Atluri, K., Aimlin, I., Arora, S., 2022. Current effective therapeutics in management of
COVID-19. J. Clin. Med. 11 (13), 3838.
S. Takazawa et al.
Virus Research 334 (2023) 199176
Kung, Y.A., Lee, K.M., Chiang, H.J., Huang, S.Y., Wu, C.J., Shih, S.R., 2022. Molecular
virology of SARS-CoV-2 and related coronaviruses. Microbiol. Mol. Biol. Rev. 86 (2),
e0002621.
Lee, J.H., Koepke, L., Kirchhoff, F., Sparrer, K.M.J., 2022. Interferon antagonists encoded
by SARS-CoV-2 at a glance. Med. Microbiol. Immunol. 1–7.
Lei, X., Dong, X., Ma, R., Wang, W., Xiao, X., Tian, Z., Wang, C., Wang, Y., Li, L., Ren, L.,
Guo, F., Zhao, Z., Zhou, Z., Xiang, Z., Wang, J., 2020. Activation and evasion of type
I interferon responses by SARS-CoV-2. Nat. Commun. 11 (1), 3810.
Liu, S., Chou, C.K., Wu, W.W., Luan, B., Wang, T.T., 2022. Stable cell clones harboring
self-replicating SARS-CoV-2 RNAs for drug screen. J. Virol. 96 (6), e0221621.
Malicoat, J., Manivasagam, S., Zuniga, S., Sola, I., McCabe, D., Rong, L., Perlman, S.,
Enjuanes, L., Manicassamy, B., 2022. Development of a single-cycle infectious SARSCoV-2 virus replicon particle system for use in biosafety level 2 laboratories. J. Virol.
96 (3), e0183721.
Nguyen, H.T., Falzarano, D., Gerdts, V., Liu, Q., 2021. Construction of a noninfectious
SARS-CoV-2 replicon for antiviral-drug testing and gene function studies. J. Virol. 95
(18), e0068721.
Ramirez, S., Fernandez-Antunez, C., Galli, A., Underwood, A., Pham, L.V., Ryberg, L.A.,
Feng, S., Pedersen, M.S., Mikkelsen, L.S., Belouzard, S., Dubuisson, J., Solund, C.,
Weis, N., Gottwein, J.M., Fahnoe, U., Bukh, J., 2021. Overcoming culture restriction
for SARS-CoV-2 in human cells facilitates the screening of compounds inhibiting
viral replication. Antimicrob. Agents Chemother. 65 (7), e0009721.
Ren, Y., Shu, T., Wu, D., Mu, J., Wang, C., Huang, M., Han, Y., Zhang, X.Y., Zhou, W.,
Qiu, Y., Zhou, X., 2020. The ORF3a protein of SARS-CoV-2 induces apoptosis in cells.
Cell Mol. Immunol. 17 (8), 881–883.
Silvas, J.A., Vasquez, D.M., Park, J.G., Chiem, K., Allue-Guardia, A., Garcia-Vilanova, A.,
Platt, R.N., Miorin, L., Kehrer, T., Cupic, A., Gonzalez-Reiche, A.S., Bakel, H.V.,
Garcia-Sastre, A., Anderson, T., Torrelles, J.B., Ye, C., Martinez-Sobrido, L., 2021.
Contribution of SARS-CoV-2 accessory proteins to viral pathogenicity in K18 human
ACE2 transgenic mice. J. Virol. 95 (17), e0040221.
Takashita, E., Kinoshita, N., Yamayoshi, S., Sakai-Tagawa, Y., Fujisaki, S., Ito, M.,
Iwatsuki-Horimoto, K., Chiba, S., Halfmann, P., Nagai, H., Saito, M., Adachi, E.,
Sullivan, D., Pekosz, A., Watanabe, S., Maeda, K., Imai, M., Yotsuyanagi, H.,
Mitsuya, H., Ohmagari, N., Takeda, M., Hasegawa, H., Kawaoka, Y., 2022. Efficacy
of antibodies and antiviral drugs against Covid-19 Omicron variant. N. Engl. J. Med.
386 (10), 995–998.
Tanaka, T., Saito, A., Suzuki, T., Miyamoto, Y., Takayama, K., Okamoto, T., Moriishi, K.,
2022. Establishment of a stable SARS-CoV-2 replicon system for application in highthroughput screening. Antivir. Res. 199, 105268.
Tews, B.A., Meyers, G., 2017. Self-replicating RNA. Methods Mol. Biol. 1499, 15–35.
The Center for Systems Science and Engineering (CSSE) at Johns Hopkins University
(JHU), 2023. COVID-19 Dashboard. https://coronavirus.jhu.edu/map.html
(Accessed 20 January 2023).
Wang, M., Cao, R., Zhang, L., Yang, X., Liu, J., Xu, M., Shi, Z., Hu, Z., Zhong, W., Xiao, G.,
2020. Remdesivir and chloroquine effectively inhibit the recently emerged novel
coronavirus (2019-nCoV) in vitro. Cell Res. 30 (3), 269–271.
Xia, H., Cao, Z., Xie, X., Zhang, X., Chen, J.Y., Wang, H., Menachery, V.D., Rajsbaum, R.,
Shi, P.Y., 2020. Evasion of type I interferon by SARS-CoV-2. Cell Rep. 33 (1),
108234.
Zhang, Q.Y., Deng, C.L., Liu, J., Li, J.Q., Zhang, H.Q., Li, N., Zhang, Y.N., Li, X.D.,
Zhang, B., Xu, Y., Ye, H.Q., 2021a. SARS-CoV-2 replicon for high-throughput
antiviral screening. J. Gen. Virol. 102 (5), 001583.
