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Article ; Online: Letter to the editor: additional evidence to support a cross-reactivity of SARS-CoV-2 with HIV chemiluminescent assay.

Cipitelli, Márcio da Costa / Dornelas-Ribeiro, Marcos / Santos, Caleb G M

2021 Volume 75, Issue 7, Page(s) 503–504

MeSH term(s)	COVID-19 ; Cross Reactions ; HIV Infections/diagnosis ; Humans ; Luminescent Measurements ; SARS-CoV-2
Language	English
Publishing date	2021-10-21
Publishing country	England
Document type	Letter
ZDB-ID	80261-x
ISSN	1472-4146 ; 0021-9746
ISSN (online)	1472-4146
ISSN	0021-9746
DOI	10.1136/jclinpath-2021-207813
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Article ; Online: Evaluation of SARS-CoV-2 ORF7a Deletions from COVID-19-Positive Individuals and Its Impact on Virus Spread in Cell Culture.

Simas, Maria Clara da Costa / Costa, Sara Mesquita / Gomes, Priscila da Silva Figueiredo Celestino / Cruz, Nádia Vaez Gonçalves da / Corrêa, Isadora Alonso / de Souza, Marcos Romário Matos / Dornelas-Ribeiro, Marcos / Nogueira, Tatiana Lucia Santos / Santos, Caleb Guedes Miranda Dos / Hoffmann, Luísa / Tanuri, Amilcar / Moura-Neto, Rodrigo Soares de / Damaso, Clarissa R / Costa, Luciana Jesus da / Silva, Rosane

Viruses

2023 Volume 15, Issue 3

Abstract: The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing the COVID-19 outbreak, posed a primary concern of public health worldwide. The most common changes in SARS-CoV-2 are single nucleotide substitutions, also reported ... ...

Abstract	The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing the COVID-19 outbreak, posed a primary concern of public health worldwide. The most common changes in SARS-CoV-2 are single nucleotide substitutions, also reported insertions and deletions. This work investigates the presence of SARS-CoV-2 ORF7a deletions identified in COVID-19-positive individuals. Sequencing of SARS-CoV-2 complete genomes showed three different ORF7a size deletions (190-nt, 339-nt and 365-nt). Deletions were confirmed through Sanger sequencing. The ORF7a∆190 was detected in a group of five relatives with mild symptoms of COVID-19, and the ORF7a∆339 and ORF7a∆365 in a couple of co-workers. These deletions did not affect subgenomic RNAs (sgRNA) production downstream of ORF7a. Still, fragments associated with sgRNA of genes upstream of ORF7a showed a decrease in size when corresponding to samples with deletions. In silico analysis suggests that the deletions impair protein proper function; however, isolated viruses with partial deletion of ORF7a can replicate in culture cells similarly to wild-type viruses at 24 hpi, but with less infectious particles after 48 hpi. These findings on deleted ORF7a accessory protein gene, contribute to understanding SARS-CoV-2 phenotypes such as replication, immune evasion and evolutionary fitness as well insights into the role of SARS-CoV-2_ORF7a in the mechanism of virus-host interactions.
MeSH term(s)	Humans ; Cell Culture Techniques ; COVID-19 ; SARS-CoV-2/genetics ; Sequence Analysis ; Sequence Deletion ; Viral Proteins/genetics ; Subgenomic RNA/genetics
Chemical Substances	ORF7a protein, SARS-CoV-2 ; Viral Proteins ; Subgenomic RNA
Language	English
Publishing date	2023-03-21
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v15030801
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Article ; Online: SARS-CoV-2 diagnostic diary: from rumors to the first case. Early reports of molecular tests from the military research and diagnostic institute of Rio de Janeiro.

Cipitelli, Marcio da Costa / Valentin, Elizabeth / da Cruz, Nadia Vaez Gonçalves / Nogueira, Tatiana Ls / de Melo, Elaine Cristina Amaro / da Silva, Rebeca Araujo / Serra, Marcelo M / Meriano, André L / Colares, Alberto Ml / Dornelas-Ribeiro, Marcos / Santos, Caleb Gm

Memorias do Instituto Oswaldo Cruz

2020 Volume 115, Page(s) e200200

Abstract: Corona virus disease (COVID-19) presents a serious threat to global health. A historical timeline of early molecular diagnostics from government alert (January 22) (D) was presented. After in silico analysis, Brazilian Army Institute of Biology (IBEx-RJ) ...

