Evolutionary Dynamics of Mexican Lineage H5N2 Avian Influenza Viruses.

We have demonstrated for the first time a comprehensive evolutionary analysis of the Mexican lineage H5N2 avian influenza virus (AIV) using complete genome sequences (n = 189), from its first isolation in 1993 until 2019. Our study showed that the Mexican lineage H5N2 AIV originated from the North American wild bird gene pool viruses around 1990 and is currently circulating in poultry populations of Mexico, the Dominican Republic, and Taiwan. Since the implementation of vaccination in 1995, the highly pathogenic AIV (HPAIV) H5N2 virus was eradicated from Mexican poultry in mid-1995. However, the low pathogenic AIV (LPAIV) H5N2 virus has continued to circulate in domestic poultry populations in Mexico, eventually evolving into five distinct clades. In the current study, we demonstrate that the evolution of Mexican lineage H5N2 AIVs involves gene reassortments and mutations gained over time. The current circulating Mexican lineage H5N2 AIVs are classified as LPAIV based on the amino acid sequences of the hemagglutinin (HA) protein cleavage site motif as well as the results of the intravenous pathogenicity index (IVPI). The immune pressure from vaccinations most likely has played a significant role in the positive selection of antigenic drift mutants within the Mexican H5N2 AIVs. Most of the identified substitutions in these viruses are located on the critical antigenic residues of the HA protein and as a result, might have contributed to vaccine failures. This study highlights and stresses the need for vaccine updates while emphasizing the importance of continued molecular monitoring of the HA protein for its antigenic changes compared to the vaccines used.

Suppressive treatment with monepantel and the fast selection for phenotypically resistant trichostrongylids of sheep.

Gastrointestinal parasite control has been a major challenge to livestock due to the failure of anthelmintic treatments. Monepantel (MNT) was introduced in 2009 as an alternative treatment option showing a new mechanism of action against nematode parasites. To study the response of MNT in a suppressive regime, 45-Suffolk and White Dorper naturally infected sheep were divided into one of three groups, G1: control ­ with no treatment, G2: MNT at 2.5 mg kg−1 live weight (LW) PO every 30 days, and G3: MNT at 4.0 mg kgLW−1 PO every 30 days for 6 months. Every 15 days, the animals were individually weighed (body weight, BW) and checked for Famacha (FMC) and body condition score (BCS). The efficacy of MNT was evaluated weekly by fecal egg count (FEC) every month. FEC showed >97% efficacy at the start of the experiment, revealing a significant reduction for G2 (28%) and G3 (39%) in the following months. There was no treatment, BW or BCS effect between treatments; however, there was a period (P < 0.0001) and a treatment vs period interaction (P < 0.0001) for BW. The data revealed that MNT at a therapeutic and suppressive dose had a non-linear polynomial efficacy regression (R2) of 0.988 and 0.992, respectively. This original experiment demonstrates how short-interval and suppressive MNT treatments would rapidly select Haemonchus contortus, showing a fast susceptible-resistance phenotypic population replacement. Therefore, it is suggested that MNT might be carefully used in parasite control programmes alongside other management strategies (i.e. FMC, BCS) to reduce treatment frequency and the selection process for resistance.

Effect of calcium addition to aerobic granular sludge systems under high (conventional SBR) and low (simultaneous fill/draw SBR) selection pressure.

This paper investigated the effect of calcium addition on the formation and properties of aerobic granules under high (conventional SBR) and low (simultaneous fill/draw SBR) selection pressure. Additionally, the simultaneous removal of carbon, nitrogen, and phosphorus, and the operational stability were assessed. The conventional SBRs showed earlier granule development (20 days) than the simultaneous fill/draw SBRs. The effect of calcium on granulation was more accentuated in conventional SBRs, forming larger granules in a shorter interval of time due to the higher EPS production. Additionally, higher amounts of calcium were found in the EPS matrix, mainly during the formation of granules. The operation regime and the addition of calcium did not affect the removal of carbon, nitrogen, and phosphorus. However, they both influenced the granulation time, settleability characteristics, size, and granule composition.

