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Volume 24, Number 2—February 2018
Research

Lethal Respiratory Disease Associated with Human Rhinovirus C in Wild Chimpanzees, Uganda, 2013

Erik J. Scully, Sarmi Basnet, Richard W. Wrangham, Martin N. Muller, Emily Otali, David Hyeroba, Kristine A. Grindle, Tressa E. Pappas, Melissa Emery Thompson, Zarin Machanda, Kelly E. Watters, Ann C. Palmenberg, James E. Gern, and Tony L. GoldbergComments to Author 
Author affiliations: Harvard University, Cambridge, Massachusetts, USA (E.J. Scully, R.W. Wrangham); University of Wisconsin‒Madison, Madison, Wisconsin, USA (S. Basnet, K.A. Grindle, T.E. Pappas, K.E. Watters, A.C. Palmenberg, J.E. Gern, T.L. Goldberg); University of New Mexico, Albuquerque, New Mexico, USA (M.N. Muller, M.E. Thompson); Makerere University, Kampala, Uganda (E. Otali, D. Hyeroba); Tufts University, Grafton, Massachusetts, USA (Z. Machanda)

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Figure 3

Phylogenetic tree of rhinovirus C variants. The tree was constructed from a codon-based alignment (6,234 positions) of the new chimpanzee-derived sequence identified in the Kanyawara chimpanzee community, Uganda, 2013 (indicated by the asterisk and chimpanzee silhouette), and all human-derived RV-C complete polyprotein gene sequences available in GenBank as of December 18, 2016, with rhinoviruses A and B from the RefSeq database included as outgroups. We created alignments using the MAFFT algori

Figure 3. Phylogenetic tree of rhinovirus C variants. The tree was constructed from a codon-based alignment (6,234 positions) of the new chimpanzee-derived sequence identified in the Kanyawara chimpanzee community, Uganda, 2013 (indicated by the asterisk and chimpanzee silhouette), and all human-derived RV-C complete polyprotein gene sequences available in GenBank as of December 18, 2016, with rhinoviruses A and B from the RefSeq database included as outgroups. We created alignments using the MAFFT algorithm (18) implemented in the computer program Translator X (19), with the Gblocks algorithm (20) applied to remove poorly aligned regions. We constructed trees using the maximum-likelihood method implemented in PhyML (22), with best-fit models of molecular evolution estimated from the data by using jModelTest (21). Circles on nodes indicate statistical confidence on the basis of 1,000 bootstrap replicates of the data (closed circles 100%; open circles >75%). Scale bar indicates nucleotide substitutions per site. GenBank accession numbers and other details of the RV-C sequences included in the analysis are in Technical Appendix Table).

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