Influenza virus stablishes a network of virus-host functional interactions, which depends on chromatin dynamic and therefore on epigenetic modifications. Using an unbiased search, we analyzed the epigenetic changes at DNA methylation and post-translational histone modification levels induced by the infection. DNA methylation was unaltered, while we found a general decrease on histone acetylation, which correlates with transcriptional inactivation and may cooperate with the impairment of cellular transcription that causes influenza virus infection. A particular increase in H3K79 methylation was observed and the use of an inhibitor of the specific H3K79 methylase, Dot1L enzyme, or its silencing, increased influenza virus replication. The antiviral response was reduced in conditions of Dot1L downregulation, since decreased nuclear translocation of NF-kB complex, and IFN-β, Mx1 and ISG56 expression was detected. The data suggested a control of antiviral signaling by methylation of H3K79 and consequently, influenza virus replication was unaffected in IFN pathway-compromised, Dot1L-inhibited cells. H3K79 methylation also controlled replication of another potent interferon-inducing virus such as vesicular stomatitis virus, but did not modify amplification of respiratory syncytial virus that poorly induces interferon signaling. Epigenetic methylation of H3K79 might have an important role in controlling interferon-induced signaling against viral pathogens.

The influenza A virus RNA polymerase is a heterotrimeric complex responsible for viral genome transcription and replication in the nucleus of infected cells. We recently carried out a proteomic analysis of purified polymerase expressed in human cells and identified a number of polymerase-associated cellular proteins. Here we characterise the role of one such host factors, SFPQ/PSF, during virus infection. Down-regulation of SFPQ/PSF by silencing with two independent siRNAs reduced the virus yield by 2–5 log in low-multiplicity infections, while the replication of unrelated viruses as VSV or Adenovirus was almost unaffected. As the SFPQ/PSF protein is frequently associated to NonO/p54, we tested the potential implication of the latter in influenza virus replication. However, down-regulation of NonO/p54 by silencing with two independent siRNAs did not affect virus yields. Down-regulation of SFPQ/PSF by siRNA silencing led to a reduction and delay of influenza virus gene expression. Immunofluorescence analyses showed a good correlation between SFPQ/PSF and NP levels in infected cells. Analysis of virus RNA accumulation in silenced cells showed that production of mRNA, cRNA and vRNA is reduced by more than 5-fold but splicing is not affected. Likewise, the accumulation of viral mRNA in cicloheximide-treated cells was reduced by 3-fold. In contrast, down-regulation of SFPQ/PSF in a recombinant virus replicon system indicated that, while the accumulation of viral mRNA is reduced by 5-fold, vRNA levels are slightly increased. In vitro transcription of recombinant RNPs generated in SFPQ/PSF-silenced cells indicated a 4–5-fold reduction in polyadenylation but no alteration in cap snatching. These results indicate that SFPQ/PSF is a host factor essential for influenza virus transcription that increases the efficiency of viral mRNA polyadenylation and open the possibility to develop new antivirals targeting the accumulation of primary transcripts, a very early step during infection.