Phylogenetic and evolutionary analysis of HoBi-like pestivirus: Insights into origin and dispersal.

The HoBi-like pestivirus (HoBiPeV), currently classified as Pestivirus H species, is a pathogen associated with a broad spectrum of clinical manifestations in ruminants, particularly in cattle. Since HoBiPeV complete genome sequencing data is scarce, in the present study we described five nearly complete new Brazilian HoBiPeV genomes and further perform a more complete genetic and evolutionary characterization with all additional genome sequences available in the GenBank database. Entropy and selection pressure analysis showed the E2 gene, a surface glycoprotein, is the most variable gene, which also displays the greatest number of sites under positive selection. Phylogenetic and Bayesian inference based on complete genome and Npro gene, respectively, from all HoBiPeV sequences available so far, confirms the existence of three main clades (a, b, and c). The abovementioned analysis suggests that this pestivirus species probably emerged in Asia and spread to different regions including Brazil, where only strains belonging to specific genetic group 'a' have been found. The hypothesis of the HoBiPeV introduction in Brazil (between 1,890 and 1,962), formulated based on Bayesian inference, coincides with a period of intensive importation of water buffalo (Bubalus arnee) and indicine cattle (Bos taurus indicus) from Asia to Brazil, suggesting that this could be the origin of the current Brazilian HoBiPeV genetic group 'a'.

Positive selection pressure on E2 protein of classical swine fever virus drives variations in virulence, pathogenesis and antigenicity: Implication for epidemiological surveillance in endemic areas.

Classical swine fever (CSF), caused by CSF virus (CSFV), is considered one of the most important infectious diseases with devasting consequences for the pig industry. Recent reports describe the emergence of new CSFV strains resulting from the action of positive selection pressure, due mainly to the bottleneck effect generated by ineffective vaccination. Even though a decrease in the genetic diversity of the positively selected CSFV strains has been observed by several research groups, there is little information about the effect of this selective force on the virulence degree, antigenicity and pathogenicity of this type of strains. Hence, the aim of the current study was to determine the effect of the positive selection pressure on these three parameters of CSFV strains, emerged as result of the bottleneck effects induced by improper vaccination in a CSF-endemic area. Moreover, the effect of the positively selected strains on the epidemiological surveillance system was assessed. By the combination of in vitro, in vivo and immunoinformatic approaches, we revealed that the action of the positive selection pressure induces a decrease in virulence and alteration in pathogenicity and antigenicity. However, we also noted that the evolutionary process of CSFV, especially in segregated microenvironments, could contribute to the gain-fitness event, restoring the highly virulent pattern of the circulating strains. Besides, we denoted that the presence of low virulent strains selected by bottleneck effect after inefficient vaccination can lead to a relevant challenge for the epidemiological surveillance of CSF, contributing to under-reports of the disease, favouring the perpetuation of the virus in the field. In this study, B-cell and CTL epitopes on the E2 3D-structure model were also identified. Thus, the current study provides novel and significant insights into variation in virulence, pathogenesis and antigenicity experienced by CSFV strains after the positive selection pressure effect.

Identifying signatures of recent selection in Holstein cattle in the Tropic / Identificación de señales de selección reciente en ganado Holstein en el trópico / Identificação de sinais de seleção recente no gado Holandês no trópico