Zhang, Y., Song, W., Chen, S., Yuan, Z., Yi, Z., 2021b. A bacterial artificial chromosome
(BAC)-vectored noninfectious replicon of SARS-CoV-2. Antivir. Res. 185, 104974.
Beigel, J.H., Tomashek, K.M., Dodd, L.E., Mehta, A.K., Zingman, B.S., Kalil, A.C.,
Hohmann, E., Chu, H.Y., Luetkemeyer, A., Kline, S., Lopez de Castilla, D., Finberg, R.
W., Dierberg, K., Tapson, V., Hsieh, L., Patterson, T.F., Paredes, R., Sweeney, D.A.,
Short, W.R., Touloumi, G., Lye, D.C., Ohmagari, N., Oh, M.D., Ruiz-Palacios, G.M.,
Benfield, T., Fatkenheuer, G., Kortepeter, M.G., Atmar, R.L., Creech, C.B.,
Lundgren, J., Babiker, A.G., Pett, S., Neaton, J.D., Burgess, T.H., Bonnett, T.,
Green, M., Makowski, M., Osinusi, A., Nayak, S., Lane, H.C., Members, A.-S.G., 2020.
Remdesivir for the treatment of Covid-19 - final report. N. Engl. J. Med. 383 (19),
1813–1826.
Centers for Disease Control and Prevention (CDC), 2022. Overview of COVID-19 vaccines
https://www.cdc.gov/coronavirus/2019-ncov/vaccines/different-vaccines/overv
iew-COVID-19-vaccines.html (accessed 20 January 2023).
Centers for Disease Control and Prevention (CDC), 2021. Interim laboratory biosafety
guidelines for handling and processing specimens associated with coronavirus
disease 2019 (COVID-19). https://www.cdc.gov/coronavirus/2019-ncov/lab/la
b-biosafety-guidelines.html (accessed 30 June 2023).
Chen, N., Zhou, M., Dong, X., Qu, J., Gong, F., Han, Y., Qiu, Y., Wang, J., Liu, Y., Wei, Y.,
Xia, J., Yu, T., Zhang, X., Zhang, L., 2020. Epidemiological and clinical
characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a
descriptive study. Lancet 395 (10223), 507–513.
Cheung, P.H., Ye, Z.W., Lui, W.Y., Ong, C.P., Chan, P., Lee, T.T., Tang, T.T., Yuen, T.L.,
Fung, S.Y., Cheng, Y., Chan, C.P., Chan, C.P., Jin, D.Y., 2022. Production of singlecycle infectious SARS-CoV-2 through a trans-complemented replicon. J. Med. Virol.
94 (12), 6078–6090.
Gao, Y., Yan, L., Huang, Y., Liu, F., Zhao, Y., Cao, L., Wang, T., Sun, Q., Ming, Z.,
Zhang, L., Ge, J., Zheng, L., Zhang, Y., Wang, H., Zhu, Y., Zhu, C., Hu, T., Hua, T.,
Zhang, B., Yang, X., Li, J., Yang, H., Liu, Z., Xu, W., Guddat, L.W., Wang, Q., Lou, Z.,
Rao, Z., 2020. Structure of the RNA-dependent RNA polymerase from COVID-19
virus. Science 368 (6492), 779–782.
He, X., Quan, S., Xu, M., Rodriguez, S., Goh, S.L., Wei, J., Fridman, A., Koeplinger, K.A.,
Carroll, S.S., Grobler, J.A., Espeseth, A.S., Olsen, D.B., Hazuda, D.J., Wang, D., 2021.
Generation of SARS-CoV-2 reporter replicon for high-throughput antiviral screening
and testing. Proc. Natl. Acad. Sci. U.S.A. 118 (15), e2025866118.
Heilmann, E., Costacurta, F., Moghadasi, S.A., Ye, C., Pavan, M., Bassani, D., Volland, A.,
Ascher, C., Weiss, A.K.H., Bante, D., Harris, R.S., Moro, S., Rupp, B., MartinezSobrido, L., von Laer, D., 2023. SARS-CoV-2 3CL(pro) mutations selected in a VSVbased system confer resistance to nirmatrelvir, ensitrelvir, and GC376. Sci. Transl.
Med. 15 (678), eabq7360.
Huang, C., Wang, Y., Li, X., Ren, L., Zhao, J., Hu, Y., Zhang, L., Fan, G., Xu, J., Gu, X.,
Cheng, Z., Yu, T., Xia, J., Wei, Y., Wu, W., Xie, X., Yin, W., Li, H., Liu, M., Xiao, Y.,
Gao, H., Guo, L., Xie, J., Wang, G., Jiang, R., Gao, Z., Jin, Q., Wang, J., Cao, B., 2020.
Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China.
Lancet 395 (10223), 497–506.
Jin, Y.Y., Lin, H., Cao, L., Wu, W.C., Ji, Y., Du, L., Jiang, Y., Xie, Y., Tong, K., Xing, F.,
Zheng, F., Shi, M., Pan, J.A., Peng, X., Guo, D., 2021. A convenient and biosafe
replicon with accessory genes of SARS-CoV-2 and its potential application in
antiviral drug discovery. Virol. Sin. 36 (5), 913–923.
Kotaki, T., Xie, X., Shi, P.Y., Kameoka, M., 2021. A PCR amplicon-based SARS-CoV-2
replicon for antiviral evaluation. Sci. Rep. 11 (1), 2229.
Kuhlmann, C., Mayer, C.K., Claassen, M., Maponga, T., Burgers, W.A., Keeton, R.,
Riou, C., Sutherland, A.D., Suliman, T., Shaw, M.L., Preiser, W., 2022. Breakthrough
infections with SARS-CoV-2 omicron despite mRNA vaccine booster dose. Lancet
399 (10325), 625–626.
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