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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)

Main Article

Figure 2

Recombination between viral genotypes rhinovirus C45 and C11 leading to RV-C45-cpz1-2013, the strain identified in the Kanyawara chimpanzee community, Uganda, 2013. Analyses were performed in RDP4 (17) on aligned rhinovirus C genome sequences of 36 known genotypes. Each alignment entry encoded the full or nearly full polyprotein gene sequence, but some sequences were missing fragments (<400 bp) of their respective 5′-UTRs (Δ seq, yellow box at left). The 3′ poly(A) tail was not included. A re

Figure 2. Recombination between viral genotypes rhinovirus C45 and C11 leading to RV-C45-cpz1-2013, the strain identified in the Kanyawara chimpanzee community, Uganda, 2013. Analyses were performed in RDP4 (17) on aligned rhinovirus C genome sequences of 36 known genotypes. Each alignment entry encoded the full or nearly full polyprotein gene sequence, but some sequences were missing fragments (<400 bp) of their respective 5′-UTRs (Δ seq, yellow box at left). The 3′ poly(A) tail was not included. A recombination event between the 2 viruses shown (GenBank nos. JN837686 and EU840952) is the most likely event among all full alignment comparisons (window size 20 bps) according to 6 of the 9 RDP4 algorithms. The average p values were RDP 2.8 × 10−81, GENECONV 3.0 × 10−70, MaxChi 1.4 × 10−18, Chimaera 2.1 × 10−21, SiScan 3.6 × 10–34, and 3Seq 1.5 × 10−27. BootScan, PhylPro, and LARD made no call for these particular parents. Purple box in the 5′-UTR denotes the 99% breakpoint confidence level (combined). Dashed box indicates the position of the most likely swapped fragment. The (Monte Carlo corrected) probability for this event is 2.8 × 10−81. The virus map is scaled to the alignment. Conf, confidence level; RV-C, rhinovirus C; Δ seq, missing sequence; UTR, untranslated region.

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