
| | - Sara Arroyo-Escalante
- División de Parasitología, Hospital General "Dr. Manuel Gea Gonzalez", Mexico City, Mexico
| | - Beatriz Zavaleta-Villa
- División de Parasitología, Hospital General "Dr. Manuel Gea Gonzalez", Mexico City, Mexico
| | - Moises Leon-Juarez
- Departamento de Inmunobioquimica, Instituto Nacional de Perinatologia, Mexico City, Mexico
| | | | | | - Angelica Olivo-Diaz
- División de Parasitología, Hospital General "Dr. Manuel Gea Gonzalez", Mexico City, Mexico
| | | | - Lourdes Suarez-Roa
- División de Parasitología, Hospital General "Dr. Manuel Gea Gonzalez", Mexico City, Mexico
| | - Hector Prado-Calleros
- División de Parasitología, Hospital General "Dr. Manuel Gea Gonzalez", Mexico City, Mexico
| | | | - Guillermina Avila-Ramirez
- Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autonoma de Mexico (UNAM), Mexico City, Mexico
| | - Ana Flisser
- Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autonoma de Mexico (UNAM), Mexico City, Mexico
| | - Pablo Maravilla
- División de Parasitología, Hospital General "Dr. Manuel Gea Gonzalez", Mexico City, Mexico
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Alarcon-Valdes P, Villalobos G, Martinez-Flores WA, Lopez-Escamilla E, Gonzalez-Arenas NR, Romero-Valdovinos M, Martinez-Hernandez F, Santillan-Benitez JG, Maravilla P. Can the pyruvate: ferredoxin oxidoreductase (PFOR) gene be used as an additional marker to discriminate among Blastocystis strains or subtypes? Parasit Vectors 2018; 11:564. [PMID: 30373630 PMCID: PMC6205798 DOI: 10.1186/s13071-018-3141-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/10/2018] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Blastocystis spp. are the most prevalent intestinal eukaryotes identified in humans, with at least 17 genetic subtypes (ST) based on genes coding for the small-subunit ribosomal RNA (18S). It has been argued that the 18S gene should not be the marker of choice to discriminate between STs of these strains because this marker exhibits high intra-genomic polymorphism. By contrast, pyruvate:ferredoxin oxidoreductase (PFOR) is a relevant enzyme involved in the core energy metabolism of many anaerobic microorganisms such as Blastocystis, which, in other protozoa, shows more polymorphisms than the 18S gene and thus may offer finer discrimination when trying to identify Blastocystis ST. Therefore, the objective of the present study was to assess the suitability of the PFOR gene as an additional marker to discriminate among Blastocystis strains or subtypes from symptomatic carrier children. METHODS Faecal samples from 192 children with gastrointestinal symptoms from the State of Mexico were submitted for coprological study. Twenty-one of these samples were positive only for Blastocystis spp.; these samples were analysed by PCR sequencing of regions of the 18S and PFOR genes. The amplicons were purified and sequenced; afterwards, both markers were assessed for genetic diversity. RESULTS The 18S analysis showed the following frequencies of Blastocystis subtypes: ST3 = 43%; ST1 = 38%; ST2 = 14%; and ST7 = 5%. Additionally, using subtype-specific primer sets, two samples showed mixed Blastocystis ST1 and ST2 infection. For PFOR, Bayesian inference revealed the presence of three clades (I-III); two of them grouped different ST samples, and one grouped six samples of ST3 (III). Nucleotide diversity (π) and haplotype polymorphism (θ) for the 18S analysis were similar for ST1 and ST2 (π = ~0.025 and θ = ~0.036); remarkably, ST3 showed almost 10-fold lower values. For PFOR, a similar trend was found: clade I and II had π = ~0.05 and θ = ~0.05, whereas for clade III, the values were almost 6-fold lower. CONCLUSIONS Although the fragment of the PFOR gene analysed in the present study did not allow discrimination between Blastocystis STs, this marker grouped the samples in three clades with strengthened support, suggesting that PFOR may be under different selective pressures and evolutionary histories than the 18S gene. Interestingly, the ST3 sequences showed lower variability with probable purifying selection in both markers, meaning that evolutionary forces drive differential processes among Blastocystis STs.
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Affiliation(s)
- Patricia Alarcon-Valdes
- Facultad de Quimica, Universidad Autonoma del Estado de Mexico (UAEMex), Paseo Colon esq. Paseo Tollocan, Toluca, Estado de Mexico, Mexico
| | - Guiehdani Villalobos
- Instituto de Ecologia, Universidad Nacional Autonoma de Mexico (UNAM), 04510, Ciudad de Mexico, Ciudad de Mexico, Mexico
| | | | - Eduardo Lopez-Escamilla
- Hospital General "Dr. Manuel Gea Gonzalez", Calzada de Tlalpan 4800, Ciudad de Mexico, 14080, Ciudad de Mexico, Mexico
| | - Nelly Raquel Gonzalez-Arenas
- Hospital General "Dr. Manuel Gea Gonzalez", Calzada de Tlalpan 4800, Ciudad de Mexico, 14080, Ciudad de Mexico, Mexico
| | - Mirza Romero-Valdovinos
- Hospital General "Dr. Manuel Gea Gonzalez", Calzada de Tlalpan 4800, Ciudad de Mexico, 14080, Ciudad de Mexico, Mexico
| | - Fernando Martinez-Hernandez
- Hospital General "Dr. Manuel Gea Gonzalez", Calzada de Tlalpan 4800, Ciudad de Mexico, 14080, Ciudad de Mexico, Mexico.
| | | | - Pablo Maravilla
- Hospital General "Dr. Manuel Gea Gonzalez", Calzada de Tlalpan 4800, Ciudad de Mexico, 14080, Ciudad de Mexico, Mexico.
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