Predominance of the SARS-CoV-2 Lineage P.1 and Its Sublineage P.1.2 in Patients from the Metropolitan Region of Porto Alegre, Southern Brazil in March 2021

Associations between epidemiological and laboratory parameters and disease severity in hospitalized patients with COVID-19 during first and second epidemic waves in middle south Mato Grosso

BACKGROUND

COVID-19 is a multisystemic disease characterized by respiratory distress. Disease severity is associated with several factors. Here we characterize virological findings and evaluate the association of laboratorial, epidemiological, virological findings and clinical outcomes of 251 patients during the first and second epidemic waves of COVID-19.

METHODS

This transversal study used biological samples and data from patients hospitalized with COVID-19 between May 2020 and August 2021 in the metropolitan region of Cuiabá, Mato Grosso Brazil. Biological samples were subjected to RT-qPCR and MinION sequencing. Univariate and multivariate logistic regression and Odds ratio were used to correlate clinical, laboratorial, epidemiological data.

FINDINGS

Patients were represented by males (61.7%) with mean age of 52.4 years, mild to moderate disease (49,0%), overweight/obese (69.3%), with comorbidities (66.1%) and evolving to death (55.38%). Severe cases showing symptoms for prolonged time, ≥ 25% of ground-glass opacities in the lungs and fatality rate increased significantly in second wave. Fatality was statistically associated to > 61 years of age,>25% ground-glass opacities in the lungs, immune, cardiac, or metabolic comorbidities. Higher viral load (p < 0.01/p = 0.02 in each wave), decreased erythrocyte (p < 0.01), hemoglobin (p < 0.05/p < 0.01), hematocrit (p < 0.01), RDW (p < 0.01), lymphocyte (p < 0.01), increased leucocyte (p < 0.01), neutrophil (p < 0.01) and CRP levels (p < 0.01) showed significant association with fatality in both waves, as did Neutrophil/Platelet (NPR; p < 0.01), Neutrophil/Lymphocyte (NLR; p < 0.01) and Monocyte/Lymphocyte ratio (MLR; p < 0.01). SARS-CoV-2 genomes from lineage B.1.1.33(n = 8) and Gamma/P.1(n = 15) shared 6/7 and 20/23 lineage-defining mutations, respectively.

MAIN CONCLUSIONS

Severity and mortality of COVID-19 associated with a panel of epidemiological and laboratorial findings, being second wave, caused by Gamma variant, more severe in this in-hospital population.

Spatiotemporal transmission of SARS-CoV-2 lineages during 2020-2021 in Pernambuco-Brazil

SARS-CoV-2 virus emerged as a new threat to humans and spread around the world, leaving a large death toll. As of January 2023, Brazil is among the countries with the highest number of registered deaths. Nonpharmacological and pharmacological interventions have been heterogeneously implemented in the country, which, associated with large socioeconomic differences between the country regions, has led to distinct virus spread dynamics. Here, we investigate the spatiotemporal dispersion of SARS-CoV-2 lineages in the Pernambuco state (Northeast Brazil) throughout the distinct epidemiological scenarios that unfolded in the first 2 years of the pandemic. We generated a total of 1,389 new SARS-CoV-2 genomes from June 2020 to August 2021. This sampling captured the arrival, communitary transmission, and the circulation of the B1.1, B.1.1.28, and B.1.1.33 lineages; the emergence of the former variant of interest P.2; and the emergence and fast replacement of all previous variants by the more transmissible variant of concern P.1 (Gamma). Based on the incidence and lineage spread pattern, we observed an East-to-West to inner state pattern of transmission, which is in agreement with the transmission of more populous metropolitan areas to medium- and small-size country-side cities in the state. Such transmission patterns may be partially explained by the main routes of traffic across municipalities in the state. Our results highlight that the fine-grained intrastate analysis of lineages and incidence spread can provide actionable insights for planning future nonpharmacological intervention for air-borne transmissible human pathogens.IMPORTANCEDuring the COVID-19 pandemic, Brazil was one of the most affected countries, mainly due its continental-size, socioeconomic differences among regions, and heterogeneous implementation of intervention methods. In order to investigate SARS-CoV-2 dynamics in the state of Pernambuco, we conducted a spatiotemporal dispersion study, covering the period from June 2020 to August 2021, to comprehend the dynamics of viral transmission during the first 2 years of the pandemic. Throughout this study, we were able to track three significant epidemiological waves of transmission caused by B1.1, B.1.1.28, B.1.1.33, P.2, and P.1 lineages. These analyses provided valuable insights into the evolution of the epidemiological landscape, contributing to a deeper understanding of the dynamics of virus transmission during the early years of the pandemic in the state of Pernambuco.

