Vol.:(0123456789) 1 3 Virus Genes https://doi.org/10.1007/s11262-019-01650-6 Diversity and distribution of Maize-associated totivirus strains from Tanzania David Alan Read 1  · Jonathan Featherston 1  · David Jasper Gilbert Rees 1  · Genevieve Dawn Thompson 1  · Ronel Roberts 2  · Bradley Charles Flett 3  · Kingstone Mashingaidze 3  · Gerhard Pietersen 4  · Barnabas Kiula 5  · Alois Kullaya 6  · Ernest R. Mbega 7 Received: 30 January 2019 / Accepted: 13 February 2019 © Springer Science+Business Media, LLC, part of Springer Nature 2019 Abstract Typically associated with fungal species, members of the viral family Totiviridae have recently been shown to be associated with plants, including important crop species, such as Carica papaya (papaya) and Zea mays (maize). Maize-associated totivirus (MATV) was frst described in China and more recently in Ecuador, where it has been found to co-occur with other viruses known to elicit maize lethal necrosis disease (MLND). In a survey for maize-associated viruses, 35 samples were selected for Illumina HiSeq sequencing, from the Tanzanian maize producing regions of Mara, Arusha, Manyara, Kilimanjaro, Morogoro and Pwani. Libraries were prepared using an RNA-tag-seq methodology. Taxonomic classifcation of the result- ing datasets showed that 6 of the 35 samples from the regions of Arusha, Kilimanjaro, Morogoro and Mara, contained reads that were assigned to MATV reference sequences. This was confrmed with PCR and Sanger sequencing. Read assembly of the six MATV-associated datasets yielded partial MATV genomes, two of which were selected for further characterization, using RACE. This yielded two full-length MATV genomes, one of which is divergent from other available MATV genomes. Keywords Totivirus · Maize · Tanzania · Maize lethal necrosis disease · Illumina sequencing Introduction Members of the viral family Totiviridae have been shown to infect a wide diversity of fungal genera and have been implicated in the “killer” phenotype of certain yeast strains [1]. They have also been hypothesized to modulate virulence in parasites, such as Leishmania, Trichomonas and Giardia [2] and shown to infect arthropod hosts, including mosquitos [3], ants [4] and shrimp [5]. More recently, members of the family Totiviridae have been detected in a number of plant species including Carica papaya (papaya) [6], Panax sp [7]. and Zea mays (maize) [8, 9]. Given the opportunities for transfer during fungal colonization, it is possible that Toti- viruses were initially transmitted to maize via a fungal host species [10]. Totivirus genomes are double-stranded RNA molecules, typically non-segmented containing two open reading frames (ORF), with the 5′ proximal ORF encoding for a coat protein (CP) and the 3′ proximal ORF encoding for an RNA-dependant-RNA-polymerase (RdRp). Genome sizes vary in length from − 4000 to 8500 bp, based on publicly available sequences in GenBank. Maize-associated totivirus Edited by Dr. Karel Petrzik. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11262-019-01650-6) contains supplementary material, which is available to authorized users. * David Alan Read readd@arc.agric.za 1 Agricultural Research Council - Biotechnology Platform, Private Bag X05, Onderstepoort 0110, South Africa 2 Agricultural Research Council - Plant Protection Research, Private Bag X134, Queenswood 0001, South Africa 3 Agricultural Research Council - Grain Crops, Private Bag X1251, Potchefstroom 2520, South Africa 4 Department of Genetics, Stellenbosch University, Stellenbosch 7600, South Africa 5 Tanzania Agricultural Research Institute (TARI, Ilonga), Kilosa, Morogoro, Tanzania 6 Tanzania Agricultural Research Institute (TARI, Mikocheni), Dar es Salaam, Tanzania 7 Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania