Viral quasispecies profiles as the result of the interplay of competition and cooperation

Viral quasispecies can be regarded as a swarm of genetically related mutants or a quasispecies (QS). A common formalism to approach QS is the replicator-mutator equation (RME). However, a problem with the RME is how to quantify the interaction coefficients between viral variants. Here, this is addressed by adopting an ecological perspective and resorting to the niche theory of competing communities, which assumes that the utilization of resources primarily determines ecological segregation between competing individuals (the different viral variants that constitute the QS). Using this novel combination of RME plus the ecological concept of niche overlapping, for describing QS, we explore the population distributions of viral variants that emerge, as well as the corresponding dynamics. We observe that the population distribution requires very long transients both to A) reach equilibrium and B) to show a clear dominating master sequence. Based on different independent and recent experimental evidence, we find that when some cooperation or facilitation between variants is included in appropriate doses we can solve both A) and B). We show that a useful quantity to calibrate the degree of cooperation is the Shannon entropy. Therefore, in order to get a typical quasispecies profile, it seems that pure competition is not enough. Rather, some degree of cooperation among viral variants is needed. This has several biological implications that might contribute to shed light on the mechanisms operating in QS dynamics and to understand the QS as a whole entity.Comment: 23 pages, 5 figure

Genetic Characterization of a Pigeon Paramyxovirus Type 1 Isolated from Columba livia in Uruguay

The isolation and molecular characterization of pigeon paramyxovirus type 1 (PPMV-1) from a sick racing pigeon in Uruguay is reported for the first time. Hemagglutination inhibition (HI) tests were performed to detect antibodies against avian paramyxovirus serotype 1 (APMV-1), and a HI titer of 1/32 was obtained. Tracheal and cloacal swabs were processed by real-time reverse transcriptionpolymerase chain reaction (rRT-PCR) with the use of the National Veterinary Services LaboratoryU.S. Department of Agriculture validated matrix (M) gene assay and were positive for APMV-1. Viral isolation in embryonated chicken eggs confirmed the molecular detection of the isolate. A fragment corresponding to the 3' region of the fusion (F) protein gene was amplified by RT-PCR, and subsequently sequenced. The deduced amino acid sequence at the F protein cleavage site displayed the motif 112RRQKR/F 117. Phylogenetic analysis of this part of the genome allowed the isolated virus to be grouped in the lineage VIb/4b, which suggests that it shares the same ecologic niche with other PPMV-1 that were found in the region, and it is not imported as other European or North American viruses.Fil: Castro, E. R.. No especifíca;Fil: Zanetti, Flavia Adriana. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Arbiza, Juan. Universidad de la Republica; Urugua

Detection and genotyping of equid herpesvirus 1 in Uruguay

Infection with equid alphaherpesvirus 1 (EHV-1) causes respiratory disease, abortion and neurological disorders in horses. Molecular epidemiology studies have demonstrated that a single nucleotide polymorphism (A2254/G2254) in the genome region of open reading frame 30 which results in an amino acid variation (N752/D752) of the EHV-1 DNA polymerase, is significantly associated with the neuropathogenic potential of naturally occurring strains. In recent years, an increase in the number of cases of equine neurological disease caused by neuropathogenic variants of EHV-1 has been observed in numerous countries. The purpose of this study was to detect the presence of the viral genome of EHV-1 and equid herpesvirus 4 (EHV-4) in the bronchopulmonary lymph nodes of 47 horses from various locations in Uruguay, obtained from a slaughterhouse, and to determine whether the EHV-1 genomes possessed the mutation associated with neuropathogenesis (G2254/D752). The genes encoding glycoprotein H (gH) of EHV-1 and glycoprotein B (gB) of EHV-4 were amplified by a semi-nested polymerase chain reaction. Of the samples analysed, 28% and 6% of lymph nodes contained the genes for gH and gB, respectively. The viral DNA olymerase gene was amplified and sequenced. Twelve of the 13 genomes sequenced presented the nucleotide G2254, while the remaining 1 showed both nucleotides, A2254 and G2254. The results confirm the presence of EHV-1 in Uruguay. Furthermore, there is evidence for the first time of the detection of EHV- 4, and high-frequency detection of the neuropathogenic variant (G2254/D752) of EHV-1 in Uruguay. These findings provide new insights into the epidemiological situation of EHV-1 and EHV-4 in that country