SARS-Coronavirus-2 (SARS-CoV-2) causes Coronavirus disease 2019 , an infectious respiratory disease causing thousands of deaths and overwhelming public health systems. The international spread of SARS-CoV-2 is associated with the ease of global travel, and societal dynamics, immunologic naiveté of the host population, and muted innate immune responses. Based on these factors and the expanding geographic scale of the disease, the World Health Organization (WHO) declared the COVID-19 outbreak a pandemicthe first caused by a coronavirus. In this review, we summarize the current epidemiological status of COVID-19 and consider the virological and immunological lessons, animal models, and tools developed in response to prior SARS-CoV and MERS-CoV outbreaks that can serve as resources for development of SARS-CoV-2 therapeutics and vaccines. In particular, we discuss structural insights into the SARS-CoV-2 spike protein, a major determinant of transmissibility, and discuss key molecular aspects that will aid in understanding and fighting this new global threat. The COVID-19 Pandemic to DateFrom Emergence in Wuhan to Global Pandemic In December 2019, a novel human coronavirus (HCoV) was identified as the causative agent of clusters of pneumonia in China. The virus was named as SARS-CoV-2, based on its phylogenetic and taxonomic similarity to SARS-CoV [1], which caused an outbreak of severe acute respiratory syndrome (SARS) in 2002. The WHO named the disease caused by SARS-CoV-2 as coronavirus disease 2019 . The first confirmed SARS-CoV-2 case was found in Wuhan, China (Figure 1A). Subsequently, medical workers and family clusters who had not visited Wuhan tested positive for SARS-CoV-2, thus confirming human-to-human transmission [2]. SARS-CoV-2 rapidly spread to most countries and has resulted in thousands of fatalities (Figure 1B-D). WHO declared a pandemic on 11 March 2020. As of 5 May 2020, over 3 500 000 cases have been confirmed in over 185 countries, with over 243 000 deaths, suggesting a case fatality rate (CFR) of 6.9% (WHO report 106) (Figure 1B-D). However, nominal CFR are strongly influenced by the extent of testing of suspected cases and under-testing can result in higher apparent CFR. In this review, we summarize current progress in epidemiology and detection methods for SARS-CoV-2 and discuss findings concerning general characteristics of pathogenic coronaviruses. These studies form the foundation for future efforts to develop vaccines and preand postexposure therapeutics.

Transcription and replication of influenza A virus are carried out in the nuclei of infected cells in the context of viral ribonucleoproteins (RNPs). The viral polymerase responsible for these processes is a protein complex composed of the PB1, PB2, and PA proteins. We previously identified a set of polymerase-associated cellular proteins by proteomic analysis of polymerase-containing intracellular complexes expressed and purified from human cells. Here we characterize the role of NXP2/MORC3 in the infection cycle. NXP2/MORC3 is a member of the Microrchidia (MORC) family that is associated with the nuclear matrix and has RNA-binding activity. Influenza virus infection led to a slight increase in NXP2/MORC3 expression and its partial relocalization to the cytoplasm. Coimmunoprecipitation and immunofluorescence experiments indicated an association of NXP2/MORC3 with the viral polymerase and RNPs during infection. Downregulation of NXP2/MORC3 by use of two independent short hairpin RNAs (shRNAs) reduced virus titers in low-multiplicity infections. Consistent with these findings, analysis of virus-specific RNA in high-multiplicity infections indicated a reduction of viral RNA (vRNA) and mRNA after NXP2/MORC3 downregulation. Silencing of NXP2/MORC3 in a recombinant minireplicon system in which virus transcription and replication are uncoupled showed reductions in cat mRNA and chloramphenicol acetyltransferase (CAT) protein accumulation but no alterations in cat vRNA levels, suggesting that NXP2/MORC3 is important for influenza virus transcription. IMPORTANCE Influenza virus infections appear as yearly epidemics Influenza viruses cause an acute respiratory disease that annually affects millions of people worldwide (Global Influenza Surveillance and Response System [GISRS] [http://www.who .int/influenza/gisrs_laboratory/en/]). The genome of influenza A viruses is about 13 kb long and consists of eight single-stranded negative-sense RNA segments. The viral proteome includes 10 viral proteins that have been studied extensively (1) and another 8 proteins, probably accessory proteins, that were identified more recently (reviewed in reference 2). The transcription and replication of influenza viruses occur in the nuclei of infected cells and are mediated by the viral polymerase, a heterotrimer composed of the PB1, PB2, and PA subunits, in the context of viral ribonucleoprotein complexes (RNPs) (3; reviewed in references 4 to 7). The virus recruits host cell factors to help carry out these processes, and in some specific cases, their roles in virus replication have been determined (reviewed in references 4 and 8 to 10). In one such study, we identified the nuclear matrix NXP2 protein as a factor associated with influenza virus polymerase in vivo by proteomic analysis of recombinant purified polymerase complexes (11). Since influenza virus RNA synthesis is connected to the nuclear matrix (12, 13), we decided to further characterize the role of NXP2 in the virus infection cycle.The NXP2 protein (also called MORC3, ZCW...