Precision medicine in cats:novel niemann-pick type C1 diagnosed by whole-genome sequencing

State-of-the-art health care includes genome sequencing of the patient to identify genetic variants that contribute to either the cause of their malady or variants that can be targeted to improve treatment. The goal was to introduce state-of-the-art health care to cats using genomics and a precision medicine approach. To test the feasibility of a precision medicine approach in domestic cats, a single cat that presented to the University of Missouri, Veterinary Health Center with an undiagnosed neurologic disease was whole-genome sequenced. The DNA variants from the cat were compared to the DNA variant database produced by the 99 Lives Cat Genome Sequencing Consortium. Approximately 25× genomic coverage was produced for the cat. A predicted p.H441P missense mutation was identified in NPC1, the gene causing Niemann-Pick type C1 on cat chromosome D3.47456793 caused by an adenine-to-cytosine transversion, c.1322A>C. The cat was homozygous for the variant. The variant was not identified in any other 73 domestic and 9 wild felids in the sequence database or 190 additionally genotyped cats of various breeds. The successful effort suggested precision medicine is feasible for cats and other undiagnosed cats may benefit from a genomic analysis approach. The 99 Lives DNA variant database was sufficient but would benefit from additional cat sequences. Other cats with the mutation may be identified and could be introduced as a new biomedical model for NPC1. A genetic test could eliminate the disease variant from the population

Food-Borne Viruses in Shellfish: Investigation on Norovirus and HAV Presence in Apulia (SE Italy)

Shellfish are an important vehicle for transmission of food-borne pathogens including norovirus (NoV) and hepatitis A virus (HAV). The risks related with consumption of shellfish are greater if these products are eaten raw or slightly cooked. As molluscs are filter-feeding organisms, they are able to concentrate pathogens dispersed in the water. Data on shellfish viral contamination are therefore useful to obtain a background information on the presence of contamination in the environment, chiefly in shellfish production areas and to generate a picture of the epidemiology of viral pathogens in local populations. From January 2013 to July 2015, 253 samples of bivalve molluscs collected in harvesting areas from a large coastal tract (860 km) of Southern Italy were screened for HAV and NoV of genogroups GI and GII, using real-time reverse transcription qualitative PCR. The RNA of HAV was not detected in any of the analyzed samples. In contrast, the RNA of NoV was identified in 14.2% of the samples with a higher prevalence of NoVs of genogroup GII (12.2%) than genogroup GI (1.6%). Upon sequence analysis of a short diagnostic region located in capsid region, the NoV strains were characterized as GII.2, GII.4 Sydney 2012, GII.6, GII.13, GI.4, and GI.6, all which were circulating in local populations in the same time span. These data confirm that consumption of mussels can expose consumers to relevant risks of infection. Also, matching between the NoV genotypes circulating in local population and detected in molluscs confirms the diffusion in the environment of NoVs

Simian Immunodeficiency Virus Infection of Chimpanzees (Pan troglodytes) Shares Features of Both Pathogenic and Non-pathogenic Lentiviral Infections.

The virus-host relationship in simian immunodeficiency virus (SIV) infected chimpanzees is thought to be different from that found in other SIV infected African primates. However, studies of captive SIVcpz infected chimpanzees are limited. Previously, the natural SIVcpz infection of one chimpanzee, and the experimental infection of six chimpanzees was reported, with limited follow-up. Here, we present a long-term study of these seven animals, with a retrospective re-examination of the early stages of infection. The only clinical signs consistent with AIDS or AIDS associated disease was thrombocytopenia in two cases, associated with the development of anti-platelet antibodies. However, compared to uninfected and HIV-1 infected animals, SIVcpz infected animals had significantly lower levels of peripheral blood CD4+ T-cells. Despite this, levels of T-cell activation in chronic infection were not significantly elevated. In addition, while plasma levels of β2 microglobulin, neopterin and soluble TNF-related apoptosis inducing ligand (sTRAIL) were elevated in acute infection, these markers returned to near-normal levels in chronic infection, reminiscent of immune activation patterns in 'natural host' species. Furthermore, plasma soluble CD14 was not elevated in chronic infection. However, examination of the secondary lymphoid environment revealed persistent changes to the lymphoid structure, including follicular hyperplasia in SIVcpz infected animals. In addition, both SIV and HIV-1 infected chimpanzees showed increased levels of deposition of collagen and increased levels of Mx1 expression in the T-cell zones of the lymph node. The outcome of SIVcpz infection of captive chimpanzees therefore shares features of both non-pathogenic and pathogenic lentivirus infections.This work was supported by the Biotechnology and Biological Sciences Research Council and by the Wellcome Trust.This is the final version of the article. It first appeared from PLOS via http://dx.doi.org/10.1371/journal.ppat.100514

