Transcriptome studies have reported the dysregulation of cell cycle-related genes and the global inhibition of host mRNA translation in COVID-19 cases. However, the key genes and cellular mechanisms that are most affected by the severe outcome of this disease remain unclear. For this work, the RNA-seq approach was used to study the differential expression in buffy coat cells of two groups of people infected with SARS-CoV-2: (a) Mild, with mild symptoms; and (b) SARS (Severe Acute Respiratory Syndrome), who were admitted to the intensive care unit with the severe COVID-19 outcome. Transcriptomic analysis revealed 1009 up-regulated and 501 down-regulated genes in the SARS group, with 10% of both being composed of long non-coding RNA. Ribosome and cell cycle pathways were enriched among down-regulated genes. The most connected proteins among the differentially expressed genes involved transport dysregulation, proteasome degradation, interferon response, cytokinesis failure, and host translation inhibition. Furthermore, interactome analysis showed Fibrillarin to be one of the key genes affected by SARS-CoV-2. This protein interacts directly with the N protein and long non-coding RNAs affecting transcription, translation, and ribosomal processes. This work reveals a group of dysregulated processes, including translation and cell cycle, as key pathways altered in severe COVID-19 outcomes.

The emergence of the COVID-19 pandemic resulted in an unprecedented need for RT-qPCR-based molecular diagnostic testing, placing a strain on the supply chain and the availability of commercially available PCR testing kits and reagents. The effect of limited molecular diagnostics-related supplies has been felt across the globe, disproportionally impacting molecular diagnostic testing in developing countries where acquisition of supplies is limited due to availability. The increasing global demand for commercial molecular diagnostic testing kits and reagents has made standard PCR assays cost prohibitive, resulting in the development of alternative approaches to detect SARS-CoV-2 in clinical specimens, circumventing the need for commercial diagnostic testing kits while mitigating the high-demand for molecular diagnostics testing. The timely availability of the complete SARS-CoV-2 genome in the beginning of the COVID-19 pandemic facilitated the rapid development and deployment of specific primers and standardized laboratory protocols for the molecular diagnosis of COVID-19. An alternative method offering a highly specific manner of detecting and genotyping pathogens within clinical specimens is based on the melting temperature differences of PCR products. This method is based on the melting temperature differences between purine and pyrimidine bases. Here, RT-qPCR assays coupled with a High Resolution Melting analysis (HRM-RTqPCR) were developed to target different regions of the SARS-CoV-2 genome (RdRp, E and N) and an internal control (human RNAse P gene). The assays were validated using synthetic sequences from the viral genome and clinical specimens (nasopharyngeal swabs, serum and saliva) of sixty-five patients with severe or moderate COVID-19 from different states within Brazil; a larger validation group than that used in the development to the commercially available TaqMan RT-qPCR assay which is considered the gold standard for COVID-19 testing. The sensitivity of the HRM-RTqPCR assays targeting the viral N, RdRp and E genes were 94.12, 98.04 and 92.16%, with 100% specificity to the 3 SARS-CoV-2 genome targets, and a diagnostic accuracy of 95.38, 98.46 and 93.85%, respectively. Thus, HRM-RTqPCR emerges as an attractive alternative and low-cost methodology for the molecular diagnosis of COVID-19 in restricted-budget laboratories.

Since COVID-19 was declared a pandemic, Brazil has become one of the countries most affected by this disease. A year into the pandemic, a second wave of COVID-19 emerged, with a rapid spread of a new SARS-CoV-2 lineage of concern. Several vaccines have been granted emergency-use authorization, leading to a decrease in mortality and severe cases in many countries. However, the emergence of SARS-CoV-2 variants raises the alert for potential new waves of transmission and an increase in pathogenicity. We compared the demographic and clinical data of critically ill patients infected with COVID-19 hospitalized in Rio de Janeiro during the first and second waves between July 2020 and October 2021. In total, 106 participants were included in this study; among them, 88% had at least one comorbidity, and 37% developed severe disease. Disease severity was associated with older age, pre-existing neurological comorbidities, higher viral load, and dyspnea. Laboratory biomarkers related to white blood cells, coagulation, cellular injury, inflammation, renal, and liver injuries were significantly associated with severe COVID-19. During the second wave of the pandemic, the necessity of invasive respiratory support was higher, and more individuals with COVID-19 developed acute hepatitis, suggesting that the progression of the second wave resulted in an increase in severe cases. These results can contribute to understanding the behavior of the COVID-19 pandemic in Brazil and may be helpful in predicting disease severity, which is a pivotal for guiding clinical care, improving patient outcomes, and defining public policies.

Introdução/Objetivo As doenças crônicas como hipertensão arterial e diabetes são condições associadas a maior morbimortalidade na infecção pelo novo coronavírus (SARS-CoV-2). Entretanto, distúrbios metabólicos como a obesidade podem também contribuir como um fator de risco para o desenvolvimento de COVID-19 grave. Este estudo objetiva determinar o perfil da COVID-19 em indivíduos com sobrepeso (Sp) e obesos (Ob) hospitalizados em hospital terciário. Métodos Foram estudados 85 indivíduos com COVID-19 confirmada laboratorialmente durante o período de julho/2020 a junho/2021, sendo classificados de acordo com o índice de massa corpórea (IMC): ≤25, não obeso (Nob), >25 e ≤29,9, Sp; ≥ 30 kg/mm 2 , Ob. Dados demográficos e clínicos foram obtidos através de fichas padronizadas e bancos de dados institucionais, sendo a análise estatística realizada pelo software R. Resultados A população geral do estudo compunha-se de indivíduos com idade média de 60,6 ± 16,3 anos, sendo 54,1% de mulheres. Destas, 71,1% foram classificadas como Sp/Ob, em contraste com 64,1% dos homens. Em 73/84 pacientes, havia ≥ 1 comorbidade, sendo 21/27 (77,8%) e 52/57 (91,2%) no grupo Nob e Sp/Ob, respectivamente. Entre as manifestações clínicas, o grupo Sp/Ob apresentou dispneia, 28/57 (49,12% x Nob, 0/27 (0,0%), febre, 26/57 (45,61% x Nob, 1/27 (3,7%,) e tosse, 26/57 (45,61% x Nob, 12/27 (44,4%). A mortalidade geral foi de 32,14% (Nob, 12/27, 44,4%; Sp/Ob, 17/57, 29,82%). Foram admitidos 49/84 (58,3%) pacientes na terapia intensiva (Nob,18/27 (66,7%) e Sp/Ob, 31/57 (54,4%), sendo a mortalidade de 42,9% (12/28) no grupo Nob versus 57,14% (16/28, p > 0.05, Odds Ratio = 0.5333, IC95% 0.1658-1.879). Conclusão Os dados indicaram que a população com Sp/Ob hospitalizada compõe-se de mulheres acima dos 60 anos, portadoras de múltiplas comorbidades. Este grupo apresenta-se mais sintomático na admissão, mas os indivíduos com IMC ≤ 25 podem apresentar discreto aumento da frequência de desfechos desfavoráveis.