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Volume 28, Number 8—August 2022
Research Letter

Lymphocytic Choriomeningitis Virus Infection, Australia

Leon CalyComments to Author , Ashleigh F. Porter, Joanna Chua, James P. Collet, Julian D. Druce, Michael G. Catton, and Sebastian Duchene
Author affiliations: Monash University, Clayton, Victoria, Australia (L. Caly); The Peter Doherty Institute of Infection and Immunity, Melbourne, Victoria, Australia (L. Caly, A.F. Porter, J. Chua, J.D. Druce, M.G. Catton, S. Duchene); University of Sydney, Sydney, New South Wales, Australia (J.P. Collet); Dubbo Hospital, Dubbo, New South Wales, Australia (J.P. Collet)

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Figure

Phylogenetic relationships of a strain of lymphocytic choriomeningitis virus from a man in Australia and the broader lymphocytic choriomeningitis virus phylogeny. Tips are labeled with GenBank sequence accession number, country of origin, year of collection, and host (mice, hamsters, humans, ticks). Trees were generated by using BEAST 1.10.4 (9) to estimate the time to the most recent common ancestor between the novel virus sequence and its closest phylogenetic relative. We used the Hasegawa-Kishino-Yano plus gamma substitution model with a strict clock and an exponential growth coalescent tree prior. Because the dataset exhibits high sequence divergence, we calibrated the molecular clock by using previous independent estimates of the substitution rate, with a fixed clock rate for the long segment of 3.7 × 10–4 substitutions/site/year and 3.3 × 10–4 substitutions/site/year for the short segment (10). Highest clade credibility tree of the short segment (GenBank accession no. OK356607) sequences (n = 29) (A) and highest clade credibility tree of the long segment (GenBank accession no. OK356608) sequences (n = 19) (B). Node labels denote the posterior support, and an asterisk represents a bootstrap percentage of >70% support for a specific clade, using 1,000 ultra-fast bootstrap replicates in a maximum-likelihood tree approach using IQ-TREE2 (11). The 95% highest posterior density for the divergence time before present of the Australia sample is annotated in the respective node.

Figure. Phylogenetic relationships of a strain of lymphocytic choriomeningitis virus from a man in Australia and the broader lymphocytic choriomeningitis virus phylogeny. Tips are labeled with GenBank sequence accession number, country of origin, year of collection, and host (mice, hamsters, humans, ticks). Trees were generated by using BEAST 1.10.4 (9) to estimate the time to the most recent common ancestor between the novel virus sequence and its closest phylogenetic relative. We used the Hasegawa-Kishino-Yano plus gamma substitution model with a strict clock and an exponential growth coalescent tree prior. Because the dataset exhibits high sequence divergence, we calibrated the molecular clock by using previous independent estimates of the substitution rate, with a fixed clock rate for the long segment of 3.7 × 10–4 substitutions/site/year and 3.3 × 10–4 substitutions/site/year for the short segment (10). Highest clade credibility tree of the short segment (GenBank accession no. OK356607) sequences (n = 29) (A) and highest clade credibility tree of the long segment (GenBank accession no. OK356608) sequences (n = 19) (B). Node labels denote the posterior support, and an asterisk represents a bootstrap percentage of >70% support for a specific clade, using 1,000 ultra-fast bootstrap replicates in a maximum-likelihood tree approach using IQ-TREE2 (11). The 95% highest posterior density for the divergence time before present of the Australia sample is annotated in the respective node.

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