Alphavirus nonstructural protein 2 (nsP2) has pivotal roles in viral RNA replication, host cell shutoff, and inhibition of antiviral responses. Mutations that individually rendered other alphaviruses noncytopathic were introduced into chikungunya virus nsP2. Results show that (i) nsP2 mutation P718S only in combination with KR649AA or adaptive mutation D711G allowed noncytopathic replicon RNA replication, (ii) prohibiting nsP2 nuclear localization abrogates inhibition of antiviral interferon-induced JAK-STAT signaling, and (iii) nsP2 independently affects RNA replication, cytopathicity, and JAK-STAT signaling.
Chikungunya virus (CHIKV) is a member of the Alphavirus genus within the Togaviridae family. In humans, infection by this mosquito-borne virus can result in the development of a high fever, rash, and incapacitating, sometimes chronic, arthralgia. In the last decade, CHIKV outbreaks occurred throughout the Indian Ocean region, including La Reunion, infecting up to onethird of the human population, before infecting millions of people in India and Southern Asia (1, 2). CHIKV is a positive-strand RNA virus that replicates in the cytoplasm of infected cells. The genome contains four nonstructural proteins (nsP1 to nsP4) that are directly translated from the genomic RNA (gRNA). The viral structural proteins are translated later in infection from subgenomic mRNA (sgRNA) (3).nsP1 is a methyltransferase and is associated with cellular membranes (4), nsP3 is a phosphoprotein that recruits host factor G3BP and consequently inhibits the formation of cellular stress granules (5, 6), and nsP4 is the viral RNA-dependent RNA polymerase (3). nsP2 contains the viral helicase, protease, and a putative C-terminal methyltransferase domain; associates with many host proteins; and can effectively shut down host cell protein synthesis (7-11). Alphavirus nsP2 also contains a nuclear localization signal (NLS) in its C-terminal domain (CHIKV nsP2 KR649-650) (Fig. 1A, top). nsP2 from related Semliki Forest virus (SFV) and Sindbis virus (SINV) has been shown to translocate to the nucleus (12-14), as specific mutations within the NLS retained SFV nsP2 in the cytoplasm and reduced its cytopathicity (15). In the nucleus, nsP2 of Old World alphaviruses (SFV, SINV, and CHIKV) has been reported to inhibit host cell mRNA transcription via degradation of a subunit of DNA-directed RNA polymerase II (RPB1) (16). Mutation of a conserved proline residue in a site homologous to CHIKV nsP2 P718 (Fig. 1A, bottom) rendered SINV noncytopathic and alleviated the transcriptional inhibition via RPB1 (16-18).In addition, alphavirus nsP2 has been shown to antagonize the host's main antiviral response, the interferon (IFN) response, in two ways: (i) beta interferon (IFN-) transcription via global host shutoff and (ii) downstream type I/II IFN-induced Janus kinase/ signal transducers and activators of transcription (JAK-STAT) signaling (16,(19)(20)(21)(22). Upon activation, phosphorylated STAT1/2 proteins translocate as dimers into the nucleus to activate t...