Simultaneous Identification of DNA and RNA Viruses Present in Pig Faeces Using Process-Controlled Deep Sequencing

Background: Animal faeces comprise a community of many different microorganisms including bacteria and viruses. Only scarce information is available about the diversity of viruses present in the faeces of pigs. Here we describe a protocol, which was optimized for the purification of the total fraction of viral particles from pig faeces. The genomes of the purified DNA and RNA viruses were simultaneously amplified by PCR and subjected to deep sequencing followed by bioinformatic analyses. The efficiency of the method was monitored using a process control consisting of three bacteriophages (T4, M13 and MS2) with different morphology and genome types. Defined amounts of the bacteriophages were added to the sample and their abundance was assessed by quantitative PCR during the preparation procedure. Results: The procedure was applied to a pooled faecal sample of five pigs. From this sample, 69,613 sequence reads were generated. All of the added bacteriophages were identified by sequence analysis of the reads. In total, 7.7 % of the reads showed significant sequence identities with published viral sequences. They mainly originated from bacteriophages (73.9%) and mammalian viruses (23.9%); 0.8 % of the sequences showed identities to plant viruses. The most abundant detected porcine viruses were kobuvirus, rotavirus C, astrovirus, enterovirus B, sapovirus and picobirnavirus. In addition, sequences with identities to the chimpanzee stool-associated circular ssDNA virus were identified. Whole genome analysis indicates that this virus, tentatively designated as pig stool-associated circular ssDNA virus (PigSCV), represents a novel pi

How do risk preferences relate to malaria care-seeking behavior and the acceptability of a new health technology in Nigeria?

BACKGROUND: To reduce the burden of disease from malaria, innovative approaches are needed to engender behavior change. One unobservable, but fundamental trait—preferences for risk—may influence individuals’ willingness to adopt new health technologies. We explore the association of risk preferences with malaria care-seeking behavior and the acceptability of malaria rapid diagnostic tests (RDTs) to inform RDT scale-up plans. METHODS: In Oyo State, Nigeria, adult customers purchasing anti-malarial medications at selected drug shops took surveys and received an RDT as they exited. After an initial risk preference assessment via a simple lottery game choice, individuals were given their RDT result and treatment advice, and called four days later to assess treatment adherence. We used bivariable and multivariable regression analysis to assess the association of risk game choices with malaria care-seeking behaviors and RDT acceptability. RESULTS: Of 448 respondents, 63.2% chose the lottery game with zero variance in expected payout, 27.9% chose the game with low variance, and 8.9% chose the game with high variance. Compared to participants who chose lower variance games, individuals choosing higher variance games were older, less educated, more likely to be male, and were more likely to patronize lower quality drug shops, seek care immediately, and report complete disability due to their illness. In contrast, individuals choosing lower variance games were more likely to follow the correct treatment directions and were more likely to report an increase in their willingness to pay for an RDT compared to other risk groups, our two measures of RDT acceptability. Differences in estimated associations between risk game choices and selected care-seeking behaviors remained after controlling sociodemographic confounders. CONCLUSIONS: The uptake of health diagnostic information in terms of translating the RDT experience into willingness to pay for an RDT and treatment adherence to test results may vary according to risk preferences. Hence, health promotion communications may want to be crafted bearing in mind differences in uptake among people of different risk preferences to encourage wider RDT adoption and more rational malaria treatment. Estimates will serve as the basis for power calculations for an expanded study