ABSTRACT
Background P.1 lineage (Gamma) was first described in the State of Amazonas, northern Brazil, in the end of 2020, and has emerged as a very important variant of concern (VOC) of SARS-CoV-2 worldwide. P.1 has been linked to increased infectivity, higher mortality and immune evasion, leading to reinfections and potentially reduced efficacy of vaccines and neutralizing antibodies. Methods The samples of 276 patients from the State of Amazonas were sent to a central referral laboratory for sequencing by gold standard techniques, through Illumina MiSeq platform. Both global and regional phylogenetic analyses of the successfully sequenced genomes were conducted through maximum likelihood method. Multiple alignments were obtained including previously obtained unique human SARS-CoV-2 sequences. The evolutionary histories of spike and non-structural proteins from ORF1a of northern genomes were described and their molecular evolution was analyzed for detection of positive (FUBAR, FEL, and MEME) and negative (FEL and SLAC) selective pressures. To further evaluate the possible pathways of evolution leading to the emergence of P.1, we performed specific analysis for copy-choice recombination events. A global phylogenomic analysis with subsampled P.1 and B.1.1.28 genomes was applied to evaluate the relationship among samples. Results Forty-four samples from the State of Amazonas were successfully sequenced and confirmed as P.1 (Gamma) lineage. In addition to previously described P.1 characteristic mutations, we find evidence of continuous diversification of SARS-CoV-2, as rare and previously unseen P.1 mutations were detected in spike and non-structural protein from ORF1a. No evidence of recombination was found. Several sites were demonstrated to be under positive and negative selection, with various mutations identified mostly in P.1 lineage. According to the Pango assignment, phylogenomic analyses indicate all samples as belonging to the P.1 lineage. Conclusion P.1 has shown continuous evolution after its emergence. The lack of clear evidence for recombination and the positive selection demonstrated for several sites suggest that this lineage emergence resulted mainly from strong evolutionary forces and progressive accumulation of a favorable signature set of mutations.
ABSTRACT
Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectivity is mediated by the androgen-promoted protease, transmembrane protease, serine 2 (TMPRSS2). Previously, we have shown that treatment with proxalutamide, a non-steroidal androgen receptor antagonist, accelerates viral clearance and clinical remission in outpatients with coronavirus disease 2019 (COVID-19) compared to placebo. The effects in hospitalized COVID-19 patients were unknown. Methods: Men and women hospitalized but not requiring mechanical ventilation were randomized (1:1 ratio) to receive 300 mg of proxalutamide per day or placebo for 14 days. The study was conducted at eight sites in the state of Amazonas, Brazil. The primary outcome measure was the clinical status (8-point ordinal scale) at 14-days post-randomization. The primary efficacy endpoint was the 14-day recovery ratio (alive hospital discharge [scores 1, 2]). Findings: A total of 645 patients were randomized (317 received proxalutamide, 328 placebo) and underwent intention-to-treat analysis. The 14-day median ordinal scale score in the proxalutamide group was 1 (interquartile range [IQR]=1–2) versus 7 (IQR=2–8) for placebo, P<0.001. The 14-day recovery rate was 81.4% for proxalutamide and 35.7% for placebo (recovery ratio, 2.28; 95% CI 1.95–2.66 [P<0.001]). The 28-day all-cause mortality rate was 11.0% for proxalutamide versus 49.4% for placebo (hazard ratio, 0.16; 95% CI 0.11–0.24). The median post-randomization time to recovery was 5 days (IQR=3–8) for proxalutamide versus 10 days (IQR=6–15) for placebo.Interpretation: Hospitalized COVID-19 patients not requiring mechanical ventilation receiving proxalutamide had a 128% higher recovery rate than those treated with placebo. Clinical Trial Registration Details: ClinicalTrials.gov number, NCT04728802Funding Information: Kintor Pharmaceuticals, Ltd.Declaration of Interests: Kintor Pharmaceuticals, Ltd. manufactures and plans to market proxalutamide, and has an investigational new drug (IND) application under United States Food and Drugs Administration to conduct a Phase 3 study for proxalutamide for COVID19. Applied Biology, Inc. has patents pending regarding antiandrogen therapy for COVID19. Dr. Goren, Dr. McCoy, and Dr. Li are employees of Applied Biology, Inc. Dr. Cadegiani has served as a clinical director for Applied Biology, Inc. Dr. Wambier has served as an advisor to Applied Biology, Inc. The other authors have no conflict of interest to declare.Ethics Approval Statement: The study was approved by an ethics committee and registered in clinicaltrials.gov (NCT04728802), and also approved by Brazilian National Ethics Committee, approval number 4.513.425; CAAE 41909121.0.0000.5553; Comitê de Ética em Pesquisa (CEP) of the Comitê Nacional de Ética em Pesquisa (CONEP) of the Ministry of Health (MS). (CEP/CONEP/MS).
