Virological characteristics of the SARS-CoV-2 BA.2.86 variant

A study by Tomokazu Tamura, Keita Mizuma, Hesham Nasser, Sayaka Deguchi, Miguel Padilla-Blanco, Keiya Uriu, Jarel Elgin M Tolentino, Shuhei Tsujino, Rigel Suzuki, Isshu Kojima, Naganori Nao, Ryo Shimizu, Michael Jonathan, Yusuke Kosugi, Ziyi Guo, Alfredo A Hinay Jr., Olivia Putri, Yoonjin Kim, Yuri L Tanaka, Hiroyuki Asakura, Mami Nagashima, Kenji Sadamasu, Kazuhisa Yoshimura, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Akatsuki Saito, Jumpei Ito, Takashi Irie, Jiri Zahradnik, Terumasa Ikeda, Kazuo Takayama, Keita Matsuno, Takasuke Fukuhara, Kei Sato

Summary

This repository contains code to analyze all available BA.2.86 (including the BA.2.86.1) sequences using genome surveillance data sourced from GISAID (https://gisaid.org/).

Contents

• epidemic dynamics analysis: a directory containing computational codes for epidemic dynamics analysis. This directory also contains the metadata, the output files of the epidemic dynamics analysis using the Bayesian hierarchical multinomial logistic model, and the acknowledgement table for GISAID data
• phylogenetic analysis: a directory containing computational codes for phylogenetic analysis, the reconstructed trees, and the acknowledgement table for GISAID data

For details, please refer to our study: Virological characteristics of the SARS-CoV-2 BA.2.86 variant, Cell Host and Microbe, doi:10.1016/j.chom.2024.01.001