ArticlePathogens (Basel, Switzerland)2022
Metagenomic Analysis of RNA Fraction Reveals the Diversity of Swine Oral Virome on South African Backyard Swine Farms in the uMgungundlovu District of KwaZulu-Natal Province.
Article in Pathogens (Basel, Switzerland), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed, 12 citations in OpenAlex.
- Serological Evidence of Hepatitis E Virus Exposure in Free-Ranging Warthogs (Phacochoerus africanus) in South Africa.EcoHealth · 2026Article
- Livestock aggregated samples for monitoring viruses infecting animals and potentially zoonotic viral pathogens.One health (Amsterdam, Netherlands) · 2026Article
- Fecal virome transplantation alleviates weaning stress-induced behavioral alterations and intestinal health by reshaping the gut microbiome.Scientific reports · 2026Article
- Picobirnavirus: how do you find where it's hiding?Critical reviews in microbiology · 2026Review
- A Review of Global Patterns in Gut Microbiota Composition, Health and Disease: Locating South Africa in the Conversation.Microorganisms · 2025Review
- Discovery and rescue of porcine bastroviruses associated with polioencephalomyelitis in domestic pigs.Journal of virology · 2025Article
- A metagenomic investigation of the faecal RNA virome structure of asymptomatic chickens obtained from a commercial farm in Durban, KwaZulu-Natal province, South Africa.BMC genomics · 2024Article
- Phylogenetic Analyses of Rotavirus A, B and C Detected on a Porcine Farm in South Africa.Viruses · 2024Article
- Overview of Diagnostic Methods, Disease Prevalence and Transmission of Mpox (Formerly Monkeypox) in Humans and Animal Reservoirs.Microorganisms · 2023Review
- Characterization of a Near Full-Length Hepatitis E Virus Genome of Subtype 3c Generated from Naturally Infected South African Backyard Pigs.Pathogens (Basel, Switzerland) · 2022Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Numerous RNA viruses have been reported in backyard swine populations in various countries. In the absence of active disease surveillance, a persistent knowledge gap exists on the diversity of RNA viruses in South African backyard swine populations. This is the first study investigating the diversity of oral RNA virome of the backyard swine in South Africa. We used three samples of backyard swine oral secretion (saliva) collected from three distantly located backyard swine farms (BSFs) in the uMgungundlovu District, KwaZulu-Natal, South Africa. Total viral RNA was extracted and used for the library preparation for deep sequencing using the Illumina HiSeq X instrument. The FASTQ files containing paired-end reads were analyzed using Genome Detective v 1.135. The assembled nucleotide sequences were analyzed using the PhyML phylogenetic tree. The genome sequence analysis identified a high diversity of swine enteric viruses in the saliva samples obtained from BSF2 and BSF3, while only a few viruses were identified in the saliva obtained from BSF1. The swine enteric viruses belonged to various animal virus families; however, two fungal viruses, four plant viruses, and five unclassified RNA viruses were also identified. Specifically, viruses of the family
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