Recombination analysis on the receptor switching event of MERS-CoV and its close relatives: implications for the emergence of MERS-CoV

A study by Jarel Elgin Tolentino, Spyros Lytras, Jumpei Ito, and Kei Sato

The Genotype-to-Phenotype (G2P) Consortium

Keita Matsuno, Naganori Nao, Hirofumi Sawa, Shinya Tanaka, Masumi Tsuda, Lei Wang, Yoshikata Oda, Zannatul Ferdous, Kenji Shishido, Takasuke Fukuhara, Tomokazu Tamura, Rigel Suzuki, Saori Suzuki, Shuhei Tsujino, Hayato Ito, Yu Kaku, Naoko Misawa, Arnon Plianchaisuk, Ziyi Guo, Alfredo A Hinay Jr., Kaoru Usui, Wilaiporn Saikruang, Keiya Uriu, Yusuke Kosugi, Shigeru Fujita, Luo Chen, Lin Pan, Mai Suganami, Mika Chiba, Ryo Yoshimura, Kyoko Yasuda, Keiko Iida, Adam P. Strange, Naomi Ohsumi, Shiho Tanaka, Kaho Okumura, Kazuhisa Yoshimura, Kenji Sadamasu, Mami Nagashima, Hiroyuki Asakura, Isao Yoshida, So Nakagawa, Akifumi Takaori-Kondo, Kotaro Shirakawa, Kayoko Nagata, Ryosuke Nomura, Yoshihito Horisawa, Yusuke Tashiro, Yugo Kawai, Kazuo Takayama, Rina Hashimoto, Sayaka Deguchi, Yukio Watanabe, Ayaka Sakamoto, Naoko Yasuhara, Takao Hashiguchi, Tateki Suzuki, Kanako Kimura, Jiei Sasaki, Yukari Nakajima, Hisano Yajima, Takashi Irie, Ryoko Kawabata, Kaori Sasaki-Tabata, Terumasa Ikeda, Hesham Nasser, Ryo Shimizu, MST Monira Begum, Michael Jonathan, Yuka Mugita, Sharee Leong, Otowa Takahashi, Kimiko Ichihara, Takamasa Ueno, Chihiro Motozono, Mako Toyoda, Akatsuki Saito, Maya Shofa, Yuki Shibatani, Tomoko Nishiuchi, Jiri Zahradnik, Prokopios Andrikopoulos, Miguel Padilla-Blanco, Aditi Konar

Summary

This repository contains the multiple sequence alignment files, phylogenetic trees, and codes for analyzing the influence of recombination on the receptor switching event in the subgenus Merbecovirus.

Contents

• phylogenetic_analysis: a directory containing computational codes for phylogenetic analysis.
• output_files: a directory containing all the aligned genome sequences, recombination-free sequences, receptor-binding domain sequences of the representative viruses, the reconstructed trees (raw), and other output files (raw).

For the details on the methods, please refer to our study: Recombination analysis on the receptor switching event of MERS-CoV and its close relatives: implications for the emergence of MERS-CoV. Virology Journal, doi: 10.1186/s12985-024-02358-2