Complete genome analyses of the first porcine rotavirus group H identified from a South African pig does not provide evidence for recent interspecies transmission events.
Martin M Nyaga1
Ina Peenze2
Christiaan A Potgieter3,4
L Mapaseka Seheri5
Nicola A Page6
Claude K Yinda7
A Duncan Steele8,9
Jelle Matthijnssens10
M Jeffrey Mphahlele11
Affiliations11 institutions
South African Medical Research Council/Diarrhoeal Pathogens Research Unit (MRC-DPRU), Department of Virology, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa. Electronic address: [email protected].
South African Medical Research Council/Diarrhoeal Pathogens Research Unit (MRC-DPRU), Department of Virology, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa. Electronic address: [email protected].
Department of Biochemistry, Centre for Human Metabonomics, North-West University, Potchefstroom, South Africa
South African Medical Research Council/Diarrhoeal Pathogens Research Unit (MRC-DPRU), Department of Virology, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa. Electronic address: [email protected].
Center for Enteric Diseases, National Institute for Communicable Diseases, National Health Laboratory Service, Sandringham, Johannesburg, South Africa. Electronic address: [email protected].
KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, B-3000 Leuven, Belgium. Electronic address: [email protected].
South African Medical Research Council/Diarrhoeal Pathogens Research Unit (MRC-DPRU), Department of Virology, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa
Enteric and Diarrhoeal Diseases Programme, Global Health Program, Bill and Melinda Gates Foundation, Seattle, WA, USA. Electronic address: [email protected].
KU Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, B-3000 Leuven, Belgium. Electronic address: [email protected].
South African Medical Research Council/Diarrhoeal Pathogens Research Unit (MRC-DPRU), Department of Virology, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa. Electronic address: [email protected].
Rotaviruses (RVs) are classified into eight species/groups (RVA-RVH) according to the migration patterns of their 11 genome segments, as well as by serological and molecular properties of Viral Protein 6 (VP6). In 1997 a new unclassified RV was reported infecting adults in Bangladesh and China. This virus was initially named novel adult diarrhoea rotavirus (ADRV-N), but later renamed as RVH. Since then, RVH has been detected in humans only very sporadically. However, RVH is increasingly being detected in pig populations in the USA, Brazil and Japan, but not yet in Africa. Unfortunately, whole genome sequence data of porcine RVH strains in GenBank is currently restricted to a single strain (SKA-1) from Japan. Porcine diarrhoeic samples were collected in South Africa and analysed for rotavirus using an RVA ELISA and electropherotyping by PAGE. One sample displayed a 4:2:1:1:1:1:1 migration pattern, typical for RVH. In order to further investigate this strain, sequence-independent amplification followed by random sequencing using the 454/Roche GS FLX Sequencer was performed, resulting in the second complete porcine RVH strain (MRC-DPRU1575) available in databases. Phylogenetically, all segments of MRC-DPRU1575 clustered closely with the SKA-1 strain and in some segments with known porcine RVH strains from Brazil and the USA. In contrast, the porcine RVH strains were only distantly related to human RVH strains from Asia and a partial RVH-like strain recently detected in bats from Cameroon. Overall, strain MRC-DPRU1575 is the first complete genome of a porcine RVH from Africa and allows for the development of improved RVH screening methods. Our analyses indicate that RVH strains cluster according to their host species, not suggesting any evidence of recent interspecies transmission events. However, more RVH genomes from a wider host range are needed to better understand their evolutionary pathways and zoonotic potential.
Complete genome sequencing and phylogenetic analysis of porcine rotavirus group H from South Africa showed clustering with other porcine RVH strains and distant relationships to human and bat RVH, indicating host-specific evolutionary separation.
Sequence-independent amplification followed by random sequencing using the 454/Roche GS FLX Sequencer was performed, resulting in the second complete porcine RVH strain (MRC-DPRU1575) available in databases. Phylogenetically, all segments of MRC-DPRU1575 clustered closely with the SKA-1 strain and in some segments with known porcine RVH strains from Brazil and the USA. In contrast, the porcine RVH strains were only distantly related to human RVH strains from Asia and a partial RVH-like strain recently detected in bats from Cameroon.
Genes or proteins
whole genome; VP6
Analysis methods
complete genome sequencing; phylogenetic analysis
Zoonotic Surveillance1 records
Zoonotic SurveillanceExtraction confidence 0.85
Key finding
Rotavirus group H was detected through laboratory screening of porcine diarrhoeic samples from South Africa, providing genomic data for surveillance of rotaviruses in pigs.
Porcine diarrhoeic samples were collected in South Africa and analysed for rotavirus using an RVA ELISA and electropherotyping by PAGE. One sample displayed a 4:2:1:1:1:1:1 migration pattern, typical for RVH.
Method
ELISA; electropherotyping by PAGE; sequence-independent amplification; random sequencing; 454/Roche GS FLX Sequencer
