Origin and Possible Genetic Recombination of the Middle East Respiratory Syndrome Coronavirus from the First Imported Case in China: Phylogenetics and Coalescence Analysis

Abstract

The Middle East respiratory syndrome coronavirus (MERS-CoV) causes a severe acute respiratory tract infection with a high fatality rate in humans. Coronaviruses are capable of infecting multiple species and can evolve rapidly through recombination events. Here, we report the complete genomic sequence analysis of a MERS-CoV strain imported to China from South Korea. The imported virus, provisionally named ChinaGD01, belongs to group 3 in clade B in the whole-genome phylogenetic tree and also has a similar tree topology structure in the open reading frame 1a and -b (ORF1ab) gene segment but clusters with group 5 of clade B in the tree constructed using the S gene. Genetic recombination analysis and lineage-specific single-nucleotide polymorphism (SNP) comparison suggest that the imported virus is a recombinant comprising group 3 and group 5 elements. The time-resolved phylogenetic estimation indicates that the recombination event likely occurred in the second half of 2014. Genetic recombination events between group 3 and group 5 of clade B may have implications for the transmissibility of the virus.

Importance: The recent outbreak of MERS-CoV in South Korea has attracted global media attention due to the speed of spread and onward transmission. Here, we present the complete genome of the first imported MERS-CoV case in China and demonstrate genetic recombination events between group 3 and group 5 of clade B that may have implications for the transmissibility of MERS-CoV.

FIG 1

Timeline of the travel history, potential virus exposure, onset of disease, and diagnosis of the first imported MERS-CoV case in China. UAE, United Arab Emirates; KSA, Kingdom of Saudi Arabia.

FIG 2

Phylogenetic relationships based on complete genomes (A), ORF1ab genes (B), and S genes (C) of MERS-CoV strains. China’s first imported MERS-CoV strain (GenBank accession no. KT006149.2), South Korea’s first MERS-CoV strain (GenBank accession no. KT029139), and the latest MERS-CoV strains prevalent in the Middle East (GenBank accession no. KT026453 to KT026456) are indicated in red. The MERS-CoV strains derived from camels are indicated in blue. All of the complete genomes were analyzed by nucleotide sequence alignment using the maximum-likelihood method implemented in the RAxML. Numbers at the nodes indicate bootstrap support for each node (percentage of 1,000 bootstrap replicates). Scale bars indicate the expected number of nucleotide substitutions per site.

FIG 3

Recombination analyses of complete MERS-CoV genomes. (A) Bootscanning analysis of MERS-CoV genome. The ChinaGD01 strain was used as a query sequence and compared with one strain from group 3 (GenBank accession no. KF600628.1), one from group 5 (GenBank accession no. KJ713296.1), and one from group 1 (GenBank accession no. KP209312.1). (B) Single-nucleotide differences between the ChinaGD01 sequence and consensus sequences of group 3 and group 5. Group 3 cons, consensus sequences of group 3 strains; group 5 cons, consensus sequences of group 5 strains; South Korea, first MERS-CoV strain (GenBank accession no. KT029139) in South Korea; KSA-2015, latest strains prevalent in Saudi Arabia (GenBank accession no. KT026453 to KT026456), Bisha-1/2012, an earlier strain used as a control.

FIG 4

Time-resolved phylogenetic analyses of complete genomes (A), nonrecombination regions (B), and recombination regions (C) of MERS-CoV strains using BEAST. The nonrecombination region is approximately bp 1 to 17,300, and the recombination region is approximately bp 17,301 to 24,000. ChinaGD01 (GenBank accession no. KT006149), South Korea’s first MERS-CoV strain (GenBank accession no. KT029139), and the latest strains prevalent in Saudi Arabia (GenBank accession no. KT026453 to KT026456) are indicated in red.