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TitleVirological characteristics of the SARS-CoV-2 Omicron EG.5.1 variant.
Journal, issue, pagesMicrobiol Immunol, Year 2024
Publish dateJul 4, 2024
AuthorsShuhei Tsujino / Sayaka Deguchi / Tomo Nomai / Miguel Padilla-Blanco / Arnon Plianchaisuk / Lei Wang / Mst Monira Begum / Keiya Uriu / Keita Mizuma / Naganori Nao / Isshu Kojima / Tomoya Tsubo / Jingshu Li / Yasufumi Matsumura / Miki Nagao / Yoshitaka Oda / Masumi Tsuda / Yuki Anraku / Shunsuke Kita / Hisano Yajima / Kaori Sasaki-Tabata / Ziyi Guo / Alfredo A Hinay / Kumiko Yoshimatsu / Yuki Yamamoto / Tetsuharu Nagamoto / Hiroyuki Asakura / Mami Nagashima / Kenji Sadamasu / Kazuhisa Yoshimura / Hesham Nasser / Michael Jonathan / Olivia Putri / Yoonjin Kim / Luo Chen / Rigel Suzuki / Tomokazu Tamura / Katsumi Maenaka / Takashi Irie / Keita Matsuno / Shinya Tanaka / Jumpei Ito / Terumasa Ikeda / Kazuo Takayama / Jiri Zahradnik / Takao Hashiguchi / Takasuke Fukuhara / Kei Sato / /
PubMed AbstractIn middle to late 2023, a sublineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron XBB, EG.5.1 (a progeny of XBB.1.9.2), is spreading rapidly around the world. We performed ...In middle to late 2023, a sublineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron XBB, EG.5.1 (a progeny of XBB.1.9.2), is spreading rapidly around the world. We performed multiscale investigations, including phylogenetic analysis, epidemic dynamics modeling, infection experiments using pseudoviruses, clinical isolates, and recombinant viruses in cell cultures and experimental animals, and the use of human sera and antiviral compounds, to reveal the virological features of the newly emerging EG.5.1 variant. Our phylogenetic analysis and epidemic dynamics modeling suggested that two hallmark substitutions of EG.5.1, S:F456L and ORF9b:I5T are critical to its increased viral fitness. Experimental investigations on the growth kinetics, sensitivity to clinically available antivirals, fusogenicity, and pathogenicity of EG.5.1 suggested that the virological features of EG.5.1 are comparable to those of XBB.1.5. However, cryo-electron microscopy revealed structural differences between the spike proteins of EG.5.1 and XBB.1.5. We further assessed the impact of ORF9b:I5T on viral features, but it was almost negligible in our experimental setup. Our multiscale investigations provide knowledge for understanding the evolutionary traits of newly emerging pathogenic viruses, including EG.5.1, in the human population.
External linksMicrobiol Immunol / PubMed:38961765
MethodsEM (single particle)
Resolution2.51 - 3.78 Å
Structure data

EMDB-37648: SARS-CoV-2 EG.5.1 spike glycoprotein (1-up state)
Method: EM (single particle) / Resolution: 3.34 Å

37650

8wmd

EMDB-37650: SARS-CoV-2 EG.5.1 spike glycoprotein (closed-2 state)
PDB-8wmd: Structure of the SARS-CoV-2 EG.5.1 spike glycoprotein (closed-2 state)
Method: EM (single particle) / Resolution: 2.71 Å

37651

8wmf

EMDB-37651: SARS-CoV-2 EG.5.1 spike glycoprotein (closed-1 state)
PDB-8wmf: Structure of the SARS-CoV-2 EG.5.1 spike glycoprotein (closed-1 state)
Method: EM (single particle) / Resolution: 2.51 Å

38453

8xlm

EMDB-38453, PDB-8xlm:
Structure of the SARS-CoV-2 EG.5.1 spike glycoprotein in complex with ACE2 (1-up state)
Method: EM (single particle) / Resolution: 3.22 Å

38454

8xln

EMDB-38454, PDB-8xln:
Structure of the SARS-CoV-2 EG.5.1 spike RBD in complex with ACE2
Method: EM (single particle) / Resolution: 3.78 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

Source
  • severe acute respiratory syndrome coronavirus 2
  • homo sapiens (human)
KeywordsVIRAL PROTEIN / VIRAL PROTEIN/PROTEIN BINDING / VIRAL PROTEIN-PROTEIN BINDING complex

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