Genomic epidemiology of SARS-CoV-2 δ sublineages of the second wave of 2021 in Antioquia, Colombia / Epidemiología genómica de los sublinajes δ del virus SARS-CoV-2 de la segunda ola de COVID en Antioquia en el 2021.

Introduction. During the development of the SARS-CoV-2 pandemic in Antioquia, we experienced epidemiological peaks related to the α, É£, ß, ƛ, and δ variants. δ had the highest incidence and prevalence. This lineage is of concern due to its clinical manifestations and epidemiological characteristics. A total of 253 δ sublineages have been reported in the PANGOLIN database. The sublineage identification through genomic analysis has made it possible to trace their evolution and propagation. Objective. To characterize the genetic diversity of the different SARS-CoV-2 δ sublineages in Antioquia and to describe its prevalence. Materials and methods. We collected sociodemographic information from 2,675 samples, and obtained 1,115 genomes from the GISAID database between July 12th, 2021, and January 18th, 2022. From the analyzed genomes, 515 were selected because of their high coverage values (>90%) to perform phylogenetic analysis and to infer allele frequencies of mutations of interest. Results. We characterized 24 sublineages. The most prevalent was AY.25. Mutations of interest as L452R, P681R, and P681H were identified in this sublineage, comprising a frequency close to 0.99. Conclusions. This study identified that the AY.25 sublineage has a transmission advantage compared to the other δ sublineages. This attribute may be related to the presence of the L452R and P681R mutations associated in other studies with higher evasion of the immune system and less efficacy of drugs against SARS-CoV-2.

Introducción. Durante el desarrollo de la pandemia por SARS-CoV-2 en Antioquia se presentaron picos epidemiológicos relacionados con las variantes α, É£, ß, ƛ y δ, donde δ tuvo la mayor incidencia y prevalencia. Este linaje se considera una variante de preocupación dadas las manifestaciones clínicas que desencadena y sus características epidemiológicas. Se han informado 253 sublinajes δ en la base de datos PANGOLIN. La identificación de estos sublinajes mediante análisis genómico ha permitido rastrear su evolución y propagación. Objetivo. Caracterizar la diversidad genética de los diferentes sublinajes δ de SARSCoV-2 en Antioquia y determinar su prevalencia. Materiales y métodos. Se recopiló información sociodemográfica de 2.675 muestras y de 1.115 genomas del repositorio GISAID entre el 12 de julio de 2021 y el 18 de enero de 2022. Se seleccionaron 501 por su alto porcentaje de cobertura (>90 %) para realizar análisis filogenéticos e inferencia de frecuencias alélicas de mutaciones de interés. Resultados. Se caracterizaron 24 sublinajes donde el más prevalente fue AY.25. En este sublinaje se identificaron mutaciones de interés como L452R, P681R y P681H, que comprendían una frecuencia cercana a 0,99. Conclusiones. Este estudio permitió identificar que el sublinaje AY.25 tiene una ventaja de transmisión en comparación con los otros sublinajes δ. Esto puede estar relacionado con la presencia de las mutaciones L452R y P681R que en otros estudios se han visto asociadas con una mayor transmisibilidad, evasión del sistema inmunitario y menor eficacia de los medicamentos contra SARS-CoV-2.

Identificación de microorganismos asociados a residuos de higuerilla (Ricinus communis) / Identification of microorganisms associated with castor (Ricinus communis) waste / Identificação de microorganismos associados resíduos de castor mamona (Ricinus communis)

El objetivo de este artículo fue aislar e identificar los microorganismos presentes en los residuos de fruto y torta de higuerilla (Ricinus communis). Se utilizaron medios de cultivo selectivos para la caracterización morfológica y bioquímica y para la identificación molecular se usó la técnica de PCR con oligonucleótidos universales RM y RB del gen 16S para bacterias y secuencias intergénicas ITS1 e ITS4 para hongos y levaduras. Las secuencias fueron analizadas identificándose nueve especies de hongos, siendo Penicillium brevicompactum predominante; 12 especies de bacterias, donde el género más recurrente fue Bacillus sp.; y dos especies de levaduras, Rhodosporidium paludigenum y Pichia burtonni. La identificación de la microbiota nativa presente en los residuos de higuerilla es muy promisoria, aportando un amplio conocimiento sobre la versatilidad metabólica de cada una de las cepas aisladas. El mayor número de aislamientos se obtuvieron de la torta por el alto contenido de nutrientes presentes en este residuo.

The aim of this article is to isolate and to identify microorganisms present in the fruit and cake waste of castor (Ricinus communis). Selective culture media for morphological and biochemical characterization were used. For molecular identification, PCR technique was performed with universal primers RM and RB from the bacterial 16S gene and the ITS5 and ITS4 intergenic sequences from molds and yeasts. Sequences were analyzed identifying 9 fungal species being predominant Penicillium brevicompactum; 12 species of bacteria, where genus Bacillus sp. was the most recurrent; and two species of yeast Pichia burtonni and Rhodosporidium paludigenum. The identification of this native microbiota in the waste of castor is very promising, providing a broad knowledge of the metabolic versatility of each of the isolates. The majority of isolates were obtained from the cake by the high content of nutrients in the waste.

O objetivo da pesquisa foi isolar e identificar os microrganismos presentes nos resíduos da fruta e bolo de mamona (Ricinus communis). Foram utilizados meios de cultura seletivos para caracterização morfológica e bioquímica. Para a identificação molecular empleou-se a técnica de PCR com primers gerais RM do gen RB 16S para bactérias e sequências intergênicas ITS1 e ITS4 para fungos e leveduras. As sequências foram analisadas e identificaram-se nove espécies de fungos, sendo o predominante Penicillium brevicompactum; 12 espécies de bactérias, nas quais o gênero mais recorrente foi o Bacillus sp.; e duas espécies de levedura Rhodosporidium paludigenum e Pichia burtonni. A identificação da microbiota nativa presente nos resíduos de rícino é muito promissoria, proporcionando um amplo conhecimento da versatilidade metabólica de cada uma das cepas isoladas. A maioria das amostras foram obtidas a partir do bolo pelo alto conteúdo de nutrientes nestos resíduos.