Abstract Background: Holstein cattle have undergone strong selection processes in the world. These selection signatures can be recognized and utilized to identify regions of the genome that are important for milk yield. Objective: To identify recent selection signatures in Holstein from the Province of Antioquia (Colombia), using the integrated haplotype score (iHS) methodology. Methods: Blood or semen was extracted from 150 animals with a commercial kit. The animals were genotyped with the BovineLD chip (6909 SNPs). The editing process was carried out while preserving the loci whose minor allele frequency (MAF) was greater than 0.05. In addition, genotypes with Mendelian errors were discarded using R and PLINK v1.07 software programs. Furthermore, the extended haplotype homozygosity (EHH), iHS and the p-value were determined with the "rehh" package of R language. Results: The minor allele frequencies showed a tendency toward intermediate frequency alleles. In total, 144 focal markers were significant (p<0.001) for selection signatures. Some chromosomes showed a greater number of signatures than others. Many of the variants were found inside genes, although they were in intronic regions. Some important regions were associated with genes TRAPPC12, PANK3, ZNF16, OPLA and DPYSL4, which are related with cellular transport, excretion or metabolism. Conclusion: Identifying signatures of selection using the iHS method made it possible to determine some important regions for selection in Holstein cattle in the high tropics, some of which had been previously reported to be associated with quantitative traits loci (QTLs).

Resumen Antecedentes: El ganado Holstein ha sido sometido a procesos fuertes de selección en el mundo. Estas señales de selección pueden ser reconocidas y utilizadas para identificar regiones del genoma importantes para la producción de leche. Objetivo: Identificar señales de selección recientes en ganado Holstein de la Provincia de Antioquia (Colombia), mediante la metodología de puntaje haplotípico integrado (iHS). Métodos: A 150 animales se les extrajo DNA de sangre o semen mediante un kit comercial y posteriormente se genotiparon los animales con el chip BovineLD (6909 SNPs). Se realizó edición conservando los loci con frecuencia del alelo menor (MAF) superior a 0,05. Además, se descartaron los genotipos con errores mendelianos, usando el software R y PLINK v1.07. La determinación de la homocigosidad haplotípica extendida (EHH), iHS y el valor p se realizó utilizando el paquete "rehh" de R. Resultados: Las frecuencias del alelo menor mostraron una tendencia hacia alelos de frecuencias intermedias. En total, 144 marcadores focales fueron significativos (p<0,001) para las señales de selección. Algunos cromosomas presentaron mayor número de señales de selección que otros. Muchas de las variantes focales se encontraron al interior de genes, aunque comúnmente en regiones intrónicas. Algunas de las regiones importantes estuvieron asociadas con genes como TRAPPC12, PANK3, ZNF16, OPLA y DPYSL4 que en general se encuentran asociados con funciones relacionadas con el transporte, excreción o metabolismo celular. Conclusión: La identificación de señales de selección usando el método iHS permitió determinar algunas regiones importantes para la selección en ganado Holstein del trópico alto, algunas de las cuales han sido previamente reportadas por su asociación a loci de características cuantitativas (QTLs).

Resumo Antecedentes: O gado holandês tem sido objeto de processos de seleção fortes no mundo. Estes sinais de seleção podem ser reconhecidos e utilizados para identificar regiões do genoma importantes para a produção de leite. Objetivo: Identificar sinais de seleção recente em gado Holandês de la Província de Antioquia (Colômbia), através da metodologia de pontuação haplotípica integrada (iHS). Métodos: Foram usados 150 animais para a extração de DNA a partir de sangre ou sêmen usando kit comercial, os animais foram posteriormente genotipados com o chip BovineLD (6909 SNPs). A edição foi feita mantendo os loci com frequência do alelo menor (MAF) de 0,05; além disso, genótipos com erros mendelianos foram descartados usando o programa R e PLINK v1.07. A determinação da homozigosidade haplotípica estendida (EHH), iHS e valor p foi realizada utilizando o pacote estatístico R "reeh". Resultados: As frequências do alelo menor mostraram uma tendência inclinada a frequências intermédias. No total, 144 marcadores focais foram significativos (p<0,001) para os sinais de seleção. Alguns cromossomos apresentaram mais numero de sinais de seleção que outros. Muitas dos variantes focais foram encontradas dentro dos genes, embora comumente em regiões intrônicas. Algumas das regiões importantes foram associadas com genes como TRAPPC12, PANK3, ZNF16, OPLA e DPYSL4 que geralmente estão associadas a funções relacionadas com o transporte, a excreção ou metabolismo celular. Conclusão: A identificação de sinais de seleção usando o método iHS permitiu determinar algumas regiões importantes para a seleção no gado holandês do tropico alto, algumas destas regiões foram previamente relatados por sua associação com loci de características quantitativas (QTLs).

