title: Whole genome detection of rotavirus mixed infections in human, porcine and bovine samples co-infected with various rotavirus strains collected from sub-Saharan Africa.
abstract: Group A rotaviruses (RVA) are among the main global causes of severe diarrhea in children under the age of 5years. Strain diversity, mixed infections and untypeable RVA strains are frequently reported in Africa. We analysed rotavirus-positive human stool samples (n=13) obtained from hospitalised children under the age of 5years who presented with acute gastroenteritis at sentinel hospital sites in six African countries, as well as bovine and porcine stool samples (n=1 each), to gain insights into rotavirus diversity and evolution. Polyacrylamide gel electrophoresis (PAGE) analysis and genotyping with G-(VP7) and P-specific (VP4) typing primers suggested that 13 of the 15 samples contained more than 11 segments and/or mixed G/P genotypes. Full-length amplicons for each segment were generated using RVA-specific primers and sequenced using the Ion Torrent and/or Illumina MiSeq next-generation sequencing platforms. Sequencing detected at least one segment in each sample for which duplicate sequences, often having distinct genotypes, existed. This supported and extended the PAGE and RT-PCR genotyping findings that suggested these samples were collected from individuals that had mixed rotavirus infections. The study reports the first porcine (MRC-DPRU1567) and bovine (MRC-DPRU3010) mixed infections. We also report a unique genome segment 9 (VP7), whose G9 genotype belongs to lineage VI and clusters with porcine reference strains. Previously, African G9 strains have all been in lineage III. Furthermore, additional RVA segments isolated from humans have a clear evolutionary relationship with porcine, bovine and ovine rotavirus sequences, indicating relatively recent interspecies transmission and reassortment. Thus, multiple RVA strains from sub-Saharan Africa are infecting mammalian hosts with unpredictable variations in their gene segment combinations. Whole-genome sequence analyses of mixed RVA strains underscore the considerable diversity of rotavirus sequences and genome segment combinations that result from a complex evolutionary history involving multiple host species.
authors.affiliation: South African Medical Research Council/Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa. Electronic address: wamodylan@gmail.com.
authors.forename: Martin M
authors.initials: MM
authors.lastname: Nyaga
authors.affiliation: South African Medical Research Council/Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa; Institute of Infection and Global Health, Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, United Kingdom. Electronic address: Khuzwayo.Jere@liverpool.ac.uk.
authors.forename: Khuzwayo C
authors.initials: KC
authors.lastname: Jere
authors.affiliation: South African Medical Research Council/Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa; Gastroenteritis and Respiratory Viruses Laboratory Branch, Division of Viral Diseases, NCIRD, CDC, Atlanta, GA, USA. Electronic address: mdi4@cdc.gov.
authors.forename: Mathew D
authors.initials: MD
authors.lastname: Esona
authors.affiliation: South African Medical Research Council/Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa. Electronic address: mpasi.seheri@gmail.com.
authors.forename: Mapaseka L
authors.initials: ML
authors.lastname: Seheri
authors.affiliation: J. Craig Venter Institute, Rockville, MD, USA. Electronic address: kstucker@jcvi.org.
authors.forename: Karla M
authors.initials: KM
authors.lastname: Stucker
authors.affiliation: J. Craig Venter Institute, Rockville, MD, USA. Electronic address: RHalpin@jcvi.org.
authors.forename: Rebecca A
authors.initials: RA
authors.lastname: Halpin
authors.affiliation: J. Craig Venter Institute, Rockville, MD, USA. Electronic address: aakopov@jcvi.org.
authors.forename: Asmik
authors.initials: A
authors.lastname: Akopov
authors.affiliation: J. Craig Venter Institute, Rockville, MD, USA. Electronic address: tstockwell@jcvi.org.
authors.forename: Timothy B
authors.initials: TB
authors.lastname: Stockwell
authors.affiliation: South African Medical Research Council/Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa. Electronic address: inapeenze@yahoo.com.
authors.forename: Ina
authors.initials: I
authors.lastname: Peenze
authors.affiliation: Albert Royer National Paediatric Hospital Laboratory, Dakar, Senegal. Electronic address: amadoudioplaba@yahoo.fr.
authors.forename: Amadou
authors.initials: A
authors.lastname: Diop
authors.affiliation: Unite de Virologie Medicale Institut Pasteur, Dakar, Senegal. Electronic address: kadern@pasteur.sn.
authors.forename: Kader
authors.initials: K
authors.lastname: Ndiaye
authors.affiliation: Mother and Child Center, Chantal Biya Foundation, Yaoundé, Cameroon. Electronic address: boulaayc@yahoo.fr.
authors.forename: Angeline
authors.initials: A
authors.lastname: Boula
authors.affiliation: The National Clinical Laboratory Service, Mbabane, Swaziland. Electronic address: gpmaphalala@gmail.com.
authors.forename: Gugu
authors.initials: G
authors.lastname: Maphalala
authors.affiliation: University of Zimbabwe, Department of Medical Microbiology, Virology Section, Harare, Zimbabwe. Electronic address: cberejena@gmail.com.
authors.forename: Chipo
authors.initials: C
authors.lastname: Berejena
authors.affiliation: World Health Organization, Regional Office for Africa, Brazzaville, People's Republic of Congo. Electronic address: mwendaj@afro.who.int.
authors.forename: Jason M
authors.initials: JM
authors.lastname: Mwenda
authors.affiliation: South African Medical Research Council/Diarrhoeal Pathogens Research Unit, 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: duncan.steele@gatesfoundation.org.
authors.forename: A Duncan
authors.initials: AD
authors.lastname: Steele
authors.affiliation: J. Craig Venter Institute, Rockville, MD, USA. Electronic address: DWentworth@cdc.gov.
authors.forename: David E
authors.initials: DE
authors.lastname: Wentworth
authors.affiliation: South African Medical Research Council/Diarrhoeal Pathogens Research Unit, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Medunsa, Pretoria, South Africa. Electronic address: jeffrey.mphahlele@mrc.ac.za.
authors.forename: M Jeffrey
authors.initials: MJ
authors.lastname: Mphahlele
mesh_terms: D017954:Africa South of the Sahara; D000820:Animal Diseases / Q000821:virology*; D000818:Animals; D002417:Cattle; D002675:Child, Preschool; D060085:Coinfection; D016679:Genome, Viral; D005838:Genotype; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D010802:Phylogeny; D012401:Rotavirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D012400:Rotavirus Infections / Q000453:epidemiology / Q000821:virology*; D017422:Sequence Analysis, DNA; D013552:Swine
keywords: Africa; Mixed infections; Reassortants; Rotavirus; Whole genome