Genomic characterization and molecular evolution of SARS-CoV-2 in Rio Grande do Sul State, Brazil

SARS-CoV-2 is the virus responsible for the COVID-19 and has afflicted the world since the end of 2019. Different lineages have been discovered and the Gamma lineage, which started the second wave of infections, was first described in Brazil, one of the most affected countries by pandemic. Therefore, this study analyzed SARS-CoV-2 sequenced genomes from Esteio city in Rio Grande do Sul, Southern Brazil. We also comparatively analyzed genomes of the two first years of the pandemic from Rio Grande do Sul state for understanding their genomic and evolutionary patterns. The phylogenomic analysis showed monophyletic groups for Alpha, Gamma, Delta and Omicron, as well as for other circulating lineages in the state. Molecular evolutionary analysis identified several sites under adaptive selection in membrane and nucleocapsid proteins which could be related to a prevalent stabilizing effect on membrane protein structure, as well as majoritarily destabilizing effects on C-terminal nucleocapsid domain.

Perspective Chapter: SARS-CoV-2 Variants - Two Years Post-Onset of the Pandemic

Since the pandemic began in China in December 2019, thousands of variants of SARS-CoV-2 have emerged globally since late 2020. The World Health Organization (WHO) defined the SARS-CoV-2 variant of concern (VOC) as a variant with increased transmissibility, virulence, and decreased response to available diagnostics, vaccines, and therapeutics. Areas of the emerging variant of concern arise from countries like the United Kingdom, South Africa, Brazil, and India. These mutations carry a lineage from N501Y, D614G, N439K, Y453F, and others, which are globally dominated by clades 20A, 20B, and 20C. SARS-CoV-2 VOC emerged after 11 months of evolution since the onset through massive human-to-human transmission with five major VOCs recognized by the WHO, namely Alpha, Beta, Gamma, Delta, and Omicron. Their emergence could be attributed to changing immunological dynamics in the human population, which has resulted in resistance or escape from neutralizing antibodies, or to mutations and/or recombinations that increase transmission or pathogenicity. This literature review intends to identify and report on SARS-CoV-2 variants that have evolved two years post-onset of the pandemic and their disease implications.

Final Results of a Randomized, Placebo-Controlled, Two-Arm, Parallel Clinical Trial of Proxalutamide for Hospitalized COVID-19 Patients: A Multiregional, Joint Analysis of the Proxa-Rescue AndroCoV Trial

Background The role of androgens on COVID-19 is well established. Proxalutamide is a second-generation, non-steroidal antiandrogen (NSAA) with the highest antiandrogen potency among NSAAs and concurrent regulation of angiotensin-converting enzyme 2 (ACE2) expression and inflammatory response. Proxalutamide has been demonstrated to be effective to prevent hospitalizations in early COVID-19 in randomized clinical trials (RCTs). Conversely, in hospitalized COVID-19 patients, preliminary results from two different arms of an RCT (The Proxa-Rescue AndroCoV Trial) also demonstrated a reduction in all-cause mortality. This study aims to report the final, joint results of the two arms (North arm and South arm) of the Proxa-Rescue AndroCoV trial of the two arms (North and South arms) combined, and to evaluate whether COVID-19 response to proxalutamide was consistent across different regions (Northern Brazil and Southern Brazil). Materials and methods Upon randomization, hospitalized COVID-19 patients received either proxalutamide 300mg/day or placebo for 14 days, in addition to usual care, in a proxalutamide:placebo ratio of 1:1 in the North arm and 4:1 in the South arm (ratio was modified due to preliminary report of high drug efficacy). Datasets of the South and North arms were combined, and statistical analysis was performed for the overall study population. Proxalutamide was compared to placebo group for 14-day and 28-day recovery (discharge alive from the hospital) and mortality rates, and overall and post-randomization hospitalization stay. Results of proxalutamide and placebo groups were also compared between the North and South arms. Analysis was also performed stratified by sex and baseline WHO COVID Ordinary Score. Results A total of 778 subjects were included (645 from the North, 317 from the proxalutamide group and 328 from the placebo group; 133 from the South arm, 106 from the proxalutamide group and 27 from the placebo group). Recovery rate was 121% higher in proxalutamide than placebo group at day 14 [81.1% vs 36.6%; Recovery ratio (RecR) 2.21; 95% confidence interval (95% CI), 1.92-2.56; p<0.0001], and 81% higher at day 28 (98.1% vs 47.6%; RecR, 1.81; 95% CI, 1.61-2.03; p<0.0001). All-cause mortality rate was 80% lower in proxalutamide than placebo group at Day 14 [8.0% vs 39.2%; Risk ratio (RR), 0.20; 95% CI, 0.14-0.29; p<0.0001], and 78% lower at Day 28 (10.6% vs 48.2%; RR, 0.22; 95% CI 0.16-0.30). Post-randomization time-to-discharge was shorter in proxalutamide [median, 5 days; interquartile range (IQR), 3-8] than placebo group (median, 9 days; IQR, 6-14) (p<0.0001). Results were statistically similar between North and South arms for all measured outcomes. Males and females presented similar results in all outcomes. Patients that did not require oxygen use (scores 3 and 4) did not present statistically significant improvement in recovery and mortality rates, whereas scores 5 and 6 presented significant improvements in all outcomes (p<0.0001 for all). Conclusion Proxalutamide increased recovery rate, reduced mortality rate and shortened hospital stay in hospitalized COVID-19 patients. Results were similar between the two different arms, providing further consistency for the efficacy of proxalutamide when used in late-stage COVID-19.

Epidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil

The emergence and widespread circulation of severe acute respiratory syndrome coronavirus 2 variants of concern (VOCs) or interest impose an enhanced threat to global public health. In Brazil, one of the countries most severely impacted throughout the pandemic, a complex dynamics involving variants co-circulation and turnover events has been recorded with the emergence and spread of VOC Gamma in Manaus in late 2020. In this context, we present a genomic epidemiology investigation based on samples collected between December 2020 and May 2021 in the second major Brazilian metropolis, Rio de Janeiro. By sequencing 244 novel genomes through all epidemiological weeks in this period, we were able to document the introduction and rapid dissemination of VOC Gamma in the city, driving the rise of the third local epidemic wave. Molecular clock analysis indicates that this variant has circulated locally since the first weeks of 2021 and only 7 weeks were necessary for it to achieve a frequency above 70 per cent, consistent with rates of growth observed in Manaus and other states. Moreover, a Bayesian phylogeographic reconstruction indicates that VOC Gamma spread throughout Brazil between December 2020 and January 2021 and that it was introduced in Rio de Janeiro through at least 13 events coming from nearly all regions of the country. Comparative analysis of reverse transcription-quantitative polymerase chain reaction (RT-qPCR) cycle threshold (Ct) values provides further evidence that VOC Gamma induces higher viral loads (N1 target; mean reduction of Ct: 2.7, 95 per cent confidence interval = ± 0.7). This analysis corroborates the previously proposed mechanistic basis for this variant-enhanced transmissibility and distinguished epidemiological behavior. Our results document the evolution of VOC Gamma and provide independent assessment of scenarios previously studied in Manaus, therefore contributing to the better understanding of the epidemiological dynamics currently being surveyed in other Brazilian regions.

The ongoing evolution of variants of concern and interest of SARS-CoV-2 in Brazil revealed by convergent indels in the amino (N)-terminal domain of the spike protein

Mutations at both the receptor-binding domain (RBD) and the amino (N)-terminal domain (NTD) of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Spike (S) glycoprotein can alter its antigenicity and promote immune escape. We identified that SARS-CoV-2 lineages circulating in Brazil with mutations of concern in the RBD independently acquired convergent deletions and insertions in the NTD of the S protein, which altered the NTD antigenic-supersite and other predicted epitopes at this region. Importantly, we detected the community transmission of different P.1 lineages bearing NTD indels ∆69-70 (which can impact several SARS-CoV-2 diagnostic protocols), ∆144 and ins214ANRN, and a new VOI N.10 derived from the B.1.1.33 lineage carrying three NTD deletions (∆141-144, ∆211, and ∆256-258). These findings support that the ongoing widespread transmission of SARS-CoV-2 in Brazil generates new viral lineages that might be more resistant to antibody neutralization than parental variants of concern.