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This study aimed to investigate the presence of murine astrovirus (MuAstV) in Brazil. Fecal samples from mice belonging to four Brazilian animal facilities were collected and tested for MuAstV using real-time polymerase chain reaction. Of the 162 samples tested, 38 (23.5%) were positive for MuAstV, 33 (91.7%) of which came from specific-pathogen free colonies. Although most of the samples were obtained from asymptomatic animals, three mice presented diarrheal symptoms, and MuAstV was the only agent detected by molecular assay. Phylogenetic analysis revealed similarities between the MuAstV strains from this study and prototypes from the USA. MuAstV's high prevalence, environmental stability, genetic diversity and potential for persistent infections must be considered when evaluating health monitoring programs for laboratory rodents.

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Chicken Parvovirus (ChPV) belongs to the genus Aveparvovirus and is implicated in enteric diseases like runting-stunting syndrome (RSS) in poultry. In RSS, chicken health is affected by diarrhea, depression, and increased mortality, causing significant economic losses in the poultry industry. This study aimed to characterize the ChPV genomes detected in chickens with RSS through a metagenomic approach and compare the molecular and evolutionary characteristics within the Aveparvovirus galliform1 species. The intestinal content of broiler flocks affected with RSS was submitted to viral metagenomics. The assembled prevalent genomes were identified as ChPV after sequence and phylogenetic analysis, which consistently clustered separately from Turkey Parvovirus (TuPV). The strain USP-574-A presented signs of genomic recombination. The selective pressure analysis indicated that most of the coding genes in A. galliform1 are evolving under diversifying (negative) selection. Protein modeling of ChPV and TuPV viral capsids identified high conservancy over the VP2 region. The prediction of epitopes identified several co-localized antigenic peptides from ChPV and TuPV, especially for T-cell epitopes, highlighting the immunological significance of these sites. However, most of these peptides presented host-specific variability, obeying an adaptive scenario. The results of this study show the evolutionary path of ChPV and TuPV, which are influenced by diversifying events such as genomic recombination and selective pressure, as well as by adaptation processes, and their subsequent immunological impact.

Asunto(s)

Pollos , Evolución Molecular , Genoma Viral , Infecciones por Parvoviridae , Filogenia , Enfermedades de las Aves de Corral , Animales , Pollos/virología , Enfermedades de las Aves de Corral/virología , Infecciones por Parvoviridae/veterinaria , Infecciones por Parvoviridae/virología , Metagenómica , Parvovirinae/genética , Parvovirinae/clasificación , Parvovirus/genética , Parvovirus/clasificación

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This study aims to characterize the molecular profile of the hepatitis B virus (HBV) among socially vulnerable immigrants residing in Brazil to investigate the introduction of uncommon HBV strains into the country. Serum samples from 102 immigrants with positive serology for the HBV core antibody (anti-HBc) were tested for the presence of HBV DNA by PCR assays. Among these, 24 were also positive for the HBV surface antigen (HBsAg). The full or partial genome was sequenced to determine genotype by phylogenetic analysis. Participants were from Haiti (79.4%), Guinea-Bissau (11.8%), Venezuela (7.8%), and Colombia (1%). Of the 21 HBV DNA-positive samples, subgenotypes A1 (52.4%), A5 (28.6%), E (9.5%), F2 (4.8%), and F3 (4.8%) were identified. Among the 78 HBsAg-negative participants, four were positive for HBV DNA, resulting in an occult HBV infection rate of 5.1%. Phylogenetic analysis suggested that most strains were likely introduced to Brazil by migration. Importantly, 80% of A5 sequences had the A1762T/G1764A double mutation, linked to an increased risk of hepatocellular carcinoma development. In conclusion, this study is the first report of HBV subgenotype A5 in Brazil, shedding new light on the diversity of HBV strains circulating in the country. Understanding the genetic diversity of HBV in immigrant communities can lead to better prevention and control strategies, benefiting both immigrants and wider society.