Single Radial Hemolysis assay (SRH) to evaluate immunity protection and factors that affect the immunity level against Equine Influenza Virus infection in horses in Uruguay

El virus de la influenza equina del subtipo H3N8 ha sido considerado como el patógeno respiratorio más importante de los caballos, debido a su naturaleza altamente contagiosa y a su rápida propagación entre animales susceptibles. Se ha demostrado que el grado de protección determinado por las vacunas inactivadas, está estrechamente relacionado con el nivel de anticuerpos circulantes contra la hemaglutinina del virus de Influenza equina. El objetivo del presente trabajo es determinar la susceptibilidad de equinos de deporte en Uruguay a la infección por el virus de influenza equina mediante la cuantificación de anticuerpos SRH (hemólisis radial simple), y estudiar su asociación con factores como la edad, raza, sexo, e historia de vacunación. Se procesaron 1.532 sueros equinos de diferentes razas, sexo y estado de vacunación por la prueba de SRH, pero para el análisis estadístico se utilizaron 1.390 que contaban con la información para todas las variables. Se realizó un análisis univariado para observar el comportamiento de las frecuencias observadas de las pruebas SRH por los factores de riesgo, utilizando la prueba Chi2 de Pearson. Se observó una baja cobertura de vacunación contra la Gripe Equina en los equinos de deporte (23%). Los niveles de protección virológica y clínica obtenidos por el ensayo de SRH fueron bajos (27% y 35% respectivamente).Se comprueba la mayor susceptibilidad a la infección por el virus H3N8, en equinos que no tienen vacunación vigente, en la raza árabe y cuarto de milla, en los equinos menores a 2 años de edad y en los machos castrados.The equine influenza virus subtype H3N8 has been considered the most important respiratory pathogen of horses, due to its highly contagious nature and its rapid spread among susceptible animals. It has been shown that the degree of protection determined by inactivated vaccines, is closely related to the level of circulating antibodies against the virus hemagglutinin Equine influenza. The aim of this study is to determine the susceptibility of sport horses in Uruguay to infection by equine influenza virus by measuring antibodies SRH (single radial hemolysis), and study its association with factors such as age, horse breed, sex, and vaccination history. 1532 equine sera of different horse breed, sex and vaccination status by SRH were processed, and giving missing values only 1390 was considered for the statistical analysis. To observe the behavior of the observed frequencies of the SRH univariate analysis was performed Low coverage of vaccination against Equine Influenza in sport horses was observed (23%) and a very low level of virological and clinical immunity (27% and 35% respectively) against infection of H3N8 virus test determined by SRH test. Increased susceptibility to infection by the H3N8 virus was observed in horses without updated vaccination, Arab and Quarter mile breed horses, horses younger than 2 years old, and in castrated males horses

Seroprevalence and factors that affect the level of seroneutralizing antibodies against EHV-1 in horses in Uruguay

