Szilvia L. Farkas

Taxonomy of the order Mononegavirales: update 2016

In 2016, the order Mononegavirales was emended through the addition of two new families (Mymonaviridae and Sunviridae), the elevation of the paramyxoviral subfamily Pneumovirinae to family status (Pneumoviridae), the addition of five free-floating genera (Anphevirus, Arlivirus, Chengtivirus, Crustavirus, and Wastrivirus), and several other changes at the genus and species levels. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).

Candidate New Rotavirus Species in Sheltered Dogs, Hungary

We identified unusual rotavirus strains in fecal specimens from sheltered dogs in Hungary by viral metagenomics. The novel rotavirus species displayed limited genome sequence homology to representatives of the 8 rotavirus species, A–H, and qualifies as a candidate new rotavirus species that we tentatively named Rotavirus I.

Genomic and phylogenetic analyses of an adenovirus isolated from a corn snake (Elaphe guttata) imply a common origin with members of the proposed new genus Atadenovirus.

Approximately 60% of the genome of an adenovirus isolated from a corn snake (Elaphe guttata) was cloned and sequenced. The results of homology searches showed that the genes of the corn snake adenovirus (SnAdV-1) were closest to their counterparts in members of the recently proposed new genus ATADENOVIRUS: In phylogenetic analyses of the complete hexon and protease genes, SnAdV-1 indeed clustered together with the atadenoviruses. The characteristic features in the genome organization of SnAdV-1 included the presence of a gene homologous to that for protein p32K, the lack of structural proteins V and IX and the absence of homologues of the E1A and E3 regions. These characteristics are in accordance with the genus-defining markers of atadenoviruses. Comparison of the cleavage sites of the viral protease in core protein pVII also confirmed SnAdV-1 as a candidate member of the genus ATADENOVIRUS: Thus, the hypothesis on the possible reptilian origin of atadenoviruses (Harrach, Acta Veterinaria Hungarica 48, 484-490, 2000) seems to be supported. However, the base composition of DNA sequence (>18 kb) determined from the SnAdV-1 genome showed an equilibrated GC content of 51%, which is unusual for an atadenovirus.

First detection and analysis of a fish circovirus

Circoviruses are present worldwide in birds and pigs but their occurrence in fish has not yet been reported. Recently, increased mortality was observed in barbel fry (Barbus barbus) in Hungary. This paper reports the detection of previously unknown circular viral DNA genomes in barbels by the use of a circovirus-specific wide-range nested PCR. The analysis of two complete genomes (Barbel circovirus, BaCV1 and BaCV2) indicated that they belonged into a new genetic group within the family Circoviridae, distinct from known circoviruses and circovirus-like genomes. Their genome size was 1957 bases and contained two major ORFs similar to the capsid and replication-associated protein genes of circoviruses. A connection between the presence of the virus and clinical manifestations of the infection could not be proved.

Zoonotic transmission of reassortant porcine G4P[6] rotaviruses in Hungarian pediatric patients identified sporadically over a 15 year period.

Genotype G4P[6] Rotavirus A (RVA) strains collected from children admitted to hospital with gastroenteritis over a 15 year period in the pre rotavirus vaccine era in Hungary were characterized in this study. Whole genome sequencing and phylogenetic analysis was performed on eight G4P[6] RVA strains. All these RVA strains shared a fairly conservative genomic configuration (G4-P[6]-I1/I5-R1-C1-M1-A1/A8-N1-T1/T7-E1-H1) and showed striking similarities to porcine and porcine-derived human RVA strains collected worldwide, although genetic relatedness to some common human RVA strains was also seen. The resolution of phylogenetic relationship between porcine and human RVA genes was occasionally low, making the evaluation of host species origin of individual genes sometimes difficult. Yet the whole genome constellations and overall phylogenetic analyses indicated that these eight Hungarian G4P[6] RVA strains may have originated by independent zoonotic transmission, probably from pigs. Future surveillance studies of human and animal RVA should go parallel to enable the distinction between direct interspecies transmission events and those that are coupled with reassortment of cognate genes.

Completion of the genome analysis of snake adenovirus type 1, a representative of the reptilian lineage within the novel genus Atadenovirus

Genome sequencing and analysis of snake adenovirus type 1 (SnAdV-1), originating from corn snake, were completed. This is the first full genomic sequence of an adenovirus from reptilian hosts. The presence of characteristic genus-common genes and transcription units, showed that SnAdV-1 shares similar genome organisation with members of the recently established genus Atadenovirus. Three novel open reading frames of yet unknown functions were found. One of these seemed to be related to a putative gene, the so-called 105R that has recently been described from the genome of the tree shrew adenovirus. The other two putative genes were found to be unique for SnAdV-1. On phylogenetic trees, SnAdV-1 clustered within the atadenovirus clade. Thereby the hypothesis on the reptilian origin of atadenoviruses was further strengthened. Interestingly, however, one of the most striking features of atadenoviruses, namely the base content heavily biased towards A+T, is not characteristic for SnAdV-1 having a genome of balanced composition with a G+C value of 50.21%.