Abstract	Corona virus disease (COVID-19) presents a serious threat to global health. A historical timeline of early molecular diagnostics from government alert (January 22) (D) was presented. After in silico analysis, Brazilian Army Institute of Biology (IBEx-RJ) tested samples in house using real-time reverse transcriptase polymerase chain reaction (RT-PCR) (fast mode) based on Centers for Disease Control and Prevention (CDC) recommendations. First cases from Brazil, Rio de Janeiro, IBEx, and diagnosis team were reported in D36, D44, D66, and D74 respectively. Therefore, after 1300 tests, we recommend N1/N2 primer sets (CDC) for preliminary and Charité protocol confirmation in case of positive results. Moreover, every professional should be tested before starting work, in addition to weekly tests for everyone involved.
MeSH term(s)	Betacoronavirus/genetics ; Betacoronavirus/isolation & purification ; Brazil/epidemiology ; COVID-19 ; Coronavirus Infections/diagnosis ; Coronavirus Infections/epidemiology ; Humans ; Military Facilities ; Pandemics ; Pneumonia, Viral/diagnosis ; Pneumonia, Viral/epidemiology ; Reverse Transcriptase Polymerase Chain Reaction ; SARS-CoV-2
Keywords	covid19
Language	English
Publishing date	2020-07-13
Publishing country	Brazil
Document type	Journal Article
ZDB-ID	953293-6
ISSN	1678-8060 ; 0074-0276
ISSN (online)	1678-8060
ISSN	0074-0276
DOI	10.1590/0074-02760200200
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Article ; Online: Different Profiles of Cytokines, Chemokines and Coagulation Mediators Associated with Severity in Brazilian Patients Infected with Dengue Virus.

Fiestas Solórzano, Victor Edgar / da Costa Faria, Nieli Rodrigues / Dos Santos, Caroline Fernandes / Corrêa, Gladys / Cipitelli, Márcio da Costa / Dornelas Ribeiro, Marcos / de Souza, Luiz José / Damasco, Paulo Vieira / da Cunha, Rivaldo Venâncio / Dos Santos, Flavia Barreto / de Oliveira Pinto, Luzia Maria / de Azeredo, Elzinandes Leal

Viruses

2021 Volume 13, Issue 9

Abstract: The incidence of dengue in Latin America has increased dramatically during the last decade. Understanding the pathogenic mechanisms in dengue is crucial for the identification of biomarkers for the triage of patients. We aimed to characterize the profile ...

Abstract	The incidence of dengue in Latin America has increased dramatically during the last decade. Understanding the pathogenic mechanisms in dengue is crucial for the identification of biomarkers for the triage of patients. We aimed to characterize the profile of cytokines (IFN-γ, TNF-α, IL-1β, IL-6, IL-18 and IL-10), chemokines (CXCL8/IL-8, CCL2/MCP-1 and CXCL10/IP-10) and coagulation mediators (Fibrinogen, D-dimer, Tissue factor-TF, Tissue factor pathway inhibitor-TFPI and Thrombomodulin) during the dengue-4 epidemic in Brazil. Laboratory-confirmed dengue cases had higher levels of TNF-α (
MeSH term(s)	Adult ; Biomarkers/blood ; Blood Coagulation Factors/classification ; Blood Coagulation Factors/immunology ; Brazil ; Chemokines/blood ; Chemokines/classification ; Chemokines/immunology ; Cytokines/blood ; Cytokines/classification ; Cytokines/immunology ; Dengue/blood ; Dengue/immunology ; Dengue Virus/immunology ; Female ; Humans ; Inflammation ; Male ; Middle Aged ; Severity of Illness Index
Chemical Substances	Biomarkers ; Blood Coagulation Factors ; Chemokines ; Cytokines
Language	English
Publishing date	2021-09-08
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v13091789
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Book ; Online: SARS-CoV-2 diagnostic diary

Cipitelli, Marcio da Costa / Valentin, Elizabeth / da Cruz, Nadia Vaez Gonçalves / Nogueira, Tatiana LS / de Melo, Elaine Cristina Amaro / da Silva, Rebeca Araujo / Serra, Marcelo M / Meriano, André L / Colares, Alberto ML / Dornelas-Ribeiro, Marcos / Santos, Caleb GM

Memórias do Instituto Oswaldo Cruz v.115 2020

from rumors to the first case. Early reports of molecular tests from the military research and diagnostic institute of Rio de Janeiro