Subject(s)
Alzheimer Disease , Porphyria, Erythropoietic , Severe Acute Respiratory Syndrome , Multiple Sclerosis , COVID-19ABSTRACT
Almost a year after the COVID-19 pandemic had begun, The United Kingdom, South Africa, and Brazil became the epicenter of new lineages, the Variant of Concern (VOCs), B.1.1.7, B.1.351, and P.1, respectively. These VOCs are increasingly associated with enhanced transmissibility, immunity evasion, and mortality. The previous most prevalent lineages in the state of Rio Grande do South (Brazil), B.1.1.28 and B.1.1.33 were rapidly replaced by P.1 and P.2, two B.1.1.28-derived lineages harboring the E484K mutation. To perform a genomic characterization of SARS-CoV-2 samples from COVID-19 patients from the metropolitan region of Porto Alegre (Rio Grande do Sul, Southern Brazil), in this second pandemic wave, we sequenced viral samples from patients of this region to: (i) identify the prevalence of SARS-CoV-2 lineages in the region, the state and bordering countries/states, (ii) characterize the mutation spectra, and (iii) hypothesize possible viral dispersal routes by using phylogenetic and phylogeographic approaches. As results, we not only confirmed that 96.4% of the samples belonged to the P.1 lineage but also that approximately 20% of which could be assigned as the newer P.1.2 (a P.1 derived new sublineage harboring new signature substitutions recently described and present in other Brazilian states and foreign countries). Moreover, P.1 sequences from this study were allocated in several distinct branches (four clades and five clusters) of the P.1 phylogeny, suggesting multiple introductions of P.1 in Rio Grande do Sul still in 2020 and placing this state as a potential core of diffusion and emergence of P.1-derived clades. It is still uncertain if the emergence of P.1.2 and other P.1 clades are related to further virological, clinical, or epidemiological consequences. However, the clear signs of viral molecular diversification from recently introduced P.1 warrant further genomic surveillance.
Subject(s)
COVID-19ABSTRACT
Importance In the COVID-19 pandemic, a limiting barrier for more successful approaches to COVID-19 is the lack of appropriate timing for its diagnosis, during the viral replication stage, when antiviral approaches could demonstrate efficacy, precluding progression to severe stages. Three major reasons that hamper the diagnosis earlier in the disease are the unspecific and mild symptoms in the first stage, the cost- and time-limitations of the rtPCR-SARS-CoV-2, and the insufficient sensitivity of this test as desired for screening purposes during the pandemic. More sensitive and earlier methods of COVID-19 detection should be considered as key for breakthrough changes in the disease course and response to specific therapeutic strategies. Our objective was to propose a clinical scoring for the diagnosis of COVID-19 (The AndroCoV Clinical Scoring for COVID-19 Diagnosis) that has been validated in a large population sample, aiming to encourage the management of patients with high pre-clinical likelihood of presenting COVID-19, at least during the pandemics, independent of a rtPCR-SARS-COV-2 test. Materials and methods This is a compounded retrospective and prospective analysis of clinical data prospectively collected from the Pre-AndroCoV and AndroCov Trials that resulted in a clinical scoring for COVID-19 diagnosis based on likelihood of presenting COVID-19 according to the number of symptoms, presence of anosmia, and known positive household contact, in a variety of combinations of scoring criteria, aiming to the detect scorings that provided the highest pre-test probability and accuracy. Sensitivity, specificity, positive predictive value, negative predictive value, positive likelihood ratio, and accuracy were calculated for subjects screened in two different periods and altogether, for females, males, and both, in a total of nine different scenarios, for combinations between one, two, or three or more symptoms, or presence of anosmia in subjects without known positive household contacts, and no symptoms, one, two, or three or more symptoms, or presence of anosmia or ageusia in subjects with known positive household contacts. Results 1,757 patients were screened for COVID-19. Among the multiple combinations, requiring two or more symptoms with or without anosmia or ageusia for subjects without known contact and one or more symptoms with or without anosmia or ageusia with known positive contacts presented the highest accuracy (80.4%), and higher pretest probability and accuracy than virtually all rtPCR-SARS-CoV-2 commercially available kit tests. Conclusion The AndroCoV Clinical Scoring for COVID-19 Diagnosis was demonstrated to be a feasible, quick, inexpensive and sensitive diagnostic tool for clinical diagnosis of COVID-19. A clinical diagnosis of COVID-19 should avoid delays and missed diagnosis, and reduce costs, and should therefore be recommended as a first-line option for COVID-19 diagnosis for public health policies, at least while SARS-CoV-2 is the prevailing circulating virus. Key Points Question Is a clinical diagnosis of COVID-19 sensitive, accurate, and feasible? Findings The present analysis of a 1,757-subject cohort of the AndroCoV trials demonstrated that clinical scoring for COVID-19 diagnosis can deliver a more sensitive and prompter diagnosis than the current gold-standard diagnostic method, rtPCR-SARS-CoV-2, with an accuracy above 80%. Meaning A clinical diagnosis of COVID-19 avoids missed diagnosis due to insufficient sensitivity or incorrect timing of the performance of rtPCR-SARS-CoV-2, reduces costs, avoid delays on specific managements, and allows the testing of potentially effective antiviral therapeutic approaches that should work if administered in the early stage of COVID-19