Asunto(s)

Carcinoma Hepatocelular , Emigrantes e Inmigrantes , Genotipo , Virus de la Hepatitis B , Hepatitis B , Neoplasias Hepáticas , Mutación , Filogenia , Humanos , Virus de la Hepatitis B/genética , Virus de la Hepatitis B/aislamiento & purificación , Brasil/epidemiología , Neoplasias Hepáticas/virología , Neoplasias Hepáticas/genética , Neoplasias Hepáticas/epidemiología , Carcinoma Hepatocelular/virología , Carcinoma Hepatocelular/genética , Carcinoma Hepatocelular/epidemiología , Femenino , Masculino , Adulto , Hepatitis B/virología , Hepatitis B/epidemiología , Hepatitis B/genética , Persona de Mediana Edad , ADN Viral/genética , Antígenos de Superficie de la Hepatitis B/genética , Antígenos de Superficie de la Hepatitis B/sangre , África/etnología , África/epidemiología , América Latina/etnología , América Latina/epidemiología

RESUMEN

The rubber tree (Hevea brasiliensis) is one of the major domesticated crops planted commercially for the production of natural rubber (NR) worldwide. In recent years, rubber trees in the Southern states of India and other rubber-producing countries have experienced a severe leaf spot disease, characterized by the appearance of several brown circular spots in the initial stage, which later spread all over the lamina of fully matured leaves, leading to yellowing and defoliation. The causal organism of this Circular Leaf Spot (CLS) disease has not been conclusively identified in any previous studies. In this study, we collected infected leaf samples from various locations in the South Indian states. We aimed to identify the actual fungal pathogen that causes the CLS disease on rubber trees. Based on the morphological and molecular analysis of the most frequently isolated fungi from infected leaf samples were identified as Colletotrichum siamense and Colletotrichum fructicola. Pathogenicity tests also confirmed the involvement of isolated Colletotrichum spp. in the development of CLS disease. These findings provide valuable insights into understanding the CLS disease and its impact on rubber cultivation. To our knowledge, it is the first report of C. siamense and C. fructicola associated with CLS disease of rubber trees in India.

Asunto(s)

Colletotrichum , Hevea , Enfermedades de las Plantas , Hojas de la Planta , Hevea/microbiología , Colletotrichum/genética , Colletotrichum/aislamiento & purificación , Colletotrichum/clasificación , Enfermedades de las Plantas/microbiología , India , Hojas de la Planta/microbiología , ADN de Hongos/genética , Filogenia , Análisis de Secuencia de ADN , Datos de Secuencia Molecular

RESUMEN

This study aimed to investigate the presence of Mycoplasma spp. and identify the species of mycoplasma isolates obtained from seabirds found on Brazilian coastal beaches. Tracheal and cloacal swab samples were collected from 50 seabirds rescued by three conservation and marine animal rehabilitation centers located in Brazil. The tracheal and cloacal samples were subjected to mycoplasma culture and the isolates were identified through PCR. A "Mollicutes-specific" 16S rRNA PCR reaction was employed for triage. Four species-specific PCR reactions were used to detect Mycoplasma gallisepticum, Mycoplasma synoviae, Mycoplasma meleagridis, or M. gallinarum. The Mollicutes positive and species negative samples were submitted do 16S rRNA sequencing. Eighteen (36%) of 50 seabirds tested positive for mycoplasma by culture. In the PCR for the genus, 28 (56%) of 50 seabirds were positive for Mycoplasma spp., with 13 (26%) detected in the trachea, one (2%) in the cloaca, and 14 (28%) in both sites. In the species-specific PCR, M. gallisepticum was detected in 17.8%, and M. meleagridis in 17.8%. Both species were detected in 14.3%. Of the isolates not characterized at species level, we obtained ten sequences and they were divided into three clusters. The first cluster was closely related to M. meleagridis, the second to M. synoviae, and the third grouped M. tully, M. gallisepticum, and M. imitans. Four and five of nine species of seabirds studied had mycoplasma detected by culture or PCR, respectively. Mycoplasmas were found in the majority of the animals studied, with the highest prevalence proportionally found in Sula leucogaster, and the lowest in Fregata magnificens. The phylogenetic analysis identified Mycoplasma spp. adapted to aquatic birds.