2020

Abstract	Corona virus disease (COVID-19) presents a serious threat to global health. A historical timeline of early molecular diagnostics from government alert (January 22) (D) was presented. After in silico analysis, Brazilian Army Institute of Biology (IBEx-RJ) tested samples in house using real-time reverse transcriptase polymerase chain reaction (RT-PCR) (fast mode) based on Centers for Disease Control and Prevention (CDC) recommendations. First cases from Brazil, Rio de Janeiro, IBEx, and diagnosis team were reported in D36, D44, D66, and D74 respectively. Therefore, after 1300 tests, we recommend N1/N2 primer sets (CDC) for preliminary and Charité protocol confirmation in case of positive results. Moreover, every professional should be tested before starting work, in addition to weekly tests for everyone involved.
Keywords	coronavirus ; SARS-CoV-2 ; RT-PCR ; global pandemic ; COVID-19 ; covid19
Language	English
Publishing date	2020-01-01
Publisher	Instituto Oswaldo Cruz, Ministério da Saúde
Publishing country	br
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A Multidimensional Approach to Assessing Anthropometric and Aerobic Fitness Profiles of Elite Brazilian Endurance Athletes and Military Personnel.

Xavier, Raphael / Sánchez, Carlos / Paulucio, Dailson / da Silva, Izadora Moreira / Velasque, Rodolfo / Nogueira, Fernando S / Ferrini, Luiz S G / Dornelas Ribeiro, Marcos / Serrato, Mauricio / Alvarenga, Renato / Pompeu, Fernando A M S / Santos, Caleb G M

Military medicine

2019 Volume 184, Issue 11-12, Page(s) 875–881

Abstract: Introduction: Military personnel must remain physically active to meet operational requirements. Military physical training not only provides the performance capabilities required for performing occupational tasks but also fosters the development of ... ...

Abstract	Introduction: Military personnel must remain physically active to meet operational requirements. Military physical training not only provides the performance capabilities required for performing occupational tasks but also fosters the development of sport. Thus, Armed Forces across the world have historically invested in developing elite- and Olympic-level athletes. This study aimed to assess the anthropometric and physiological differences among groups of Brazilian military athletes (MA), non-military athletes (A), and military non-athletes (M). Materials and methods: Seventy-five individuals participated in the study: 17 MA (23.7 ± 4.8 years), 27 A (24.7 ± 5.3 years), and 31 M (26.9 ± 3.3 years). MA and A individuals specialized in endurance sports, and had a mean weekly training volume of (100.0 ± 34.8 and 106.3 ± 40.5 Km; F = 0.894, p = 0.6), respectively. Anthropometric measures and maximal oxygen uptake (V̇O2máx) were assessed in all participants. Ergospirometry and anthropometry variables were analyzed with one-way analysis of variance (ANOVA) for independent measures. Comparisons of weekly training volume (km) and training experience (years) were performed only between the A and MA using the Student's t-test for independent samples. For a multidimensional approach, Partial least squares discriminant analysis (PLS-DA) was performed for all variables using the online tool MetaboAnalyst. Results: We found no differences in anthropometric and physiological profiles between A and MA, but significant differences between M and MA/A in body mass index (kg/m2) (BMI), body fat percentage, fat mass (kg), waist circumference (cm) (WC), somatotype, and V̇O2máx (mL min-1 kg-1). Conclusion: In conclusion, military endurance athletes have similar anthropometric and physiological profiles to non-military athletes and superior levels to non-athlete military. These findings indicate that the Brazilian Armed Forces scouting system has been successful in identifying endurance athletic talent in line with their historic role of developing sport in Brazil.
MeSH term(s)	Adult ; Analysis of Variance ; Anthropometry/methods ; Athletes/statistics & numerical data ; Body Mass Index ; Brazil ; Exercise/physiology ; Female ; Humans ; Male ; Military Personnel/statistics & numerical data ; Oxygen Consumption/physiology ; Physical Fitness/physiology
Language	English
Publishing date	2019-04-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	391061-1
ISSN	1930-613X ; 0026-4075
ISSN (online)	1930-613X
ISSN	0026-4075
DOI	10.1093/milmed/usz003
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Article: Different Profiles of Cytokines, Chemokines and Coagulation Mediators Associated with Severity in Brazilian Patients Infected with Dengue Virus

Fiestas Solórzano, Victor Edgar / da Costa Faria, Nieli Rodrigues / dos Santos, Caroline Fernandes / Corrêa, Gladys / Cipitelli, Márcio da Costa / Dornelas Ribeiro, Marcos / de Souza, Luiz José / Damasco, Paulo Vieira / da Cunha, Rivaldo Venâncio / dos Santos, Flavia Barreto / de Oliveira Pinto, Luzia Maria / de Azeredo, Elzinandes Leal