ESTABLECIMIENTO DE UN SISTEMA DE SELECCIÓN IN VITRO DE VARIEDADES VENEZOLANAS DE ARROZ (Oryza sativa L.) RESISTENTES AL HONGO Pyricularia grisea / Establishment of an in vitro Selection of Venezuelan Cultivars of Rice (Oryza sativa L.) Resistant to the Fungus Pyricularia grisea

RESUMEN. El arroz, luego del trigo, es el cereal más importante del mundo, sin embargo, es susceptible al ataque de numerosos patógenos, siendo Pyricularia grisea, el más dañino. Este trabajo estableció un sistema de selección in vitro de variedades venezolanas a P. grisea, optimizando el sistema de regeneración por embriogénesis somática (inducción, regeneración y estrés por desecación), sometiendo el callo embriogénico (E) a presión de selección del filtrado crudo "FC" a través de cambios a la misma concentración "MC" o por incrementos progresivos en la concentración "IPC", obteniendo plantas tolerantes al fitopatógeno. El máximo porcentaje de inducción de callo embriogénico oscilo entre 30-65 %, en las cuatro variedades (Araure-4 y Venezuela 21: 1 mg.L-1 + 2 mg.L-1 K; Cimarrón: 3 mg.L-1 + 2 mg.L-1 K; Centauro: 1 mg.L-1 + 2 mg.L-1 BAP), mientras que la regeneración estuvo entre 44 y 52 % con 0.5 mg.L-1 + 2 mg.L-1 BAP a 48 h de desecación para Centauro y 24 h para las otras tres variedades. La frecuencia regenerativa de los callos E disminuyo a medida que se incrementó la concentración del FC, independientemente del método de presión selectiva. El promedio de plantas diferenciada por variedad, dependió del método de presión usado, siendo el sistema IPC (25 % para Centauro y 50 % para las otras tres variedades) el que mostro los resultados más favorables, evidenciándose que para las condiciones de los sistemas selectivos de FC evaluados, la resistencia expresada a nivel de planta in vivo no corresponde a la encontrada in vitro.

ABSTRACT. Rice after wheat is the most important cereal in the world, however, it is susceptible to attack by many pathogens, which Pyricularia grisea being the most harmful. In the current study we established an in-vitro selection system of P. grisea on Venezuelan rice varieties. A somatic embryogenesis regeneration system was optimized (induction, regeneration and desiccation) to expose embryogenic callus (E) to crude filtrate "CF" selection pressure through changes at the same concentration "SC" or progressive concentration increments " PIC "of P. grisea, and thus obtain plants tolerant to the pathogen. The maximum percentage of embryogenic callus induction ranged between 30-65 % in the four varieties (Araure-4 and Venezuela- 21: 1 mg.L-1 + 2 mg.L-1 K; Cimarron: 3 mg.L-1 mg.L-1 + 2 K; Centauro: 1 mg.L-1 + 2 mg.L-1 BAP) while regeneration was between 44 and 52 % with 0.5 mg.L-1 + 2 mg.L- 1 BAP 48 h of desiccation for Centauro and 24 h for the other three varieties. The regeneration frequency of embryogenic callus decreased as the concentration of FC increased, regardless of the method of selective pressure. The average differentiated plants per variety, depended on the pressure method used, with the PIC system being the most favorable (25 % for Centauro and 50 % for the other three varieties). The result demonstrated, to resistance expressed for plants in vivo does not correspond to the in vitro conditions

Effect of particulate organic substrate on aerobic granulation and operating conditions of sequencing batch reactors.