Asunto(s)

Enfermedades de las Aves , Cloaca , Infecciones por Mycoplasma , Mycoplasma , Filogenia , ARN Ribosómico 16S , Animales , Mycoplasma/aislamiento & purificación , Mycoplasma/genética , Mycoplasma/clasificación , Infecciones por Mycoplasma/veterinaria , Infecciones por Mycoplasma/microbiología , Brasil , ARN Ribosómico 16S/genética , Cloaca/microbiología , Enfermedades de las Aves/microbiología , Tráquea/microbiología , ADN Bacteriano/genética , Reacción en Cadena de la Polimerasa , Aves/microbiología

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Adaptation or acclimation of thermal requirements to environmental conditions can reduce thermoregulation costs and increase fitness, especially in ectotherms, which rely heavily on environmental temperatures for thermoregulation. Insight into how thermal niches have shaped thermal requirements across evolutionary history may help predict the survival of species during climate change. The lizard genus Sceloporus has a widespread distribution and inhabits an ample variety of habitats. We evaluated the effects of geographical gradients (i.e. elevation and latitude) and local environmental temperatures on thermal requirements (i.e. preferred body temperature, active body temperature in the field, and critical thermal limits) of Sceloporus species using published and field-collected data and performing phylogenetic comparative analyses. To contrast macro- and micro-evolutional patterns, we also performed intra-specific analyses when sufficient reports existed for a species. We found that preferred body temperature increased with elevation, whereas body temperature in the field decreased with elevation and increased with local environmental temperatures. Critical thermal limits were not related to the geographic gradient or environmental temperatures. The apparent lack of relation of thermal requirements to geographic gradient may increase vulnerability to extinction due to climate change. However, local and temporal variations in thermal landscape determine thermoregulation opportunities and may not be well represented by geographic gradient and mean environmental temperatures. Results showed that Sceloporus lizards are excellent thermoregulators, have wide thermal tolerance ranges, and the preferred temperature was labile. Our results suggest that Sceloporus lizards can adjust to different thermal landscapes, highlighting opportunities for continuous survival in changing thermal environments.

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Background and Aim: Leptospirosis is a re-emerging zoonosis that is under-reported in tropical countries, and canines can be a potential reservoir of the disease. The objective of this study was to diagnose Leptospira spp. that is actively infected and re-infected in stray dogs and cats from Bogota, D.C., Colombia. Materials and Methods: A sample of 200 animals, including dogs and cats from the animal protection programs of Bogota, Colombia, were used in this study. Blood was collected from these animals for serum and DNA analysis. Conventional polymerase chain reaction (PCR) was performed using the 16s rRNA primer set, and higher-quality amplification products were sequenced by Sanger. For serodiagnosis, a group of PCR-positive samples was tested using the microagglutination test (MAT). Results: The overall PCR positivity of stray dogs and cats was 56%, 52.9%, and 65.3% in dogs and cats, respectively. The MAT seropositivity was 77.3%, and only dogs showed titers higher than 1:400. Canicola, Icterohaemorrhagiae, Pomona, Hardjo Prajitno, and Canicola and Hardjo prajitno were the serogroups associated with dogs and cats, respectively. Phylogenetic analysis revealed that the strains belonging to Leptospira interrogans serovars related to isolated samples of American, European, and Asian bats (Myotis myotis), dogs, and bovines of American origin. Conclusion: These results showed that stray dogs and cats were previously exposed to different serovars of Leptospira spp. and re-infected with other serovars that actively participated in the transmission cycle. These findings highlight the importance of actively diagnosing infectious animals to design effective intervention strategies.

RESUMEN

Cassava (Manihot esculenta Crantz) is a staple crop widely cultivated by small farmers in tropical countries. However, despite the low level of technology required for its management, it can be affected by several diseases, with anthracnose as the main threat. There is little information about the main species of Colletotrichum that infect cassava in Brazil. Thus, the objective of this work was to study the diversity, prevalence and virulence of Colletotrichum species that cause anthracnose in cassava leaves in northern Brazil. Twenty municipalities of the Pará and Tocantins states were selected, and leaves with symptoms were collected in those locations. Pure cultures were isolated in the laboratory. Species were identified using phylogenetic analyses of multiple loci, and their pathogenicity, aggressivity and virulence levels were assessed. Our results showed the greatest diversity of Colletotrichum associated with anthracnose in cassava plants of the "Formosa" cultivar in the Tocantins and Pará states. We determined the presence of Colletotrichum chrysophilum, C. truncatum, C. siamense, C. fructicola, C. plurivorum, C. musicola and C. karsti, with C. chrysophilum as the most aggressive and virulent. Our findings provide accurate identifications of species of Colletotrichum causing anthracnose in cassava crops, which are of great relevance for cassava breeding programs (e.g., the search for genotypes with polygenic resistance since the pathogen is so diverse) and for developing anthracnose management strategies that can work efficiently against species complexes of Colletotrichum.

