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Volume 27, Number 10—October 2021
Dispatch

Confirmation of Rickettsia conorii Subspecies indica Infection by Next-Generation Sequencing, Shandong, China

Nannan Xu1, Wei Gai1, Yan Zhang, Wei Wang, Gang WangComments to Author , Gregory A. Dasch, and Marina E. Eremeeva
Author affiliations: Qilu Hospital of Shandong University, Jinan, Shandong, China (N. Xu, G. Wang); Gene Research Institute, WillingMed Technology (Beijing) Co. Ltd., Beijing, China (W. Gai, Y. Zhang); The University of Texas MD Anderson Cancer Center, Houston, Texas, USA (W. Wang); Centers for Disease Control and Prevention, Atlanta, Georgia, USA (G.A. Dasch); Georgia Southern University, Statesboro, Georgia, USA (M.E. Eremeeva)

Main Article

Figure 2

Genetic relationships of the spotted fever group rickettsia detected in blood of patient 1 in study of confirmation of Rickettsia conorii subspecies indica infection by next-generation sequencing, Shandong, China. This analysis used concatenated sequences from 27 spotted fever rickettsial genomes homologous to the patient sequences (shown in bold text). A) Analysis of 1,379 positions in the tRNA-associated sequences; B) analysis of 1,519 positions in the protein gene–associated sequences. Each tree was constructed upon concatenation of 6 different genome sites (Appendix Table 2); the consensus of reads from sites with overlapping reads was used. The evolutionary relationships were inferred by using UPGMA implemented in MEGA X (15). The optimal trees are shown. The percentage of replicate trees in which the taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches. The evolutionary distances computed by using the Kimura 2-parameter method are in the units of the number of base substitutions per site. The proportion of sites where >1 unambiguous base is present in >1 sequence for each descendent clade is shown next each internal node in the tree. All ambiguous positions were removed for each sequence pair (pairwise deletion option). Scale bars indicate the percentage of nucleotide variation between the sequences.

Figure 2. Genetic relationships of the spotted fever group rickettsia detected in blood of patient 1 in study of confirmation of Rickettsia conorii subspecies indica infection by next-generation sequencing, Shandong, China. This analysis used concatenated sequences from 27 spotted fever rickettsial genomes homologous to the patient sequences (shown in bold text). A) Analysis of 1,379 positions in the tRNA-associated sequences; B) analysis of 1,519 positions in the protein gene–associated sequences. Each tree was constructed upon concatenation of 6 different genome sites (Appendix Table 2); the consensus of reads from sites with overlapping reads was used. The evolutionary relationships were inferred by using UPGMA implemented in MEGA X (15). The optimal trees are shown. The percentage of replicate trees in which the taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches. The evolutionary distances computed by using the Kimura 2-parameter method are in the units of the number of base substitutions per site. The proportion of sites where >1 unambiguous base is present in >1 sequence for each descendent clade is shown next each internal node in the tree. All ambiguous positions were removed for each sequence pair (pairwise deletion option). Scale bars indicate the percentage of nucleotide variation between the sequences.

Main Article

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1These authors contributed equally to this article.

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Page updated: September 19, 2021
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