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Tanino Y, Nishioka K, Yamamoto C, Watanabe Y, Daidoji T, Kawamoto M, Uda S, Kirito S, Nakagawa Y, Kasamatsu Y, Kawahara Y, Sakai Y, Nobori S, Inaba T, Ota B, Fujita N, Hoshino A, Nukui Y, Nakaya T. Emergence of SARS-CoV-2 with Dual-Drug Resistant Mutations During a Long-Term Infection in a Kidney Transplant Recipient. Infect Drug Resist 2024; 17:531-541. [PMID: 38348230 PMCID: PMC10860503 DOI: 10.2147/idr.s438915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/22/2024] [Indexed: 02/15/2024] Open
Abstract
Introduction Various therapeutic agents are being developed for the treatment of coronavirus disease 2019 (COVID-19). Therefore, it is crucial to accumulate information regarding the features of drug-resistant viruses to these antiviral drugs. Methods We investigated the emergence of dual-drug resistance in a kidney transplant recipient who received sotrovimab (from day 0) and remdesivir (RDV) (from day 8 to day 17). We sequenced the whole viral genomes from nasopharyngeal swabs taken on day 0 and seven points after starting treatment (on days 12, 19, 23, 37, 43, 48, and 58). The genetic traits of the wild-type (day 0) and descendant viruses (after day 12) were determined by comparing the genomes with those of a Wuhan strain and the day 0 wild-type strain, respectively. Three viral isolates (from samples collected on days 0, 23, and 37) were investigated for their escape ability and growth kinetics in vitro. Results The sotrovimab resistant mutation (S:E340K) and the RDV resistant mutation RdRp:V792I (nt: G15814A) emerged within 12 days (day 12) and 11 days (day 19) after the treatment, respectively. The day 23 isolate harboring S:E340K/RdRp:V791I was resistant to both sotrovimab and RDV, showing 364- and 2.73-fold higher resistance respectively, compared with the wild-type. Moreover, compared with the day 23 isolate, the day 37 isolate accumulated multiple additional mutations and had a higher level of resistance to both drugs. Conclusion Drug-resistant variants with double mutations (S:E340K/RdRp:V791I) became dominant within 23 days after starting treatment, suggesting that even a combination therapy involving sotrovimab and RDV, dual-drug resistant viruses may emerge rapidly in immunocompromised patients. The dual-resistant variants had lower virus yields than those of the wild-type virus in vitro, suggesting that they paid a fitness cost.
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Affiliation(s)
- Yoko Tanino
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Keisuke Nishioka
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Chie Yamamoto
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yohei Watanabe
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
- JST, MIRAI, Tokyo, Japan
| | - Tomo Daidoji
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan
| | - Masataka Kawamoto
- Department of Forensics Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Sayaka Uda
- Department of Pulmonary Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Shoko Kirito
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuta Nakagawa
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yu Kasamatsu
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshiyuki Kawahara
- Kyoto Prefectural Institute of Public Health and Environment, Kyoto, Japan
| | - Yuri Sakai
- Kyoto Prefectural Institute of Public Health and Environment, Kyoto, Japan
| | - Shuji Nobori
- Department of Organ Transplantation and General Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tohru Inaba
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Bon Ota
- Department of Emergency Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Naohisa Fujita
- Kyoto Prefectural Institute of Public Health and Environment, Kyoto, Japan
| | - Atsushi Hoshino
- Department of Cardiovascular Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoko Nukui
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takaaki Nakaya
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
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