Subject(s)
COVID-19 , Olfaction DisordersABSTRACT
Background: Antiandrogens have demonstrated a protective effect for COVOD-19 patients in observational and interventional studies. The goal of this study was to determine if proxalutamide, an androgen receptor antagonist, could be an effective treatment for men with COVID-19 in an outpatient setting. Study design and methods: A randomized, double-blinded, placebo-controlled clinical trial was conducted at two outpatient centers (Brasilia, Brazil). Patients were recruited from October 21 to December 24, 2020 (ClinicalTrials.gov number, NCT04446429). Male patients with confirmed COVID-19 but not requiring hospitalization (COVID-19 8-point ordinal scale <3) were administered proxalutamide 200mg/day or placebo for up to 7 days. The primary endpoint was hospitalization rate at 30 days post-randomization.Results: A total of 268 men were randomized in a 1:1 ratio. 134 patients receiving proxalutamide and 134 receiving placebo were included in the intention-to-treat analysis. The 30-day hospitalization rate was 2.2% in men taking proxalutamide compared to 26% in placebo, P<0.001. The 30-day hospitalization risk ratio was 0.09; 95% confidence interval (CI) 0.03 to 0.27. Patients in the proxalutamide arm more frequently reported gastrointestinal adverse events, however, no patient discontinued treatment. In placebo group, 6 patients were lost to follow-up, and 2 patients died from acute respiratory distress syndrome.Conclusion: The hospitalization rate in proxalutamide treated men was reduced by 91% compared to usual care. Trial Registration: NCT04446429
Subject(s)
COVID-19 , Respiratory Distress SyndromeABSTRACT
Importance: SARS-CoV-2 cell entry and infectivity is indirectly dependent on androgenic status and phenotype through the regulation of transmembrane protease serine 2 (TMPRSS2), an androgen-mediated proteolytic enzyme that facilitates SARS-CoV-2 entry. Males, particularly those affected by androgenetic alopecia (AGA) are overrepresented in severe COVID-19, while the use of 5-alpha-reductase inhibitors (5ARis), an antiandrogenic drug class, may reduce COVID-19 severity. Objective: Our objective was to determine if dutasteride, a wide and potent 5ARi, would bring biochemical and virological benefits in early COVID-19.Design, Setting, and Participants: A double-blinded, randomized, prospective, investigational study of dutasteride for the treatment of COVID-19, as add-on therapy to the local standard of care, for mild or moderate, non-hospitalized subjects confirmed for SARS-CoV-2 (The Duta AndroCoV Trial).Interventions: Dutasteride 0.5mg/day or placebo for 30 days or until full COVID-19 remission. Nitazoxanide was given 500mg twice a day for six days and azithromycin was given 500mg/day for five days for all subjects.Main Outcome(s) and Measure(s): Remission times for fatigue, ageusia, anosmia, and overall disease, oxygen saturation (%), real-time polymerase chain reaction (rtPCR-SARS-CoV-2), ultrasensitive C-reactive protein (usCRP), D-dimer, lactate, dehydrogenase lactate (DHL), erythrocyte sedimentation rate (ESR), ultrasensitive troponin and ferritin.Results: Compared to placebo group (n=44) with similar baseline characteristics, dutasteride (n=43) presented reduced fatigue, anosmia and overall disease duration (46.6%, 49.6% and 43.2% lower duration, respectively; p<.0001 for all), and in Day 7 presented higher rates of virologic cure (64.3% versus 11.8% cure; p=.0094), , increased recovery rate (84.7% versus 57.5%; p=.03), higher mean [SD] oxygen saturation (97.0% [1.4%] versus 95.7% [2.0%]; p=.02), lower median [IQR] usCRP (0.34mg/L [0.23mg/L -0.66mg/L] versus 1.47mg/L [0.70mg/L-3.37mg/L]; p<.0001), lower median [IQR] lactate (2.01mmol/L [1.12mmol/L-2.43mmol/L] versus 2.66mmol/L [2.05mmol/L-3.55mmol/L]; p=.0049), lower median [IQR] ESR (5.0mm/1h [3.0mm/1h-11.0mm/1h] versus 14.0mm/1h [7.25mm/1h-18.5mm/1h]; p=.0007), lower median [IQR] LDH (165U/L [144U/L -198U/L] versus 210U/L [179U/L-249U/L]; p=.0013 and lower median [IQR] troponin levels (0.005ng/mL [0.003ng/mL-0.009ng/mL] versus 0.007ng/mL [0.006ng/mL-0.010ng/mL]; p=.048).Conclusions and Relevance: These findings suggest that dutasteride reduces clinical and virologic disease duration and inflammatory markers in males with mild-to-moderate, early-stage COVID-19, and should be considered as a therapeutic option in the current context of the COVID-19 pandemic.Trial Registration: NCT04446429