ABSTRACT
Monitoring SARS-CoV-2 spread and evolution through genome sequencing is essential in handling the COVID-19 pandemic. The availability of patient hospital records is crucial for linking the genomic sequence information to virus function during the course of infections. Here, we sequenced 892 SARS-CoV-2 genomes collected from patients in Saudi Arabia from March to August 2020. From the assembled sequences, we estimate the SARS-CoV-2 effective population size and infection rate and outline the epidemiological dynamics of import and transmission events during this period in Saudi Arabia. We show that two consecutive mutations (R203K/G204R) in the SARS-CoV-2 nucleocapsid (N) protein are associated with higher viral loads in COVID-19 patients. Our comparative biochemical analysis reveals that the mutant N protein displays enhanced viral RNA binding and differential interaction with key host proteins. We found hyper-phosphorylation of the adjacent serine site (S206) in the mutant N protein by mass-spectrometry analysis. Furthermore, analysis of the host cell transcriptome suggests that the mutant N protein results in dysregulated interferon response genes. We provide crucial information in linking the R203K/G204R mutations in the N protein as a major modulator of host-virus interactions and increased viral load and underline the potential of the nucleocapsid protein as a drug target during infection.
ABSTRACT
BackgroundSince the emergence of COVID-19, the world has been desperate to find effective therapeutics and vaccinations to treat hundreds of thousands of affected patients and to suppress the spread of this global pandemic. Lopinavir-ritonavir (LPV/RTV) is an HIV antiviral combination that has been considered for treatment of this disease. Aim of the studyThis systematic review and meta-analysis aimed to assess the efficacy and safety of lopinavir/ritonavir in COVID-19 patients in the extant published research. A systematic review protocol was developed based on PRISMA-P and the PRISMA statement. Published English and non-English articles written since December 1, 2019 were selected for review from 8 electronic databases. Readily accessible full articles (cohort studies and clinical trials) which specifically mentioned lopinavir/ritonavir and patients with lab-confirmed SARS-CoV-2 or COVOID-19 of any age were included. Three researchers separately evaluated the bias in the reported articles. We conducted a systematic review and meta-analysis with the objective of evaluation of the safety and efficacy of LPV/RTV alone or in combination with other drugs with regard to time to becoming PCR negative, time to body temperature normalization and cough relief, radiological progression, and safety. Review Manager (RevMan) was used to conduct all statistical analyses and generate the forest plots. Meta-analyses were performed using the Mantel Hazel method or the inverse variance method for dichotomous data and continuous data respectively. ResultsNon-duplicate articles (n=76) were evaluated for possible inclusion. A consensus was reached to select 29 articles for full-text screening, only 11 articles comprised 1,192 patients were included in this study, and six of which were included for meta-analysis. In terms of virological cure (PCR negative), three studies reported less time in days to achieve a virological cure for LPV/RTV arm relative to no antiviral therapy (conventional) (mean difference = -0.81 day; 95% CI, -4.44 to 2.81; P = 0.007, I2 = 80%). However, the overall effect was not significant (P = 0.66). When comparing LPV/RTV arm to umifenovir arm, a favorable affect was observed for umifenovir arm, but not statically significant (mean difference = 0.95 day; 95% CI, -1.11 to 3.01; P = 0.09, I2 = 58%). In terms of time to body normalization and cough relief (clinical cure), two studies reported on time to temperature normalization with no significant effect of LPV/RTV (n = 93) versus umifenovir (n = 71) arm), (OR = 0.87 day; 95% CI, 0.42 to 1.78; (P = 0.70), I2 = 0%), or alleviation of cough duration (p = 0.69). In terms of CT evidence of radiological progression of pneumonia/lung damage, treatment with lopinavir/ritonavir resulted in no significant decrease in the radiological progression (OR = 0.80; 95% CI, 0.42 to 1.54; P = 0.59, I2 = 81%), In terms of safety, a greater number of adverse events were reported for lopinavir/ritonavir (n=45) relative to the umifenovir arm (n=14) and conventional treatments (n=10), P = 0.004, 0,0007, respectively ConclusionsThe small number of studies included in this systematic review and meta-analysis study did not reveal any statistically significant advantage in efficacy of lopinavir-ritonavir in COVID-19 patients, over conventional or other antiviral treatments. This result might not reflect the actual evidence.