RESUMEN

The whole genome sequence of a low pathogenicity avian influenza virus (H6N2) was sequenced from a Brazilian teal (Amazonetta brasiliensis) in Brazil, 2023. Phylogenetic analysis of the whole genome revealed a distinct genome pertaining to South American LPAIV from 2014 to 2016, indicating extensive circulation among South American wild birds.

RESUMEN

The Mayaro virus (MAYV) is an arbovirus with emerging potential, though with a limited understanding of its epidemiology and evolution due to the lack of studies and surveillance. Here, we investigated 71 MAYV genome sequences from the Americas available at GenBank and characterized the phylogenetic relationship among virus strains. A phylogenetic analysis showed that sequences were grouped according to the genotypes L, D, and N. Genotype D sequences were closely related to sequences collected in adjacent years and from their respective countries, suggesting that isolates may have originated from circulating lineages. The coalescent analysis demonstrated similar results, indicating the continuous circulation of the virus between countries as well. An unidentified sequence from the USA was grouped with genotype D, suggesting the insertion of this genotype in the country. Furthermore, the recombination analysis detected homologous and three heterologous hybrids which presented an insertion into the nsP3 protein. Amino acid substitutions among sequences indicated selective pressure sites, suggesting viral adaptability. This also impacted the binding affinity between the E1-E2 protein complex and the Mxra8 receptor, associated with MAYV entry into human cells. These results provide information for a better understanding of genotypes circulating in the Americas.

Asunto(s)

Evolución Molecular , Variación Genética , Genoma Viral , Genotipo , Filogenia , Américas/epidemiología , Humanos , Alphavirus/genética , Alphavirus/clasificación , Alphavirus/aislamiento & purificación , Animales , Recombinación Genética , Infecciones por Alphavirus/virología , Infecciones por Alphavirus/epidemiología

RESUMEN

Thanks to advancements in genome sequencing and bioinformatics, thousands of bacterial genome sequences are available in public databases. This presents an opportunity to study bacterial diversity in unprecedented detail. This chapter describes a complete bioinformatics workflow for comparative genomics of bacterial genomes, including genome annotation, pangenome reconstruction and visualization, phylogenetic analysis, and identification of sequences of interest such as antimicrobial-resistance genes, virulence factors, and phage sequences. The workflow uses state-of-the-art, open-source tools. The workflow is presented by means of a comparative analysis of Salmonella enterica serovar Typhimurium genomes. The workflow is based on Linux commands and scripts, and result visualization relies on the R environment. The chapter provides a step-by-step protocol that researchers with basic expertise in bioinformatics can easily follow to conduct investigations on their own genome datasets.

Asunto(s)

Biología Computacional , Genoma Bacteriano , Genómica , Filogenia , Programas Informáticos , Genómica/métodos , Biología Computacional/métodos , Flujo de Trabajo , Bases de Datos Genéticas , Anotación de Secuencia Molecular , Salmonella typhimurium/genética

RESUMEN

Agave durangensis commonly known as agave cenizo, is an endemic Agave species in Mexico used for mescal production, yet its taxonomic delimitation is still controversial. This study aimed to enhance taxonomic clarity by characterizing its chloroplast genome. Chloroplast DNA was isolated from 2-year-old A. durangensis leaves. The complete chloroplast genome size was 156,441 bp, comprising a large single-copy region (LSC), a pair of inverted repeat regions (IR), and a small single-copy region (SSC). Annotation revealed 87 protein-coding genes, 38 tRNAs, and 8 rRNAs, with notable gene inversions. Phylogenetic analysis suggests, A. durangensis forms a separate lineage within the Agave genus.

