Genotypic and phenotypic characterisation of RP2- and RPGR-associated X-linked inherited retinal dystrophy, including female manifestations

BACKGROUND

With the promise of gene replacement therapy, eligible males and females with X-linked inherited retinal dystrophy (XL-IRD) should be identified.

METHODS

Retrospective observational cohort study to establish the phenotypic and genotypic spectrum of XL-IRD within New Zealand (NZ). Thirty-two probands, including 9 females, with molecularly proven XL-IRD due to RP2 or RPGR mutations, and 72 family members, of which 43 were affected, were identified from the NZ IRD Database. Comprehensive ophthalmic phenotyping, familial cosegregation, genotyping, and bioinformatics were undertaken. Main outcome measures were: RP2 and RPGR pathogenic variant spectrum, phenotype in males and females (symptoms, age of onset, visual acuity, refraction, electrophysiology, autofluorescence, retinal appearance), and genotype-phenotype correlation.

RESULTS

For 32 families, 26 unique pathogenic variants were identified; in RP2 (n = 6, 21.9% of all families), RPGR exons 1-14 (n = 10, 43.75%), and RPGR-ORF15 (n = 10, 34.3%). Three RP2 and 8 RPGR exons 1-14 variants are novel, rare, and cosegregate. Thirty-one percent of carrier females were significantly affected, with 18.5% of families initially classified as autosomal dominant. Of five Polynesian families, 80% had novel disease-causing variants. One Māori family showed keratoconus segregating with an ORF15 variant.

CONCLUSIONS

Significant disease was present in 31% of genetically proven female carriers, often leading to an erroneous presumption of the inheritance pattern. Pathogenic variants in 44% of the families were in exon 1-14 of RPGR, more frequent than usually described, which may inform the gene testing algorithm. Proving cosegregation in families for novel variants and identifying affected females and males translates to optimised clinical care and potential for gene therapy.

Circular replication-associated protein encoding DNA viruses identified in the faecal matter of various animals in New Zealand

In recent years, innovations in molecular techniques and sequencing technologies have resulted in a rapid expansion in the number of known viral sequences, in particular those with circular replication-associated protein (Rep)-encoding single-stranded (CRESS) DNA genomes. CRESS DNA viruses are present in the virome of many ecosystems and are known to infect a wide range of organisms. A large number of the recently identified CRESS DNA viruses cannot be classified into any known viral families, indicating that the current view of CRESS DNA viral sequence space is greatly underestimated. Animal faecal matter has proven to be a particularly useful source for sampling CRESS DNA viruses in an ecosystem, as it is cost-effective and non-invasive. In this study a viral metagenomic approach was used to explore the diversity of CRESS DNA viruses present in the faeces of domesticated and wild animals in New Zealand. Thirty-eight complete CRESS DNA viral genomes and two circular molecules (that may be defective molecules or single components of multicomponent genomes) were identified from forty-nine individual animal faecal samples. Based on shared genome organisations and sequence similarities, eighteen of the isolates were classified as gemycircularviruses and twelve isolates were classified as smacoviruses. The remaining eight isolates lack significant sequence similarity with any members of known CRESS DNA virus groups. This research adds significantly to our knowledge of CRESS DNA viral diversity in New Zealand, emphasising the prevalence of CRESS DNA viruses in nature, and reinforcing the suggestion that a large proportion of CRESS DNA viruses are yet to be identified.

Molecular characterization and field survey of Iranian potato virus X isolates

Six hundred and one symptomatic potato samples were collected from nine provinces in Iran. Screening by double-antibody sandwich enzyme linked immunosorbent assay using a potato virus X (PVX) together with a few potyviruses polyclonal antibodies, produced positive reactions in 4.3 % of samples against PVX. Based on symptoms on different test plant, the isolates were divided into two groups: the first groups causing blistering and malformation of leaves and the second showed mild mosaic and vein clearing in Nicotiana glutinosa. The almost complete nucleotide sequence of two isolates as a representative of severe and a mild isolates were determined. Genomes of two PVX Iranian isolates are identical to that of the most PVX isolates comprise 6435 nucleotides in length excluding 101 nucleotide in the 5' end of the genome and shares 94.8-96.7 % identities with European and Asian, and 77-96.1 % with American isolates. Furthermore, the 3'-terminal sequences, including the coat protein coding region of other 13 Iranian isolates were determined and compared with the GenBank sequences. Phylogenetic analysis of the cp gene of 13 Iranian isolates together all those available in public databases indicated that the 13 Iranian isolates all belong to low diversity clade I.