Adenovirus and mycoplasma infection in an ornate box turtle (Terrapene ornata ornata) in Hungary

A female, adult ornate box turtle (Terrapene ornata ornata) with fatty liver was submitted for virologic examination in Hungary. Signs of an adenovirus infection including degeneration of the liver cells, enlarged nuclei and intranuclear inclusion bodies were detected by light microscopic examination. The presence of an adenovirus was later confirmed by obtaining partial sequence data from the adenoviral DNA-dependent DNA-polymerase. Phylogenetic analyses revealed that this novel chelonian adenovirus was distinct from previously described reptilian adenoviruses, not belonging to any of the recognized genera of the family Adenoviridae. As a part of the routine diagnostic procedure for chelonians the detection of herpes-, rana- and iridoviruses together with Mycoplasma spp. was attempted. Amplicons were generated by a general mycoplasma polymerase chain reaction (PCR) targeting the 16S/23S ribosomal RNA (rRNA) intergenic spacer region, as well as, a specific Mycoplasma agassizii PCR targeting the 16S rRNA gene. Based on the analyses of partial sequences of the 16S rRNA gene, the Mycoplasma sp. of the ornate box turtle seemed to be identical with the recently described eastern box turtle (Terrapene carolina carolina) Mycoplasma sp. This is the first report of a novel chelonian adenovirus and a mycoplasma infection in an ornate box turtle (T. ornata ornata) in Europe.

One Year Survey of Human Rotavirus Strains Suggests the Emergence of Genotype G12 in Cameroon

In this study the emergence of rotavirus A genotype G12 in children <5 years of age is reported from Cameroon during 2010/2011. A total of 135 human stool samples were P and G genotyped by reverse transcriptase PCR. Six different rotavirus VP7 genotypes were detected, including G1, G2, G3, G8, G9, and G12 in combinations with P[4], P[6] and P[8] VP4 genotypes. Genotype G12 predominated in combination with P[8] (54.1%) and P[6] (10.4%) genotypes followed by G1P[6] (8.2%), G3P[6] (6.7%), G2P[4] (5.9%), G8P[6] (3.7%), G2P[6] (0.7%), G3P[8] (0.7%), and G9P[8] (0.7%). Genotype P[6] strains in combination with various G‐types represented a substantial proportion (N = 44, 32.6%) of the genotyped strains. Partially typed strains included G12P[NT] (2.2%); G3P[NT] (0.7%); G(NT)P[6] (1.5%); and G(NT)P[8] (0.7%). Mixed infections were found in five specimens (3.7%) in several combinations including G1 + G12P[6], G2 + G3P[6] + P[8], G3 + G8P[6], G3 + G12P[6] + P[8], and G12P[6] + P[8]. The approximately 10% relative frequency of G12P[6] strains detected in this study suggests that this strain is emerging in Cameroon and should be monitored carefully as rotavirus vaccine is implemented in this country, as it shares neither G‐ nor P‐type specificity with strains in the RotaTeq® and Rotarix® vaccines. These findings are consistent with other recent reports of the global spread and increasing epidemiologic importance of G12 and P[6] strains. J. Med. Virol. 85:1485–1490, 2013.

Novel NSP4 genotype in a camel G10P[15] rotavirus strain

In this study a Kuwaiti camel rotavirus strain, RVA/Camel-wt/KUW/s21/2010/G10P[15], is characterized by sequencing and phylogenetic analysis. The strain had multiple genes with high nucleotide sequence similarities to ovine and bovine strains (VP2, ≤ 96%; NSP2 and NSP5, ≤ 97%, NSP3, ≤ 94%), or, to porcine strains (VP1, ≤ 89%). Other genes had moderate sequence similarities (VP4, ≤ 87%; VP6, ≤ 81%; VP7, ≤ 82%) with reference strains from ruminants. The NSP4 gene shared limited sequence identity (≤ 71%) with other mammalian and avian rotavirus NSP4 types, and was designated a novel genotype, E15. This study demonstrates genetic diversity in the outer capsid and some backbone genes of an old-world camelid rotavirus strain and uncovers its common evolutionary roots with strains from other ruminants.

Full genome characterization of human Rotavirus A strains isolated in Cameroon, 2010-2011: diverse combinations of the G and P genes and lack of reassortment of the backbone genes.

Over the past few years whole genome sequencing of rotaviruses has become a routine laboratory method in many strain surveillance studies. To study the molecular evolutionary pattern of representative Cameroonian Rotavirus A (RVA) strains, the semiconductor sequencing approach was used following random amplification of genomic RNA. In total, 31 RVA strains collected during 2010-2011 in three Cameroonian study sites located 120 to 1240 km from each other were sequenced and analyzed. Sequence analysis of the randomly selected representative strains showed that 18 RVAs were Wa-like, expressing G1P[6], G12P[6], or G12P[8] neutralization antigens on the genotype 1 genomic constellation (I1-R1-C1-M1-A1-N1-T1-E1-H1), whereas 13 other strains were DS-1-like, expressing G2P[4], G2P[6], G3P[6], and G6P[6] on the genotype 2 genomic constellation (I2-R2-C2-M2-A2-N2-T2-E2-H2). No inter-genogroup reassortment in the backbone genes was observed. Phylogenetic analysis of the Cameroonian G6P[6] strains indicated the separation of the strains identified in the Far North region (Maroua) and the Northwest region (Bamenda and Esu) into two branches that is consistent with multiple introductions of G6P[6] strains into this country. The present whole genome based molecular characterization study indicates that the emerging G6P[6] strain is fully heterotypic to Rotarix, the vaccine introduced during 2014 in childhood immunization program in Cameroon. Continuous strain monitoring is therefore needed in this area and elsewhere to see if G6s, besides genotype G1 to G4, G8, G9 and G12, may become a new, regionally important genotype in the post vaccine licensure era in Africa.