RESUMEN

Background: As the COVID-19 pandemic persists, infections continue to surge globally. Presently, the most effective strategies to curb the disease and prevent outbreaks involve fostering immunity, promptly identifying positive cases, and ensuring their timely isolation. Notably, there are instances where the SARS-CoV-2 virus remains infectious even after patients have completed their quarantine. Objective: Understanding viral persistence post-quarantine is crucial as it could account for localized infection outbreaks. Therefore, studying and documenting such instances is vital for shaping future public health policies. Design: This study delves into a unique case of SARS-CoV-2 persistence in a 60-year-old female healthcare worker with a medical history of hypertension and hypothyroidism. The research spans 55 days, marking the duration between her initial and subsequent diagnosis during Chile's first COVID-19 wave, with the analysis conducted using RT-qPCR. Results: Genomic sequencing-based phylogenetic analysis revealed that the SARS-CoV-2 detected in both Nasopharyngeal swab samples (NPSs) was consistent with the 20B clade of the Nextstrain classification, even after a 55-day interval. Conclusion: This research underscores the need for heightened vigilance concerning cases of viral persistence. Such instances, albeit rare, might be pivotal in understanding sporadic infection outbreaks that occur post-quarantine.

RESUMEN

The analysis of SARS-CoV-2 in wastewater has enabled us to better understand the spread and evolution of the virus worldwide. To deepen our understanding of its epidemiological and genomic characteristics, we analyzed 10,147 SARS-CoV-2 sequences from 5 continents and 21 countries that were deposited in the GISAID database up until January 31, 2023. Our results revealed over 100 independent lineages of the virus circulating in water samples from March 2020 to January 2023, including variants of interest and concern. We observed four clearly defined periods of global distribution of these variants over time, with one variant being replaced by another. Interestingly, we found that SARS-CoV-2 water-borne sequences from different countries had a close phylogenetic relationship. Additionally, 40 SARS-CoV-2 water-borne sequences from Europe and the USA did not show any phylogenetic relationship with SARS-CoV-2 human sequences. We also identified a significant number of non-synonymous mutations, some of which were detected in previously reported cryptic lineages. Among the countries analyzed, France and the USA showed the highest degree of sequence diversity, while Austria reported the highest number of genomes (6,296). Our study provides valuable information about the epidemiological and genomic diversity of SARS-CoV-2 in wastewater, which can be employed to support public health initiatives and preparedness.

RESUMEN

INTRODUCTION: Bats are a diverse group of mammals that have unique features allowing them to act as reservoir hosts for several zoonotic pathogens such as Leptospira. Leptospires have been classified into pathogenic, intermediate, and saprophytic groups and more recently into clades P1, P2, S1, and S2, being all the most important pathogenic species related to leptospirosis included within the P1/pathogenic clade. Leptospira has been detected from bats in several regions worldwide; however, the diversity of leptospires harboured by bats is still unknown. AIM: The aim of the present study was to determine the genetic diversity of Leptospira spp. harboured by bats worldwide. METHODS: A systematic review was conducted on four databases to retrieve studies in which Leptospira was detected from bats. All studies were screened to retrieve all available Leptospira spp. 16S rRNA sequences from the GenBank database and data regarding their origin. Sequences obtained were compared with each other and reference sequences of Leptospira species and analysed through phylogenetic analysis. RESULTS: A total of 418 Leptospira spp. 16S rRNA sequences isolated from 55 bat species from 14 countries were retrieved from 15 selected manuscripts. From these, 417 sequences clustered within the P1/pathogenic group, and only one sequence clustered within the P2/intermediate group. Six major clades of P1/pathogenic Leptospira spp. were identified, three of them composed exclusively of sequences obtained from bats. CONCLUSION: We identified that bats harbour a great genetic diversity of Leptospira spp. that form part of the P1/pathogenic clade, some of which are closely related to leptospirosis-associated species. This finding contributes to the knowledge of the diversity of leptospires hosted by bats worldwide and reinforces the role of bats as reservoirs of P1/pathogenic Leptospira spp.

Asunto(s)

Quirópteros , Variación Genética , Leptospira , Leptospirosis , Filogenia , Animales , Quirópteros/microbiología , Leptospira/genética , Leptospira/clasificación , Leptospira/aislamiento & purificación , Leptospirosis/veterinaria , Leptospirosis/microbiología , Leptospirosis/epidemiología , Reservorios de Enfermedades/veterinaria , Reservorios de Enfermedades/microbiología , ARN Ribosómico 16S/genética , Zoonosis