Viruses. 2021 Sept. 08, v. 13, no. 9

2021

Abstract	The incidence of dengue in Latin America has increased dramatically during the last decade. Understanding the pathogenic mechanisms in dengue is crucial for the identification of biomarkers for the triage of patients. We aimed to characterize the profile of cytokines (IFN-γ, TNF-α, IL-1β, IL-6, IL-18 and IL-10), chemokines (CXCL8/IL-8, CCL2/MCP-1 and CXCL10/IP-10) and coagulation mediators (Fibrinogen, D-dimer, Tissue factor-TF, Tissue factor pathway inhibitor-TFPI and Thrombomodulin) during the dengue-4 epidemic in Brazil. Laboratory-confirmed dengue cases had higher levels of TNF-α (p < 0.001), IL-6 (p = 0.005), IL-10 (p < 0.001), IL-18 (p = 0.001), CXCL8/IL-8 (p < 0.001), CCL2/MCP-1 (p < 0.001), CXCL10/IP-10 (p = 0.001), fibrinogen (p = 0.037), D-dimer (p = 0.01) and TFPI (p = 0.042) and lower levels of TF (p = 0.042) compared to healthy controls. A principal component analysis (PCA) distinguished between two profiles of mediators of inflammation and coagulation: protective (TNF-α, IL-1β and CXCL8/IL-8) and pathological (IL-6, TF and TFPI). Lastly, multivariate logistic regression analysis identified high aspartate aminotransferase-to-platelet ratio index (APRI) as independent risk factors associated with severity (adjusted OR: 1.33; 95% CI 1.03–1.71; p = 0.027), the area under the receiver operating characteristics curve (AUC) was 0.775 (95% CI 0.681–0.869) and an optimal cutoff value was 1.4 (sensitivity: 76%; specificity: 79%), so it could be a useful marker for the triage of patients attending primary care centers.
Keywords	Dengue virus ; aspartic acid ; biomarkers ; coagulation ; dengue ; fibrinogen ; inflammation ; interleukin-10 ; interleukin-18 ; interleukin-6 ; principal component analysis ; regression analysis ; Brazil ; Latin America
Language	English
Dates of publication	2021-0908
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v13091789
Database	NAL-Catalogue (AGRICOLA)

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Article: SARS-CoV-2 diagnostic diary: from rumors to the first case. Early reports of molecular tests from the military research and diagnostic institute of Rio de Janeiro

Mem Inst Oswaldo Cruz

Abstract	Corona virus disease (COVID-19) presents a serious threat to global health. A historical timeline of early molecular diagnostics from government alert (January 22) (D) was presented. After in silico analysis, Brazilian Army Institute of Biology (IBEx-RJ) tested samples in house using real-time reverse transcriptase polymerase chain reaction (RT-PCR) (fast mode) based on Centers for Disease Control and Prevention (CDC) recommendations. First cases from Brazil, Rio de Janeiro, IBEx, and diagnosis team were reported in D36, D44, D66, and D74 respectively. Therefore, after 1300 tests, we recommend N1/N2 primer sets (CDC) for preliminary and Charité protocol confirmation in case of positive results. Moreover, every professional should be tested before starting work, in addition to weekly tests for everyone involved.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #646249
Database	COVID19

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Article ; Online: Trichosporon asahii secretes a 30-kDa aspartic peptidase.

Valle, Roberta S / Ramos, Lívia S / Reis, Vanessa J / Ziccardi, Mariangela / Dornelas-Ribeiro, Marcos / Sodré, Cátia L / Branquinha, Marta H / Santos, André L S

Microbiological research

2017 Volume 205, Page(s) 66–72

Abstract: Trichosporon asahii is a fungal opportunistic pathogen that causes superficial and deep-seated infections presenting high mortality. Very little is known about the virulence attributes produced by this fungus. Herein, aspartic peptidase production was ... ...

