A novel group of avian astroviruses from Neotropical passerine birds broaden the diversity and host range of Astroviridae.

Metagenomics is helping to expand the known diversity of viruses, especially of those with poorly studied hosts in remote areas. The Neotropical region harbors a considerable diversity of avian species that may play a role as both host and short-distance vectors of unknown viruses. Viral metagenomics of cloacal swabs from 50 Neotropical birds collected in French Guiana revealed the presence of four complete astrovirus genomes. They constitute an early diverging novel monophyletic clade within the Avastrovirus phylogeny, representing a putative new astrovirus species (provisionally designated as Avastrovirus 5) according to the International Committee on Taxonomy of Viruses (ICTV) classification criteria. Their genomic organization shares some characteristics with Avastrovirus but also with Mamastrovirus. The pan-astrovirus RT-PCR analysis of the cloacal samples of 406 wild Neotropical birds showed a community-level prevalence of 4.9% (5.1% in passerines, the highest described so far in this order of birds). By screening birds of a remote region, we expanded the known host range of astroviruses to the avian families Cardinalidae, Conopophagidae, Furnariidae, Thamnophilidae, Turdidae and Tyrannidae. Our results provide important first insights into the unexplored viral communities, the ecology, epidemiology and features of host-pathogen interactions that shape the evolution of avastroviruses in a remote Neotropical rainforest.

A Gene Constellation in Avian Influenza A (H7N9) Viruses May Have Facilitated the Fifth Wave Outbreak in China.

The 2016-2017 epidemic of influenza A (H7N9) virus in China prompted concern that a genetic change may underlie increased virulence. Based on an evolutionary analysis of H7N9 viruses from all five outbreak waves, we find that additional subclades of the H7 and N9 genes have emerged. Our analysis indicates that H7N9 viruses inherited NP genes from co-circulating H7N9 instead of H9N2 viruses. Genotypic diversity among H7N9 viruses increased following wave I, peaked during wave III, and rapidly deceased thereafter with minimal diversity in wave V, suggesting that the viruses entered a relatively stable evolutionary stage. The ZJ11 genotype caused the majority of human infections in wave V. We suggest that the largest outbreak of wave V may be due to a constellation of genes rather than a single mutation. Therefore, continuous surveillance is necessary to minimize the threat of H7N9 viruses.

Phylogenetic analysis of ORF5 and ORF7 of porcine reproductive and respiratory syndrome (PRRS) virus and the frequency of wild-type PRRS virus in México.

Porcine reproductive and respiratory syndrome (PRRS) is caused by a genetically diverse RNA virus and is an economically significant disease in the swine industry. In this study, a total of 8,126 serum samples were obtained from 275 technified and semi-technified farms belonging to 30 of the 32 states of Mexico and representative of the eight regions of the country. Anti-PRRSv antibodies against the PRRS vaccine and an isolated wild Mexican virus were tested by ELISA. Antibodies were found in 15%-49% of the tested sera, with 2.4%-9.8% against the vaccine and 7.7%-26% against the wild virus. The PRRSv virus was detected by RT-PCR in 77 of the 1,630 pooled samples tested, representing seven of the eight geographic regions into which the Mexican Republic is divided. The complete sequences of open reading frames 5 and 7 from 20 PRRSv-positive samples were determined. The analysis of the sequences together with the previously published sequences of historic strains revealed that all the strains belonged to the one, five and eight lineages of the PRRSV2. Striking differences, particularly in ORF5 and ORF7, were found between sequences of the strains and the reference virus, due to insertions and substitutions in positions that play key roles in the recognition, structure and function of the virus. Overall, these results established the magnitude of PRRS virus genetic diversity, and the most frequent virus strain that predominates in Mexico. The PRRSV2 is presented in the porcine population of Mexico; the circulating strains have important changes in ORF5 and ORF7, which probably explain the results obtained in the serological analysis of the wild virus and vaccine strains.

Identification and Characterization of Citrus Chlorotic Spot Virus, a New Dichorhavirus Associated with Citrus Leprosis-Like Symptoms.