RESUMEN

BACKGROUND: Chikungunya virus (CHIKV) is an arbovirus from the Togaviridae family which has four genotypes: West African (WA), East/Central/South African (ECSA) and Asian/Caribbean lineage (AL) and Indian Ocean Lineage (IOL). The ECSA genotype was first registered in Brazil in Feira de Santana and spread to all Brazilian regions. This study reports the characterization of CHIKV isolates recovered from sera samples of fifty patients from seventeen cities in Maranhão, a state from Brazilian northeast region and part of the Legal Amazon area. METHODS AND RESULTS: Primers were developed to amplify the partial regions coding structural proteins (E1, E3, E2, 6 K, and Capsid C). The consensus sequences have 2871 bp, covering approximately 24% of the genome. The isolates were highly similar (> 99%) to the ECSA isolate from Feira de Santana (BHI3734/H804698), presenting 30 non-synonymous mutations in E1 (5.95%), 18 in E2 (4.46%), and 1 in E3 (3.03%), taking the BHI3734/H804698 isolate as standard. Although the mutations described have not previously been related to increased infectivity or transmissibility of CHIKV, in silico analysis showed changes in physicochemical characteristics, antigenicity, and B cell epitopes of E1 and E2. CONCLUSIONS: These findings demonstrate the importance of molecular approaches for monitoring the viral adaptations undergone by CHIKV and its geographic distribution.

Asunto(s)

Fiebre Chikungunya , Virus Chikungunya , Humanos , Virus Chikungunya/genética , Fiebre Chikungunya/epidemiología , Brasil , Brotes de Enfermedades , Filogenia , Genotipo

RESUMEN

OBJECTIVE: this study aims to identify and characterise genomic and phylogenetically isolated SARS-CoV-2 viral isolates in patients from Lambayeque, Peru. METHODS: Nasopharyngeal swabs were taken from patients from the Almanzor Aguinaga Asenjo Hospital, Chiclayo, Lambayeque, Peru, which had been considered mild, moderate, and severe cases of COVID-19. Patients had to have tested positive for COVID-19, using a positive RT-PCR for SARS-CoV-2. Subsequently, the SARS-CoV-2 complete viral genome sequencing was carried out using Illumina MiSeq®. The sequences obtained from the sequence were analysed in Nextclade V1.10.0 to assign the corresponding clades, identify mutations in the SARS-CoV-2 genes and perform quality control of the sequences obtained. All sequences were aligned using MAFFT v7.471. The SARS-CoV-2 isolate Wuhan NC 045512.2 was used as a reference sequence to analyse mutations at the amino acid level. The construction of the phylogenetic tree model was achieved with IQ-TREE v1.6.12. RESULTS: It was determined that during the period from December 2020 to January 2021, the lineages s C.14, C.33, B.1.1.485, B.1.1, B.1.1.1, and B.1.111 circulated, with lineage C.14 being the most predominant at 76.7% (n = 23/30). These lineages were classified in clade 20D mainly and also within clades 20B and 20A. On the contrary, the variants found in the second batch of samples of the period from September to October 2021 were Delta (72.7%), Gamma (13.6%), Mu (4.6%), and Lambda (9.1%), distributed between clades 20J, 21G, 21H, 21J, and 21I. CONCLUSIONS: This study reveals updated information on the viral genomics of SARS-CoV-2 in the Lambayeque region, Peru, which is crucial to understanding the origins and dispersion of the virus and provides information on viral pathogenicity, transmission and epidemiology.

RESUMEN

In 2019-2020, dengue virus (DENV) type 4 emerged to cause the largest DENV outbreak in Paraguay's history. This study sought to characterize dengue relative to other acute illness cases and use phylogenetic analysis to understand the outbreak's origin. Individuals with an acute illness (≤7 days) were enrolled and tested for DENV nonstructural protein 1 (NS1) and viral RNA by real-time RT-PCR. Near-complete genome sequences were obtained from 62 DENV-4 positive samples. From January 2019 to March 2020, 799 participants were enrolled: 253 dengue (14 severe dengue, 5.5%) and 546 other acute illness cases. DENV-4 was detected in 238 dengue cases (94.1%). NS1 detection by rapid test was 52.5% sensitive (53/101) and 96.5% specific (387/401) for dengue compared to rRT-PCR. DENV-4 sequences were grouped into two clades within genotype II. No clustering was observed based on dengue severity, location, or date. Sequences obtained here were most closely related to 2018 DENV-4 sequences from Paraguay, followed by a 2013 sequence from southern Brazil. DENV-4 can result in large outbreaks, including severe cases, and is poorly detected with available rapid diagnostics. Outbreak strains seem to have been circulating in Paraguay and Brazil prior to 2018, highlighting the importance of sustained DENV genomic surveillance.