The formation and application of aerobic granules for the treatment of real wastewaters still remains challenging. The high fraction of particulate organic matter (XS) present in real wastewaters can affect the granulation process. The present study aims at understanding to what extent the presence of XS affects the granule formation and the quality of the treated effluent. A second objective was to evaluate how the operating conditions of an aerobic granular sludge (AGS) reactor must be adapted to overcome the effects of the presence of XS. Two reactors fed with synthetic wastewaters were operated in absence (R1) or presence (R2) of starch as proxy for XS. Different operating conditions were evaluated. Our results indicated that the presence of XS in the wastewater reduces the kinetic of granule formation. After 52 d of operation, the fraction of granules reached only 21% in R2, while in R1 this fraction was of 54%. The granules grown in presence of XS had irregular and filamentous outgrowths in the surface, which affected the settleability of the biomass and therefore the quality of the effluent. An extension of the anaerobic phase in R2 led to the formation of more compact granules with a better settling ability. A high fraction of granules was obtained in both reactors after an increase of the selection pressure for fast-settling biomass, but the quality of the effluent remained low. Operating the reactors in a simultaneous fill-and-draw mode at a low selection pressure for fast-settling biomass showed to be beneficial for substrate removal efficiency and for suppressing filamentous overgrowth. Average removal efficiencies for total COD, soluble COD, ammonium, and phosphate were 87 ± 4%, 95 ± 1%, 92 ± 10%, and 87 ± 12% for R1, and 72 ± 12%, 86 ± 5%, 71 ± 12%, and 77 ± 11% for R2, respectively. Overall our study demonstrates that the operating conditions of AGS reactors must be adapted according to the wastewater composition. When treating effluents that contain XS, the selection pressure should be significantly reduced.

Genetic variability in G2 and F2 region between biological clones of human respiratory syncytial virus with or without host immune selection pressure

Human respiratory syncytial virus (HRSV) is an important respiratory pathogens among children between zero-five years old. Host immunity and viral genetic variability are important factors that can make vaccine production difficult. In this work, differences between biological clones of HRSV were detected in clinical samples in the absence and presence of serum collected from children in the convalescent phase of the illness and from their biological mothers. Viral clones were selected by plaque assay in the absence and presence of serum and nucleotide sequences of the G2 and F2 genes of HRSV biological clones were compared. One non-synonymous mutation was found in the F gene (Ile5Asn) in one clone of an HRSV-B sample and one non-synonymous mutation was found in the G gene (Ser291Pro) in four clones of the same HRSV-B sample. Only one of these clones was obtained after treatment with the child's serum. In addition, some synonymous mutations were determined in two clones of the HRSV-A samples. In conclusion, it is possible that minor sequences could be selected by host antibodies contributing to the HRSV evolutionary process, hampering the development of an effective vaccine, since we verify the same codon alteration in absence and presence of human sera in individual clones of BR-85 sample.

Development of physiological resistance and its stage specificity in Culex quinquefasciatus after selection with deltamethrin in Assam, India

The study investigated the development and stage specificity of physiological resistance to insecticides in a colony of Culex quinquefasciatus Say (Diptera: Culicidae) mosquitoes, which are vectors of bancroftian filariasis in India, after selection with deltamethrin. Resistance was selected by exposing the larvae to the concentration of deltamethrin that caused 50 percent mortality in the tested population (i.e., LC50). Under continuous selection pressure, the LC50 increased steadily in subsequent generations. The estimated LC50 for the F0 generation was 0.409 μg/L; the LC50 first displayed a substantial increase in the F5 generation (5.616 μg/L) and reached 121.902 μg/L in the F10 generation. The objective of this study was to establish a deltamethrin-resistant colony to develop a research programme that will study the evolution of physiological resistance patterns and stage-specific resistance responses in Cx. quinquefasciatus larvae and adults under laboratory conditions. An approximately 298-fold increase in resistance was recorded after 10 generations, as evidenced by the resistance ratio (RR50). The progress and effect of the selection pressure in the adult stage was monitored with the World Health Organisation (WHO) diagnostic test. The mortality, as observed using the WHO diagnostic test, declined significantly from the F5 generation (85 percent) onwards and the highest rate of survival (65 percent) was observed in the F10 generation.