AbstractChikungunya virus (CHIKV) is a re-emerging Alphavirus transmitted by Aedes mosquitoes and causing fever, rash and arthralgia. Currently there are no vaccines or antiviral agents against CHIKV, therefore it is important to understand the molecular details of CHIKV replication. In this regard, the function of the Alphavirus non-structural protein 3 (nsP3) remains enigmatic. Building on previous studies (Gao et al, 2019), we generated a panel of mutants in a conserved and surface exposed cluster in the nsP3 alphavirus unique domain (AUD) and tested their replication phenotype using a sub-genomic replicon (SGR) in mammalian and mosquito cells. We identified three mutants that replicated poorly in mammalian cells but showed no defect in mosquito cells. We further showed that these mutants were temperature-sensitive, rather than species-specific, as they exhibited no replication defect in mammalian cells at sub-physiological temperature (28°C). Similar effects were observed in the context of infectious CHIKV as well as a closely related virus: O’Nyong Nyong virus (ONNV). Intriguingly, this analysis also revealed that the wildtype SGR replicated much more efficiently at sub-physiological temperature as compared to 37°C. This was not due to impaired interferon responses as this enhancement was also observed in Vero cells. Neither was this due to a defect in the phosphorylation of eIF2α as treatment with ISRIB, an inhibitor of global translation attenuation, did not compensate for replication defects at 37°C. However, we noticed significant differences between the sizes and numbers of virus-induced stress granules (SG) at physiological and sub-physiological temperatures. As cells in the periphery will be at sub-physiological temperatures, and these will be the first cells infected in the mammalian host following a mosquito bite, we propose that alphaviruses have evolved mechanisms to limit antiviral responses in these cells to promote viral genome replication.Author summaryChikungunya virus (CHIKV) is a re-emerging arbovirus. It is transmitted by Aedes species of mosquitos and poses massive epidemic threats. Arboviruses are unique in that they must be able to replicate efficiently in both the mosquito vector and the mammalian host, and therefore at different temperatures. Importantly, the first cells infected in the mammalian host following a mosquito bite will be in the skin and therefore at sub-physiological temperature (lower than 37°C). Here we show that mutants within one of the CHIKV proteins (nsP3) were unable to replicate at 37°C but replicated efficiently in mammalian cells at a sub-physiological temperature (28°C). We also showed that the wildtype virus replicated more efficiently at 28°C in comparison to at 37°C in mammalian cells. We investigated the mechanism behind this phenomenon and showed that at sub-physiological temperatures the virus induced the formation of smaller and more numerous cytoplasmic stress granules. We propose that alphaviruses have evolved mechanisms to promote their replication in mammalian cells at sub-physiological temperatures to facilitate infection of mammals via a cutaneous mosquito bite.