Inter- and intracontinental migrations and local differentiation have shaped the contemporary epidemiological landscape of canine parvovirus in South America

Canine parvovirus (CPV) is a fast-evolving single-stranded DNA virus that causes one of the most significant infectious diseasesof dogs. Although the virus dispersed over long distances in the past, current populations are considered to be spatiallyconfined and with only a few instances of migration between specific localities. It is unclear whether these dynamicsoccur in South America where global studies have not been performed. The aim of this study is to analyze the patterns ofgenetic variability in South American CPV populations and explore their evolutionary relationships with global strains.Genomic sequences of sixty-three strains from South America and Europe were generated and analyzed using a phylodynamicapproach. All the obtained strains belong to the CPV-2a lineage and associate with global strains in four monophyleticgroups or clades. European and South American strains from all the countries here analyzed are representative of awidely distributed clade (Eur-I) that emerged in Southern Europe during 1990?98 to later spread to South America in theearly 2000s. The emergence and spread of the Eur-I clade were correlated with a significant rise in the CPV effective populationsize in Europe and South America. The Asia-I clade includes strains from Asia and Uruguay. This clade originated in Asia during the late 1980s and evolved locally before spreading to South America during 2009?10. The third clade (Eur-II)comprises strains from Italy, Brazil, and Ecuador. This clade appears in South America as a consequence of an early introductionfrom Italy to Ecuador in the middle 1980s and has experienced extensive local genetic differentiation. Some strainsfrom Argentina, Uruguay, and Brazil constitute an exclusive South American clade (SA-I) that emerged in Argentina in the1990s. These results indicate that the current epidemiological scenario is a consequence of inter- and intracontinentalmigrations of strains with different geographic and temporal origins that set the conditions for competition and local differentiationof CPV populations. The coexistence and interaction of highly divergent strains are the main responsible for thedrastic epidemiological changes observed in South America in the last two decades. This highlights the threat of invasionfrom external sources and the importance of whole-genome resolution to robustly infer the origin and spread of new CPVvariants. From a taxonomic standpoint, the findings herein show that the classification system that uses a single aminoacid to identify variants (2a, 2b, and 2c) within the CPV-2a lineage does not reflect phylogenetic relationships and is not suitableto analyze CPV evolution. In this regard, the identification of clades or sublineages within circulating CPV strains is thefirst step towards a genetic and evolutionary classification of the virus.Fil: Grecco, Sofia. Universidad de la República; UruguayFil: Iraola, Gregorio. Universidad de la República; UruguayFil: Decaro, Nicola. Università degli Studi di Bari; ItaliaFil: Alfieri, Alice. Universidade Estadual de Londrina; BrasilFil: Alfieri, Amauri. Universidade Estadual de Londrina; BrasilFil: Gallo Calderon, Marina Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Ciencia y Tecnología "Dr. César Milstein". Fundación Pablo Cassará. Instituto de Ciencia y Tecnología "Dr. César Milstein"; ArgentinaFil: da Silva, Ana Paula. Universidade Estadual de Londrina; BrasilFil: Name, Daniela. Universidad de la República. Facultad de Ciencias; UruguayFil: Aldaz, Jaime. Universidad Estatal de Bolivar; EcuadorFil: Calleros, Lucia. Universidad de la República. Facultad de Ciencias; UruguayFil: Marandino, Ana. Universidad de la República. Facultad de Ciencias; UruguayFil: Gonzalo, Tomas. Universidad de la República. Facultad de Ciencias; Urugua

Descifrando el viroma de las abejas melíferas en Uruguay

Involucrado en los episodios de pérdidas de colonias de abejas reportados alrededor del mundo, el ácaro Varroa destructor es la principal amenaza biótica de Apis mellifera. Este parásito obligado se alimenta de los cuerpos grasos de las pupas, reduciendo la vida media de las abejas y transmitiendo diversos virus. Su letalidad lleva a la muerte de las colonias si no son tratadas con acaricidas a tiempo. Sin embargo, en nuestro país existe una población de abejas que sobreviven naturalmente a la parasitación con este ácaro sin necesidad de tratamientos. Este fenómeno podría deberse a la presencia de diferentes cepas o variantes de los virus transmitidos por V. destructor. El objetivo de este trabajo es caracterizar los virus presentes en colonias de A. mellifera sobrevivientes y susceptibles a V. destructor. Para ello se utilizó un protocolo de enriquecimiento de partículas virales puesto a punto en la sección genética y que fue exitoso para analizar abejas. Posteriormente se realizó la secuenciación masiva a partir de muestras de abejas de colonias sobrevivientes y susceptibles a V. destructor. Los resultados permitieron realizar la caracterización genómica de los principales virus de interés apícola: Acute Bee Paralysis Virus, Black Queen Cell Virus, Deformed Wing Virus y Sacbrood Virus y contigs de algunos virus que aún no se habían detectado en nuestro país, como el Lake Sinai virus y el Apis mellifera filamentous virus. Este trabajo nos permitirá estudiar en profundidad los perfiles virales de las colonias sobrevivientes y susceptibles a V. destructor de nuestro país.Agencia Nacional de Investigación e Innovació