Early-onset progressive retinal atrophy associated with an IQCB1 variant in African black-footed cats (Felis nigripes)

African black-footed cats (Felis nigripes) are endangered wild felids. One male and full-sibling female African black-footed cat developed vision deficits and mydriasis as early as 3 months of age. The diagnosis of early-onset progressive retinal atrophy (PRA) was supported by reduced direct and consensual pupillary light reflexes, phenotypic presence of retinal degeneration, and a non-recordable electroretinogram with negligible amplitudes in both eyes. Whole genome sequencing, conducted on two unaffected parents and one affected offspring was compared to a variant database from 51 domestic cats and a Pallas cat, revealed 50 candidate variants that segregated concordantly with the PRA phenotype. Testing in additional affected cats confirmed that cats homozygous for a 2 base pair (bp) deletion within IQ calmodulin-binding motif-containing protein-1 (IQCB1), the gene that encodes for nephrocystin-5 (NPHP5), had vision loss. The variant segregated concordantly in other related individuals within the pedigree supporting the identification of a recessively inherited early-onset feline PRA. Analysis of the black-footed cat studbook suggests additional captive cats are at risk. Genetic testing for IQCB1 and avoidance of matings between carriers should be added to the species survival plan for captive management

Food-Borne Viruses in Shellfish: Investigation on Norovirus and HAV Presence in Apulia (SE Italy)

Shellfish are an important vehicle for transmission of food-borne pathogens including norovirus (NoV) and hepatitis A virus (HAV). The risks related with consumption of shellfish are greater if these products are eaten raw or slightly cooked. As molluscs are filter-feeding organisms, they are able to concentrate pathogens dispersed in the water. Data on shellfish viral contamination are therefore useful to obtain a background information on the presence of contamination in the environment, chiefly in shellfish production areas and to generate a picture of the epidemiology of viral pathogens in local populations. From January 2013 to July 2015, 253 samples of bivalve molluscs collected in harvesting areas from a large coastal tract (860 km) of Southern Italy were screened for HAV and NoV of genogroups GI and GII, using real-time reverse transcription qualitative PCR. The RNA of HAV was not detected in any of the analyzed samples. In contrast, the RNA of NoV was identified in 14.2% of the samples with a higher prevalence of NoVs of genogroup GII (12.2%) than genogroup GI (1.6%). Upon sequence analysis of a short diagnostic region located in capsid region, the NoV strains were characterized as GII.2, GII.4 Sydney 2012, GII.6, GII.13, GI.4, and GI.6, all which were circulating in local populations in the same time span. These data confirm that consumption of mussels can expose consumers to relevant risks of infection. Also, matching between the NoV genotypes circulating in local population and detected in molluscs confirms the diffusion in the environment of NoVs

SIVagm Infection in Wild African Green Monkeys from South Africa: Epidemiology, Natural History, and Evolutionary Considerations

Pathogenesis studies of SIV infection have not been performed to date in wild monkeys due to difficulty in collecting and storing samples on site and the lack of analytical reagents covering the extensive SIV diversity. We performed a large scale study of molecular epidemiology and natural history of SIVagm infection in 225 free-ranging AGMs from multiple locations in South Africa. SIV prevalence (established by sequencing pol, env, and gag) varied dramatically between infant/juvenile (7%) and adult animals (68%) (p<0.0001), and between adult females (78%) and males (57%). Phylogenetic analyses revealed an extensive genetic diversity, including frequent recombination events. Some AGMs harbored epidemiologically linked viruses. Viruses infecting AGMs in the Free State, which are separated from those on the coastal side by the Drakensberg Mountains, formed a separate cluster in the phylogenetic trees; this observation supports a long standing presence of SIV in AGMs, at least from the time of their speciation to their Plio-Pleistocene migration. Specific primers/probes were synthesized based on the pol sequence data and viral loads (VLs) were quantified. VLs were of 104-106 RNA copies/ml, in the range of those observed in experimentally-infected monkeys, validating the experimental approaches in natural hosts. VLs were significantly higher (107-108 RNA copies/ml) in 10 AGMs diagnosed as acutely infected based on SIV seronegativity (Fiebig II), which suggests a very active transmission of SIVagm in the wild. Neither cytokine levels (as biomarkers of immune activation) nor sCD14 levels (a biomarker of microbial translocation) were different between SIV-infected and SIV-uninfected monkeys. This complex algorithm combining sequencing and phylogeny, VL quantification, serology, and testing of surrogate markers of microbial translocation and immune activation permits a systematic investigation of the epidemiology, viral diversity and natural history of SIV infection in wild African natural hosts. © 2013 Ma et al