Local chlorotic spots resembling early lesions characteristic of citrus leprosis (CL) were observed in leaves of two sweet orange (Citrus sinensis L.) trees in Teresina, State of Piauí, Brazil, in early 2017. However, despite the similarities, these spots were generally larger than those of a typical CL and showed rare or no necrosis symptoms. In symptomatic tissues, transmission electron microscopy revealed the presence of viroplasms in the nuclei of the infected parenchymal cells and rod-shaped particles with an average size of approximately 40 × 100 nm, resembling those typically observed during infection by dichorhaviruses. A bipartite genome of the putative novel virus, tentatively named citrus chlorotic spot virus (CiCSV) (RNA1 = 6,518 nucleotides [nt] and RNA2 = 5,987 nt), revealed the highest nucleotide sequence identity values with the dichorhaviruses coffee ringspot virus strain Lavras (73.8%), citrus leprosis virus N strain Ibi1 (58.6%), and orchid fleck virus strain So (56.9%). In addition to citrus, CiCSV was also found in local chlorotic lesions on leaves of the ornamental plant beach hibiscus (Talipariti tiliaceum (L.) Fryxell). Morphological characterization of mites recovered from the infected plants revealed at least two different types of Brevipalpus. One of them corresponds to Brevipalpus yothersi. The other is slightly different from B. yothersi mites but comprises traits that possibly place it as another species. A mix of the two mite types collected on beach hibiscus successfully transmitted CiCSV to arabidopsis plants but additional work is required to verify whether both types of flat mite may act as viral vectors. The current study reveals a newly described dichorhavirus associated with a citrus disease in the northeastern region of Brazil.

Genetic relatedness of dengue viruses in Key West, Florida, USA, 2009-2010.

Sequencing of dengue virus type 1 (DENV-1) strains isolated in Key West/Monroe County, Florida, indicate endemic transmission for >2 years of a distinct and predominant sublineage of the American-African genotype. DENV-1 strains isolated elsewhere in Florida grouped within a separate Central American lineage. Findings indicate endemic transmission of DENV into the continental United States.

Characterization of an influenza A virus in Mexican swine that is related to the A/H1N1/2009 pandemic clade.

In the spring of 2009, swine-origin influenza H1N1pdm09 viruses caused the first influenza pandemic of this century. We characterized the influenza viruses that circulated early during the outbreak in Mexico, including one newly sequenced swine H1N1pdm09 virus and three newly sequenced human H1N1pdm09 viruses that circulated in the outbreak of respiratory disease in La Gloria, Veracruz. Phylogenetic analysis revealed that the swine isolate (A/swine/Mexico/4/2009) collected in April 2009 is positioned in a branch that is basal to the rest of the H1N1pdm09 clade in two (NP and PA) of the eight single-gene trees. In addition, the concatenated HA-NA and the complete whole-genome trees also showed a basal position for A/swine/Mexico/4/2009. Furthermore, this swine virus was found to share molecular traits with non-H1N1pdm09 H1N1 viral lineages. These results suggest that this isolate could potentially be the first one detected from a sister lineage closely related to the H1N1pdm09 viruses.

Analysis of oropouche virus L protein amino acid sequence showed the presence of an additional conserved region that could harbour an important role for the polymerase activity.

We described here the complete nucleotide sequence of the L RNA segment of Oropouche virus (genus Orthobunyavirus, family Bunyaviridae). We found the L RNA segment is 6846 nucleotides long and encodes a putative RNA polymerase of 2250 amino acids. Phylogenetic analysis showed that ORO virus cluster to the Orthobunyavirus genus confirming the serological classification. It also showed that Bunyamwera and California viruses, from the Orthobunyavirus genus, are more closely related to each other than to ORO virus. Sequence comparisons performed between the L proteins of 15 bunyaviruses and the PB1 proteins of 3 influenza viruses revealed that ORO L protein contains the 3 regions characteristic of arenaviruses and bunyaviruses. These comparisons also showed the existence of an additional fourth conserved region in the L protein of bunyaviruses that contains at least two active sites.

Molecular characterization of strains of Human herpesvirus 8 from Japan, Argentina and Kuwait.

Current genotyping systems for Human herpesvirus 8 (HHV-8) are based on the highly variable gene encoding the K1 glycoprotein. Most strains collected worldwide cluster into two subtypes (I/A and II/C). Sequenced African strains have belonged to subtypes I/A and IV/B. Members of all three of these subtypes can have either the M or P allele at the right-hand side (RHS) of the genome. Strains obtained predominantly from aboriginal or relatively isolated populations have formed clades that branch at a distance from subtypes I/A and II/C, all being of the RHS P allele. The characterization is reported here of 16 Japanese, two Kuwaiti and five Argentine HHV-8 strains obtained from human immunodeficiency virus-infected and non-infected patients with Kaposi's sarcoma (KS), primary effusion lymphoma, multicentric Castleman's disease or renal transplants. K1 sequences of five Japanese, one Kuwaiti and two Argentine strains were identified as subtype I/A and eight Japanese, one Kuwaiti and three Argentine strains were subtype II/C. Three strains from elderly classic KS patients originally from Hokkaido, a northern Japanese island, were relatively closely related to strains of subtypes III/D and E. Consistent with previous observations, both the M and P alleles were identified at the RHS of subgroup I/A and II/C genomes; only the P allele was detected among the three Hokkaido strains. Distances among the Hokkaido strains were similar to the distance between subtypes I/A and II/C, suggesting that the Hokkaido strains may represent two distinct subtypes and that, as more strains are analysed, the currently recognized III/D subgroups will probably emerge as independent subtypes.