Introduction Early literature on the COVID-19 pandemic indicated striking ethnic inequalities in SARS-CoV-2-related outcomes. This systematic review and meta-analysis aimed to describe the presence... Show moreIntroduction Early literature on the COVID-19 pandemic indicated striking ethnic inequalities in SARS-CoV-2-related outcomes. This systematic review and meta-analysis aimed to describe the presence and magnitude of associations between ethnic groups and COVID-19-related outcomes. Methods PubMed and Embase were searched from December 2019 through September 2020. Studies reporting extractable data (ie, crude numbers, and unadjusted or adjusted risk/ORs) by ethnic group on any of the five studied outcomes: confirmed COVID-19 infection in the general population, hospitalisation among infected patients, and disease severity, intensive care unit (ICU) admission and mortality among hospitalised patients with SARS-CoV-2 infection, were included using standardised electronic data extraction forms. We pooled data from published studies using random-effects meta-analysis. Results 58 studies were included from seven countries in four continents, mostly retrospective cohort studies, covering a total of almost 10 million individuals from the first wave until the summer of 2020. The risk of diagnosed SARS-CoV-2 infection was higher in most ethnic minority groups than their White counterparts in North American and Europe with the differences remaining in the US ethnic minorities after adjustment for confounders and explanatory factors. Among people with confirmed infection, African-Americans and Hispanic-Americans were also more likely than White-Americans to be hospitalised with SARS-CoV-2 infection. No increased risk of COVID-19 outcomes (ie, severe disease, ICU admission and death) was found among ethnic minority patients once hospitalised, except for a higher risk of death among ethnic minorities in Brazil. Conclusion The risk of SARS-CoV-2 diagnosis was higher in most ethnic minorities, but once hospitalised, no clear inequalities exist in COVID-19 outcomes except for the high risk of death in ethnic minorities in Brazil. The findings highlight the necessity to tackle disparities in social determinants of health, preventative opportunities and delay in healthcare use. Ethnic minorities should specifically be considered in policies mitigating negative impacts of the pandemic. PROSPERO registration number CRD42020180085. Show less
Replication of positive-stranded RNA viruses requires the activity of proteases that cleave the viral replicase polyproteins. For Middle East respiratory coronavirus (MERS-CoV), the virus-encoded... Show moreReplication of positive-stranded RNA viruses requires the activity of proteases that cleave the viral replicase polyproteins. For Middle East respiratory coronavirus (MERS-CoV), the virus-encoded papain-like protease (PLpro) is one of such proteases. This protease also functions as a deubiquitinating enzyme (DUB) that removes ubiquitin from substrates, most likely to suppress the ubiquitin-dependent activation of the innate immune response. The work described in this thesis provides novel insights in the interaction between PLpro and ubiquitin. The crystal structure of the PLpro-ubiquitin complex facilitated the design of substitutions in PLpro that selectively disrupted its DUB activity. DUB-negative MERS-CoV induced enhanced immune responses compared to wild-type virus, while showing similar replication in infected cells. Relative to wild-type virus, the virulence of DUB-negative MERS-CoV was reduced in mice and earlier, better-regulated immune responses were measured in their lungs. In the search for novel antivirals, ubiquitin sequence variants were selected that bound with very high affinity to MERS-CoV PLpro. Expression of those ubiquitin variants affected the activity of PLpro and concomitantly inhibited virus replication resulting in severely less virus progeny. Collectively, the gained knowledge can be used to design novel coronavirus vaccines or further develop ubiquitin variants as antiviral agents against viruses that encode DUBs. Show less
The interplay between nidoviruses and the infected host cell was investigated. Arterivirus RNA-synthesising activity was shown to depend on intact membranes and on a cytosolic host protein which... Show moreThe interplay between nidoviruses and the infected host cell was investigated. Arterivirus RNA-synthesising activity was shown to depend on intact membranes and on a cytosolic host protein which does not cosediment with the RTC. Furthermore, the immunosuppressant drug cyclosporin A (CsA) blocks replication of EAV and the swine arterivirus PRRSV in cell culture. Cyclophilin A appears to be an important host factor for EAV replication. CsA may be a nidovirus-wide inhibitor of replication since this compound also blocked replication of the coronaviruses SARS-CoV, HCoV-229E, and MHV. We further described a kinase siRNA library screen that identified ninety antiviral and forty proviral hits and signalling pathways involved in the SARS-CoV replicative cycle. PKR (antiviral) and COPB2 (proviral) were validated in follow-up experiments. We also investigated MERS-CoV replication characteristics and we described an assay t o screen for compounds that block MERS-CoV infection. CsA and pegylated IFN-_ (PEG-IFN) significantly inhibited infection, and MERS-CoV was shown to be much more sensitive to PEG-IFN treatment than SARS-CoV, an observation that may have implications for the treatment of MERS-CoV infection. The data presented in this thesis might contribute to better understand virus replication and hopefully provide additional starting points for the development of antiviral strategies. Show less
This thesis discusses the purification and activities of the SARS-coronavirus (SARS-CoV) RNA-dependent RNA polymerases (RdRps) nsp12 and nsp(7+8). The first is a large monomeric RdRp, whose... Show moreThis thesis discusses the purification and activities of the SARS-coronavirus (SARS-CoV) RNA-dependent RNA polymerases (RdRps) nsp12 and nsp(7+8). The first is a large monomeric RdRp, whose stability is greatly influenced by N-terminal additions. In contrast, the latter RdRp is a remarkable hexadecameric complex that is capable of both de novo initiation and primer-extension. In addition these RNA polymerase activities, the thesis also expatiates upon the calibration of magnetic tweezers for force measurements and the dynamics of the equine arteritis virus (EAV) RNA helicase as function of NTP hydrolysis. Show less
Viruses depend on their host cell for the production of their progeny. The genetic information that is required to regulate this process is contained in the viral genome. In the case of plus... Show moreViruses depend on their host cell for the production of their progeny. The genetic information that is required to regulate this process is contained in the viral genome. In the case of plus-stranded RNA viruses, like nidoviruses, the RNA genome is directly involved in translation (resulting in the synthesis of viral enzymes), replication, transcription and encapsidation into progeny virions. The multifunctional nature of these viral RNA genomes requires the tight control of all these processes for which they are equipped with RNA sequence motifs and higher order RNA structures. At 25-32 kilobases, nidoviruses possess the largest known RNA genomes. One characteristic of nidoviruses is that in infected cells they produce a nested set of subgenomic (sg) mRNAs. The sg mRNAs of two nidovirus families, arteri- and coronaviruses, consist of two RNA stretches that are noncontiguous in the genome. It was demonstrated that primary and higher order RNA structures play a crucial role during the synthesis of these special sg mRNAs. The obtained knowledge of arterivirus RNA synthesis, formed the basis for an virus inhibitor study in which regulatory RNA sequences were targeted in an attempt to block virus replication in cell culture using phosphorodiamidate morpholino oligomers (P-PMOs). Show less