Biological and molecular characterization of Brazilian isolates of Zucchini yellow mosaic virus

Zucchini yellow mosaic virus (ZYMV) causes substantial economic losses in cucurbit crops. Although ZYMV has been present in Brazil for more than 20 years, there is little information about the biological and molecular characteristics of the isolates found in the country. This study aimed to characterize the experimental hosts, pathotypes and genetic diversity of a collection of eleven Brazilian ZYMV isolates within the coat protein gene. For biological analysis, plant species from Amaranthaceae, Chenopodiaceae, Cucurbitaceae, Fabaceae, Solanaceae, and Pedaliaceae were mechanically inoculated and pathotypes were identified based on the reaction of a resistant Cucumis melo, accession PI414723. All of the cucurbit species/varieties and Sesamum indicum were systemically infected with all isolates. The nucleotide sequence variability of the coat protein gene ranged from 82 % to 99 % compared to the corresponding sequences of ZYMV isolates from different geographical locations. No recombination event was detected in the coat protein gene of the isolates.

Biological and molecular characterization of Brazilian isolates of Zucchini yellow mosaic virus

Zucchini yellow mosaic virus (ZYMV) causes substantial economic losses in cucurbit crops. Although ZYMV has been present in Brazil for more than 20 years, there is little information about the biological and molecular characteristics of the isolates found in the country. This study aimed to characterize the experimental hosts, pathotypes and genetic diversity of a collection of eleven Brazilian ZYMV isolates within the coat protein gene. For biological analysis, plant species from Amaranthaceae, Chenopodiaceae, Cucurbitaceae, Fabaceae, Solanaceae, and Pedaliaceae were mechanically inoculated and pathotypes were identified based on the reaction of a resistant Cucumis melo, accession PI414723. All of the cucurbit species/varieties and Sesamum indicum were systemically infected with all isolates. The nucleotide sequence variability of the coat protein gene ranged from 82 % to 99 % compared to the corresponding sequences of ZYMV isolates from different geographical locations. No recombination event was detected in the coat protein gene of the isolates.(AU)

Identification of Porcine parvovirus from wild boars by partial sequencing of the VP-2 coding gene / Identificação de parvovírus suíno em javalis a partir do sequenciamento parcial do gene VP-2

Este estudo descreve a detecção e a identificação de DNA de parvovírus suíno (PVS) em amostras de órgãos de dois javalis, por PCR e sequenciamento direcionado ao gene VP-2. Pools de órgãos (baço, rins, fígado, linfonodos e tonsila) de três javalis adultos e assintomáticos de Paraguaçu Paulista, SP, criados com propósitos comerciais, foram submetidos à detecção de PVS, resultando em duas amostras positivas após reações de nested-PCR direcionadas aos genes NS-1 e VP-2. Os fragmentos parciais de VP-2 foram sequenciados e comparados a sequências homólogas de cepas NADL-2 e Kresse, demonstrando identidade nucleotídica de 100%. Com relação a 29 cepas de PVS previamente isoladas no Brasil, o grau de identidade nucleotídica variou de 99 a 100% (uma a três substituições de nucleotídeos). Estes resultados demonstram, pela primeira vez, a detecção direta por PCR de parvovírus suíno em javalis, confirmada por análise de sequenciamento genético.(AU)

Surveillance epidemiological: parvovirus B19 genotype 1 / Vigilância epidemiológica: parvovirus B19 genótipo 1

Human parvovirus B19 was identified and characterized in sample collected from a patient who was infected in Japan, and the symptoms as fever and rash appeared after arriving to Brazil. The occurrence of virus infection was confirmed by both assays: Elisa parvovirus B19-specific IgM antibody detection and polymerase chain reaction (PCR). A fragment of NS1-VP1 region was directly submitted to nucleotide sequencing. Partial phylogenetic analysis of B19 sequences, including several sequences available in GenBank, indicated that the isolated HPV B19 corresponded to genotype 1.

O parvovirus humano B19 foi isolado e caracterizado de amostra clínica de um paciente, infectado no Japão, e que apresentou os sintomas de febre e erupção cutânea após sua chegada ao Brasil. A infecção por parvovírus foi confirmada por meio de seguintes ensaios: Elisa para detecção de anticorpos IgM antiparvovirus B19 e técnica de polymerase chain reaction (PCR). Um fragmento da região NS1-VP1 foi diretamente submetido ao seqüenciamento do nucleotídeo. A análise filogenética parcial do B19, frente às várias seqüências disponíveis no GenBank, indicou que PV B19 isolado correspondeu ao genótipo 1.

Partial molecular characterization of the Nile tilapia (Oreochromis niloticus) alpha-cardiac muscle actin gene and its relationship to actin isoforms of other fish species

An alpha actin gene segment, isolated from Nile tilapia (Oreochromis niloticus), was characterized by nucleotide sequencing, predicted amino acid sequence and Southern blot hybridization. Genomic DNA amplification resulted in a 1063-bp fragment corresponding to a partial alpha-cardiac muscle actin gene containing exons 3 to 6. Southern blot analysis of the restriction-digested DNA revealed that the Nile tilapia genome contains multiple muscle actin isoforms. Although comparison of the nucleotide sequence, amino acid residues and exon-intron organization of the isolated actin gene with those of other vertebrates showed a high level of identity, diagnostic amino acid residues can still be correlated to distinct actin genes in fish species.