La Rinoneumonitis Equina (RE) es un término que describe un conjunto de enfermedades en caballos que pueden incluir cuadros clínicos respiratorios, aborto, neumonitis neonatal de los potros, o mieloencefalopatía, y está causada por los virus EHV-1 y EHV-4. La distribución de estos agentes se considera mundialmente enzoótica provocando importantes pérdidas económicas especialmente en países con buen desarrollo de la industria hípico-deportiva. En el Uruguay se considera enzoótica desde hace muchos años. El objetivo de este trabajo es estimar la seroprevalencia de EHV-1 en equinos de deporte en el Uruguay y determinar si está asociada con factores como la edad, raza, sexo, y los antecedentes de vacunación. Se colectaron 1517 sueros equinos en el período diciembre 2013 a marzo 2014, reseñando la raza, edad, sexo y registro de vacunación, la totalidad de las muestras fueron procesadas por la prueba de seroneutralización viral, y los resultados fueron estudiados mediante modelo de regresión logística. Se comprueba que el virus EHV-1 se encuentra ampliamente distribuido en la población de equinos de deporte en nuestro país, con una prevalencia estimada del 29% (IC 95% = 27%-31%). Se observa que la presencia de anticuerpos para EHV-1 está asociada a factores como la raza y la vacunación contra RE (p<0,05).Equine herpesvirus 1 (EHV-1) infection causes disease in horses and extensive economic losses associated with outbreaks of respiratory disease, abortion, neonatal foal death, and myeloencephalopathy, with worldwide distribution and probably are endemic in Uruguay. The objective of this research is to consider the seroprevalence of EHV-1 in horses in Uruguay and to determine if it is associated with factors like the age, breed, sex, and the vaccination antecedents. A total of 1517 serum samples were selected from December 2013 to March 2014. The data registered were the breed, age, sex and vaccination history. All samples were processed by the seroneutralization test and the results obtained were statistically analyzed by a logistic regression model. It is verified that the EHV-1 is widely distributed in the horse population in Uruguay, whose estimated prevalence is of 29% (IC 95%= 27%-31%). The presence of positive serology for EHV-1 was associated to factors like the breed and the vaccination against EHV-1 (p<0.05)

PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes

We have developed a web tool, PupaSuite, for the selection of single nucleotide polymorphisms (SNPs) with potential phenotypic effect, specifically oriented to help in the design of large-scale genotyping projects. PupaSuite uses a collection of data on SNPs from heterogeneous sources and a large number of pre-calculated predictions to offer a flexible and intuitive interface for selecting an optimal set of SNPs. It improves the functionality of PupaSNP and PupasView programs and implements new facilities such as the analysis of user's data to derive haplotypes with functional information. A new estimator of putative effect of polymorphisms has been included that uses evolutionary information. Also SNPeffect database predictions have been included. The PupaSuite web interface is accessible through and through

Complete genome sequence of Hepatitis E Virus Genotype 3 obtained from a chronically infected individual in Uruguay

Hepatitis E virus (HEV) is a leading cause of acute viral hepatitis worldwide. We report the full-length genome sequence of an HEV-3 strain obtained from a chronically infected patient from Uruguay. This strain shared only 86% nucleotide sequence identity with the most closely related reference strain belonging to subtype 3m.CSIC: I+D 2018 number 24

Genetic analysis of porcine circovirus type 2 from pigs affected with PMWS in Chile reveals intergenotypic recombination

Background: Porcine circovirus type 2 (PCV2) is a very small, non-enveloped and icosahedral virus, with circular single stranded DNA genome. This virus is the most ubiquitous and persistent pathogen currently affecting the swine industry worldwide. PCV2 has been implicated as the major causative agent of postweaning multisystemic wasting syndrome (PMWS), a disease which is characterized by severe immunosuppressive effects in the porcine host. Worldwide PCV2 isolates have been classified into four different genotypes, PCV2a, PCV2b, PCV2c and PCVd. The goal of this work was to conduct the first phylogenetic analysis of PCV2 in Chile. Methods: PCV2 partial ORF2 sequences (462 nt) obtained from 29 clinical cases of PMWS in 22 Chilean intensive swine farms, covering over the 90% of the local pork-production, were analyzed. Results: 14% and 52% of sequences belonged to the genotypes PCV2a and PCV2b, respectively. Surprisingly, 34% of sequences were PCV2a/PCV2d recombinant viruses. Conclusions: Our findings suggested that a novel cluster of Chilean sequences emerged resulting from intergenotypic recombination between PCV2a and PCV2d