Governabilidade estrutural do subsistema natural do Ecossistema Babitonga (Santa Catarina: Brasil)

Editoria

Phylogenetic and genome-wide deep-sequencing analyses of canine parvovirus reveal co-infection with field variants and emergence of a recent recombinant strain.

Canine parvovirus (CPV), a fast-evolving single-stranded DNA virus, comprises three antigenic variants (2a, 2b, and 2c) with different frequencies and genetic variability among countries. The contribution of co-infection and recombination to the genetic variability of CPV is far from being fully elucidated. Here we took advantage of a natural CPV population, recently formed by the convergence of divergent CPV-2c and CPV-2a strains, to study co-infection and recombination. Complete sequences of the viral coding region of CPV-2a and CPV-2c strains from 40 samples were generated and analyzed using phylogenetic tools. Two samples showed co-infection and were further analyzed by deep sequencing. The sequence profile of one of the samples revealed the presence of CPV-2c and CPV-2a strains that differed at 29 nucleotides. The other sample included a minor CPV-2a strain (13.3% of the viral population) and a major recombinant strain (86.7%). The recombinant strain arose from inter-genotypic recombination between CPV-2c and CPV-2a strains within the VP1/VP2 gene boundary. Our findings highlight the importance of deep-sequencing analysis to provide a better understanding of CPV molecular diversity

Deep-sequencing profile of the distinguishing nucleotides between CPV-2a (KM457143) and 364-rec recombinant (KM457139) strains in sample 364.

a<p> The left fragment (NS gene) of the 364-rec strain was derived from a CPV-2c strain, and the right fragment was from a CPV-2a strain.</p>b<p> Coverage: number of times a nucleotide is read during the sequencing process.</p>c<p> The recombination breakpoint in the 364-rec recombinant strain falls in a 117-nt region between two constant parental markers (positions 2433 and 2549).</p>d<p> The difference in the 2907 position corresponds to a single-nucleotide polymorphism in the 2a homologous region of the co-infecting strains.</p><p>Deep-sequencing profile of the distinguishing nucleotides between CPV-2a (KM457143) and 364-rec recombinant (KM457139) strains in sample 364.</p

Deep-sequencing profile of the distinguishing nucleotides between CPV-2a (KM457141) and CPV-2c (KM457142) strains in sample 370.

a<p>Coverage: number of times a nucleotide is read during the sequencing process.</p><p>Deep-sequencing profile of the distinguishing nucleotides between CPV-2a (KM457141) and CPV-2c (KM457142) strains in sample 370.</p

CPV recombination network.

<p>The phylogenetic network was generated from alignment of 42 complete CPV genome sequences. There are two main clades encompassing CPV-2c and CPV-2a strains (circles), and an edge (split) that reveals a possible recombination event involving strain 364-rec (KM457139). The Phi test for recombination was significant at p = 0.003.</p

Uruguayan dog fecal samples used in this study.

a<p> (C) Capital city (Montevideo); (P) Periphery: cities/regions located in or near (within 15 km) the boundary of Montevideo; (I) Interior (remainder of the country). The VP2 gene sequences for some of these strains have been previously reported <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111779#pone.0111779-Maya1" target="_blank">[31]</a>.</p><p>Uruguayan dog fecal samples used in this study.</p

Phylogenetic incongruence analysis.

<p>Phylogenetic reconstructions were performed with non-recombinant fragments of the 4269-bp CPV coding region containing nt 1–2500 (A), and nt 2501–4269 (B). The 364-rec strain (arrowhead) associates with both the CPV-2c (A) and CPV-2a (B) clades. 2a-UY: Uruguayan CPV-2a clade; 2c-UY: Uruguayan CPV-2c clade; FPV-US.06: feline panleukopenia virus (EU659115); MEV-CH.09: mink enteritis virus (FJ592174); CPV2-US.79: Canine parvovirus type 2 (M38245); CPV2a-15 United States 2a isolate (M24003); CPV2a-s5/2010 Chinese 2a isolate (KF638400.1). CPV2c-56/00 Italian 2c isolate. CH: China; US: United States; UY: Uruguay.</p