Abstract	Trichosporon asahii is a fungal opportunistic pathogen that causes superficial and deep-seated infections presenting high mortality. Very little is known about the virulence attributes produced by this fungus. Herein, aspartic peptidase production was identified in Brazilian clinical isolates of T. asahii by different methodologies. Initially, T. asahii strain 250 (from skin lesion) was inoculated in both liquid and solid culture media containing bovine serum albumin (BSA) as the sole nitrogenous source. A translucent halo around the fungal colony was observed from the 5th day of culture. The cell-free culture supernatant revealed that soluble BSA was hydrolyzed along the growth, generating low molecular mass polypeptides as observed by electrophoresis. Subsequently, the secretions from four clinical strains of T. asahii were analyzed by BSA-SDS-PAGE and a single proteolytic band of 30-kDa was detected under acidic pH at 37°C. The secreted aspartic peptidase of T. asahii efficiently cleaved the cathepsin D peptide substrate, but not the substrates with specificity to HIV-1 peptidase and rennin. The capability to cleave either cathepsin D substrate in a fluorogenic assay or BSA immobilized within a gel matrix varied according to the T. asahii isolate. T. asahii extracellular peptidase activity was strongly inhibited by pepstatin A and HIV peptidase inhibitors, classifying it as an aspartic-type peptidase. Human serum albumin, mucin, non-immune immunoglobulin G and gelatin induced, in different levels, the secretion of this aspartic peptidase. With these results, T. asahii must be included in the list of many human fungal opportunistic pathogens able to secrete an aspartic-type peptidase.
Language	English
Publishing date	2017-12
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1189614-0
ISSN	1618-0623 ; 0944-5013
ISSN (online)	1618-0623
ISSN	0944-5013
DOI	10.1016/j.micres.2017.08.015
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Article ; Online: Candida haemulonii complex: species identification and antifungal susceptibility profiles of clinical isolates from Brazil.

Ramos, Lívia S / Figueiredo-Carvalho, Maria Helena G / Barbedo, Leonardo S / Ziccardi, Mariangela / Chaves, Alessandra L S / Zancopé-Oliveira, Rosely M / Pinto, Marcia R / Sgarbi, Diana B G / Dornelas-Ribeiro, Marcos / Branquinha, Marta H / Santos, André L S

The Journal of antimicrobial chemotherapy

2015 Volume 70, Issue 1, Page(s) 111–115

Abstract: Objectives: The emerging fungal pathogens comprising the Candida haemulonii complex (Candida haemulonii, Candida haemulonii var. vulnera and Candida duobushaemulonii) are notable for their antifungal resistance. Twelve isolates with phenotypic ... ...

Abstract	Objectives: The emerging fungal pathogens comprising the Candida haemulonii complex (Candida haemulonii, Candida haemulonii var. vulnera and Candida duobushaemulonii) are notable for their antifungal resistance. Twelve isolates with phenotypic similarity to C. haemulonii were recovered from patients in Brazilian hospitals. Here we aimed to identify these isolates by a molecular approach, using the current classification of this fungal complex, and to evaluate their antifungal susceptibility profiles. Methods: The fungal isolates were rechecked to certify their authentication by mycology methodologies and then characterized by ITS1-5.8S-ITS2 gene sequencing. A susceptibility assay was performed using the broth microdilution method published by CLSI (M27-A3/M27-S3). Results: Based on biochemical tests, all Brazilian isolates were identified as C. haemulonii. After employing ITS sequencing, five isolates were identified as C. haemulonii, four as C. duobushaemulonii and three as C. haemulonii var. vulnera. All 12 clinical isolates were resistant to amphotericin B (MICs ranged from 2 to >16 mg/L) and fluconazole (MICs ≥ 64 mg/L). One isolate of C. haemulonii var. vulnera and two isolates of C. duobushaemulonii were susceptible-dose dependent to itraconazole, while the remaining isolates (75%) were resistant to this antifungal. Eight out of 12 isolates (66.7%) were resistant to voriconazole (MICs ≥ 16 mg/L), while all isolates were susceptible to caspofungin (MICs ≤ 0.5 mg/L). Conclusions: Our results reinforce the importance of molecular identification in differentiating species of the C. haemulonii complex. Moreover, the antifungal multiresistant profile of clinical isolates of the C. haemulonii complex represents a challenge to the treatment of such infections.
MeSH term(s)	Antifungal Agents/pharmacology ; Brazil ; Candida/classification ; Candida/drug effects ; Candida/genetics ; Candida/isolation & purification ; Candidiasis/microbiology ; Cluster Analysis ; DNA, Fungal/chemistry ; DNA, Fungal/genetics ; DNA, Ribosomal Spacer/chemistry ; DNA, Ribosomal Spacer/genetics ; Hospitals ; Humans ; Microbial Sensitivity Tests ; Molecular Sequence Data ; Mycological Typing Techniques ; Phylogeny ; Sequence Analysis, DNA
Chemical Substances	Antifungal Agents ; DNA, Fungal ; DNA, Ribosomal Spacer
Language	English
Publishing date	2015-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	191709-2
ISSN	1460-2091 ; 0305-7453
ISSN (online)	1460-2091
ISSN	0305-7453
DOI	10.1093/jac/dku321
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