Asunto(s)

Virus del Dengue , Dengue , Humanos , Virus del Dengue/genética , Dengue/diagnóstico , Dengue/epidemiología , Paraguay/epidemiología , Filogenia , Enfermedad Aguda , Genotipo , Brotes de Enfermedades

RESUMEN

The characteristics of the whole PEDV genome that has circulated in Mexico from the first outbreak to the present are unknown. We chose samples obtained from 2013 to 2017 and sequenced them, which enabled us to identify the genetic variation and phylogeny in the virus during the first four years that it circulated in Mexico. A 99% identity was found among the analyzed pandemic strains; however, the 1% difference affected the structure of the S glycoprotein, which is essential for the binding of the virus to the cellular receptor. The S protein induces the most efficacious antibodies; hence, these changes in structure could be implicated in the clinical antecedents of the outbreaks. Antigenic changes could also help PEDV avoid neutralization, even in the presence of previous immunity. The characterization of the complete genome enabled the identification of three circulating strains that have a deletion in ORF1a, which is present in attenuated Asian vaccine strains. The phylogenetic analysis of the complete genome indicates that the first PEDV outbreaks in Mexico were caused by INDEL strains and pandemic strains related to USA strains; however, the possibility of the entry of European strains exists, which may have caused the 2015 and 2016 outbreaks.

Asunto(s)

Infecciones por Coronavirus , Virus de la Diarrea Epidémica Porcina , Enfermedades de los Porcinos , Animales , Porcinos , Virus de la Diarrea Epidémica Porcina/genética , Filogenia , Infecciones por Coronavirus/epidemiología , Infecciones por Coronavirus/veterinaria , México/epidemiología , Brotes de Enfermedades , Enfermedades de los Porcinos/epidemiología , Glicoproteína de la Espiga del Coronavirus/genética , Glicoproteína de la Espiga del Coronavirus/química , Diarrea

RESUMEN

BACKGROUND: Nematodes of the Ascarididae, Ancylostomatidae and Onchocercidae families are parasites of human and veterinary importance causing infections with high prevalence worldwide. Molecular tools have significantly improved the diagnosis of these helminthiases, but the selection of genetic markers for PCR or metabarcoding purposes is often challenging because of the resolution these may show. METHODS: Nuclear 18S rRNA, internal transcribed spacers 1 (ITS-1) and 2 (ITS-2), mitochondrial gene cytochrome oxidase 1 (cox1) and mitochondrial rRNA genes 12S and 16S loci were studied for 30 species of the mentioned families. Accordingly, their phylogenetic interspecies resolution, pairwise nucleotide p-distances and sequence availability in GenBank were analyzed. RESULTS: The 18S rRNA showed the least interspecies resolution since separate species of the Ascaris, Mansonella, Toxocara or Ancylostoma genus were intermixed in phylogenetic trees as opposed to the ITS-1, ITS-2, cox1, 12S and 16S loci. Moreover, pairwise nucleotide p-distances were significantly different in the 18S compared to the other loci, with an average of 99.1 ± 0.1%, 99.8 ± 0.1% and 98.8 ± 0.9% for the Ascarididae, Ancylostomatidae and Onchocercidae families, respectively. However, ITS-1 and ITS-2 average pairwise nucleotide p-distances in the three families ranged from 72.7% to 87.3%, and the cox1, 12S and 16S ranged from 86.4% to 90.4%. Additionally, 2491 cox1 sequences were retrieved from the 30 analyzed species in GenBank, whereas 212, 1082, 994, 428 and 143 sequences could be obtained from the 18S, ITS-1, ITS-2, 12S and 16S markers, respectively. CONCLUSIONS: The use of the cox1 gene is recommended because of the high interspecies resolution and the large number of sequences available in databases. Importantly, confirmation of the identity of an unknown specimen should always be complemented with the careful morphological examination of worms and the analysis of other markers used for specific parasitic groups.

Asunto(s)

Nematodos , Sarcocystis , Sarcocistosis , Humanos , Animales , ARN Ribosómico 18S/genética , Sarcocistosis/veterinaria , Filogenia , Nematodos/genética , Nucleótidos