Eyes on the RNA virus polymerase – one major target for antiviral development

Structure of severe fever with thrombocytopenia syndrome virus L

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RNA virus, including positive-sense (+ssRNA) or negative-sense (-ssRNA) and retrovirus, groups a large number of pathogens to cause infectious diseases in plants, animals and humans. For example, the current pandemic of COVID-19 is caused by a +ssRNA virus, 2019-nCoV. Despite large variations in RNA virus lifecycles, they all use RNA-dependent polymerase -RNA-dependent RNA polymerase (RdRp) for +ssRNA/-ssRNA viruses and RNA-dependent DNA polymerase or reverse transcriptase (RT) for retrovirus - to synthesise nucleic acids for viral replication and transcription. Due to the central role of RNA-dependent polymerase in the virus lifecycle, it is widely accepted to be a major target for antiviral development. For example, the RT inhibitors Zidovudine/Lamivudine/Zalcitabine/Didanosine/Stavudine are used as anti-HIV therapeutics, and the RdRp inhibitor Sofosbuvir is used to cure HCV infection. In very recent studies, Remdesivir, an RdRp inhibitor, has shown potential for treating COVID-19 patients.

The tick-borne Severe Fever with Thrombocytopenia Syndrome virus (SFTSV) belongs to the Phenuiviridae family within the Bunyavirales order and has homology with Rift Valley Fever Virus (RVFV) and several other human pathogens. Infection of SFTSV results in fever, thrombocytopenia, and multi-system organ failure accompanied by hemorrhage. Since its first outbreak in 2009, thousands of infections have been reported, with a mortality ratio of up to 30%, and the incidence of SFTSV infection has recently increased rapidly worldwide. The World Health Organization (WHO) has included SFTSV in the list of priority target pathogens requiring urgent attention.

Whereas +ssRNA viruses and retroviruses encode a “small” polymerase, the -ssRNA viruses, including SFTSV, encode a large RdRp (so-called L protein) with multiple enzymatic functions to facilitate virus transcription and replication. As a segmented –ssRNA virus, SFTSV-L employs a ‘‘cap-snatching’’ mechanism to cannibalize the cap structure from host cell mRNA to prime the synthesis of viral mRNA. Segmented negative-sense RNA viruses (sNSRV) encode a single-polypeptide large (L) protein (for example, bunyavirus and arenavirus) or a hetrotrimeric polymerase complex (for example, orthomyxovirus) to cannibalize host mRNA cap structures serving as primers of transcription and catalyze RNA synthesis. By using cryo-electron microscopy (cryo-EM), the structure of the full-length SFTSV-L was determined to atomic level (3.4-Å). Knowing the complete architecture of L protein in this family for the first time enabled identification of an Arg-finger that plays a key role in initiation of the cap-snatching process and the subsequent transcription. Moreover, the catalytic machinery for RNA synthesis in SFTSV-L shows relatively high structural homology with other viral RdRp. These observations indicate that, alongside the conventional RdRp inhibitor (nucleotide analogue chain terminator), more strategies for antiviral discovery targeting multiple processes in L protein functions would be helpful for further therapeutic development.

Figure 1. Structure of SFTSV L on the background of a virion.

We would like to say that the structural study of viral RdRp, in particular –ssRNA viral RdRp, significantly benefits from the significant progress of cryo-EM. In our study, though SFTSV-L has high purity, only ~10% particles can be selected out to reconstruct the structure shown in the paper. A set of different classes with variable conformations, which may represent different status in SFTSV-L function, can be found and the reconstructions are underway.

Our report can be found at https://www.nature.com/articles/s41564-020-0712-2 .

Zhiyong Lou

Professor, Tsinghua University

Zhiyong Lou is a professor of molecular virology at Tsinghua University. He is active in virology, structural biology (protein crystallography and cryo Electron Microscopy), as well as antiviral research.

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