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Volume 27, Number 2—February 2021
Dispatch

Shuni Virus in Cases of Neurologic Disease in Humans, South Africa

Thopisang P. Motlou and Marietjie VenterComments to Author 
Author affiliation: University of Pretoria, Pretoria, South Africa

Main Article

Figure

A) Phylogenetic confirmation that the orthobunyavirus small (S) segment specific reverse transcription PCR (14) positive products identified in this study clustered with SHUV strains. The 155-bp sequence of the nucleocapsid gene of the S segment of the human clinical isolates were aligned to SHUV strains previously identified in animals and other Orthobunyaviruses in the Simbu serogroup. The evolutionary history was inferred by using the maximum likelihood method and Kimura 2-parameter model. The tree with the highest log likelihood (−1043.27) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying neighbor-joining and BioNJ algorithms to a matrix of pairwise distances estimated using the maximum composite likelihood (MCL) approach and then selecting the topology with superior log likelihood value. A discrete gamma distribution was used to model evolutionary rate differences among sites (5 categories [+G parameter = 0.6884]). This analysis involved 28 nt sequences. All positions containing gaps and missing data were eliminated (complete deletion option). There were a total of 151 positions in the final dataset. Evolutionary analyses were conducted in MEGA X (http://www.megasoftware.net). Black circles indicate the newly sequenced positive human samples (ZRUH208/17, ZRUH131/17, ZRUH219/17, ZRUH212/17, ZRUH213/17, ZRUH400/17, ZRUH039/17). B) Phylogenetic analysis of a human SHUV-positive case using a larger region of the S-segment amplified with SHUV-specific primers. The evolutionary history was inferred by using the maximum likelihood method and Tamura-Nei model. The tree with the highest log likelihood (−3135.73) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying neighbor-joining and BioNJ algorithms to a matrix of pairwise distances estimated using the MCL approach and then selecting the topology with superior log likelihood value. A discrete gamma distribution was used to model evolutionary rate differences among sites (5 categories [+G, parameter = 0.3230]). This analysis involved 28 nt sequences. All positions containing gaps and missing data were eliminated (complete deletion option). There were a total of 324 positions in the final dataset. Evolutionary analyses were conducted in MEGA X. Black circle indicates the newly sequenced positive human strain (ZRUH131/17, GenBank accession no. MN937197). Sequence data are available upon request; numbers in parentheses for related strains indicate GenBank accession numbers. Scale bars indicate nucleotide substitutions per site. AINOV, Aino virus; AKAV, Akabane virus; BUTV, Buttonwillow virus; DOUV, Douglas virus; FPV, Faceys Paddock virus; INGV, Ingwavuma virus; KAIV, Kaikalur virus; KAIRV, Kairi virus; MERV, Mermet virus; OROV, Oropouche virus; PEAV, Peaton virus; SABOV, Sabo virus; SANV, Sango virus; SATV, Sathuperi virus; SBV, Schmallenburg virus; SHAV, Shamonda virus; SHUV, Shuni virus; SIMV, Simbu virus; TINV, Tinaroo virus; THIV, Thimiri virus; YABA, Yaba-7 virus.

Figure. A) Phylogenetic confirmation that the orthobunyavirus small (S) segment specific reverse transcription PCR (14) positive products identified in this study clustered with SHUV strains. The 155-bp sequence of the nucleocapsid gene of the S segment of the human clinical isolates were aligned to SHUV strains previously identified in animals and other Orthobunyaviruses in the Simbu serogroup. The evolutionary history was inferred by using the maximum likelihood method and Kimura 2-parameter model. The tree with the highest log likelihood (−1043.27) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying neighbor-joining and BioNJ algorithms to a matrix of pairwise distances estimated using the maximum composite likelihood (MCL) approach and then selecting the topology with superior log likelihood value. A discrete gamma distribution was used to model evolutionary rate differences among sites (5 categories [+G parameter = 0.6884]). This analysis involved 28 nt sequences. All positions containing gaps and missing data were eliminated (complete deletion option). There were a total of 151 positions in the final dataset. Evolutionary analyses were conducted in MEGA X (http://www.megasoftware.net). Black circles indicate the newly sequenced positive human samples (ZRUH208/17, ZRUH131/17, ZRUH219/17, ZRUH212/17, ZRUH213/17, ZRUH400/17, ZRUH039/17). B) Phylogenetic analysis of a human SHUV-positive case using a larger region of the S-segment amplified with SHUV-specific primers. The evolutionary history was inferred by using the maximum likelihood method and Tamura-Nei model. The tree with the highest log likelihood (−3135.73) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. Initial tree(s) for the heuristic search were obtained automatically by applying neighbor-joining and BioNJ algorithms to a matrix of pairwise distances estimated using the MCL approach and then selecting the topology with superior log likelihood value. A discrete gamma distribution was used to model evolutionary rate differences among sites (5 categories [+G, parameter = 0.3230]). This analysis involved 28 nt sequences. All positions containing gaps and missing data were eliminated (complete deletion option). There were a total of 324 positions in the final dataset. Evolutionary analyses were conducted in MEGA X. Black circle indicates the newly sequenced positive human strain (ZRUH131/17, GenBank accession no. MN937197). Sequence data are available upon request; numbers in parentheses for related strains indicate GenBank accession numbers. Scale bars indicate nucleotide substitutions per site. AINOV, Aino virus; AKAV, Akabane virus; BUTV, Buttonwillow virus; DOUV, Douglas virus; FPV, Faceys Paddock virus; INGV, Ingwavuma virus; KAIV, Kaikalur virus; KAIRV, Kairi virus; MERV, Mermet virus; OROV, Oropouche virus; PEAV, Peaton virus; SABOV, Sabo virus; SANV, Sango virus; SATV, Sathuperi virus; SBV, Schmallenburg virus; SHAV, Shamonda virus; SHUV, Shuni virus; SIMV, Simbu virus; TINV, Tinaroo virus; THIV, Thimiri virus; YABA, Yaba-7 virus.

Main Article

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