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1.
Einstein (Sao Paulo) ; 20: eAO6175, 2022.
Article in English | MEDLINE | ID: covidwho-2026529

ABSTRACT

OBJECTIVE: To describe the first COVID-19 pandemic at Casa Ondina Lobo, a philanthropic nursing home in São Paulo city, and the containment measures against the pandemic that proved to be effective. METHODS: Several preventive measures were taken before and during the pandemic, with emphasis on universal testing by reverse transcription polymerase chain reaction for COVID-19. All residents and employees were tested twice in a D9 period. RESULTS: Among the 62 residents and 55 employees, in both testing, eight residents and nine employees tested positive for COVID-19. Of 22% of employees and 75% of residents evolved asymptomatic, emphasizing the importance of universal testing for the detection and isolation of these cases. A quarter of residents evolved without any symptoms, however, with COVID-19 signs, reinforcing the importance of monitoring vital signs. The second testing did not detect any new cases among residents, demonstrating the effectiveness of the containment measures, however, it found four new cases among employees. This emphasized their role in COVID-19 outbreaks in nursing homes. Only one patient died, a 12.5% lethality among those known to be infected and a 1.6% mortality in the total population of residents were seen. CONCLUSION: The adoption of appropriate containment measures enabled to contain an COVID-19 pandemic in studied nursing home. Universal reverse transcription polymerase chain reaction testing for COVID-19 has proved to be particularly important and effective.


Subject(s)
COVID-19 , Brazil/epidemiology , COVID-19/prevention & control , COVID-19 Testing , Humans , Nursing Homes , Pandemics/prevention & control
2.
Transplantation ; 2022 Aug 05.
Article in English | MEDLINE | ID: covidwho-1985218

ABSTRACT

BACKGROUND: Comparative studies of third heterologous doses following the CoronaVac vaccine against coronavirus disease 2019 (COVID-19) in kidney transplant recipients are lacking. METHODS: This prospective, single-center cohort study included kidney transplant recipients without previous COVID-19. Patients received a third heterologous (BNT162b2 mRNA) or homologous dose at least 4 wk after 2 doses of the CoronaVac vaccine. Immunoglobulin G antibody response and seroprevalence for neutralizing anti-severe acute respiratory syndrome coronavirus 2 antibodies immediately before and 28 d after third doses were compared between the groups. RESULTS: There were 307 patients in the heterologous group and 777 in the homologous group. Patients in the heterologous group were older (54 versus 50 y; P < 0.0001), with a longer time since transplant (11 versus 6 y; P < 0.0001). Immediately before the third dose, immunoglobulin G seroprevalence (36% versus 34%; P = 0.597) and antibody titers (246 versus 268 AU/mL; P = 0.279) were similar. After booster, seroconversion was higher in the heterologous group (49% versus 32%; P < 0.0001), resulting in a higher seroprevalence (67% versus 55%; P = 0.0003); however, 42% of all patients remained seronegative. Antibody titers after booster in seropositive patients were higher in the heterologous group (7771 versus 599 AU/mL; P < 0.0001). These results persisted after adjusting for confounding variables. Lastly, a similar proportion of patients became seropositive for neutralizing antibodies (98% versus 94%; P = 0.098). CONCLUSIONS: In kidney transplant recipients fully vaccinated with CoronaVac, a third dose with an mRNA vaccine produced a higher seroconversion rate and antibody titers than a third homologous dose. However, both boosters achieved equivalent seroprevalence for neutralizing antibodies. The high proportion of still seronegative patients indicates the need for alternative strategies of protection.

3.
Commun Med (Lond) ; 2: 72, 2022.
Article in English | MEDLINE | ID: covidwho-1895609

ABSTRACT

Background: The Complete Blood Count (CBC) is a commonly used low-cost test that measures white blood cells, red blood cells, and platelets in a person's blood. It is a useful tool to support medical decisions, as intrinsic variations of each analyte bring relevant insights regarding potential diseases. In this study, we aimed at developing machine learning models for COVID-19 diagnosis through CBCs, unlocking the predictive power of non-linear relationships between multiple blood analytes. Methods: We collected 809,254 CBCs and 1,088,385 RT-PCR tests for SARS-Cov-2, of which 21% (234,466) were positive, from 900,220 unique individuals. To properly screen COVID-19, we also collected 120,807 CBCs of 16,940 individuals who tested positive for other respiratory viruses. We proposed an ensemble procedure that combines machine learning models for different respiratory infections and analyzed the results in both the first and second waves of COVID-19 cases in Brazil. Results: We obtain a high-performance AUROC of 90 + % for validations in both scenarios. We show that models built solely of SARS-Cov-2 data are biased, performing poorly in the presence of infections due to other RNA respiratory viruses. Conclusions: We demonstrate the potential of a novel machine learning approach for COVID-19 diagnosis based on a CBC and show that aggregating information about other respiratory diseases was essential to guarantee robustness in the results. Given its versatile nature, low cost, and speed, we believe that our tool can be particularly useful in a variety of scenarios-both during the pandemic and after.

4.
Einstein (Sao Paulo, Brazil) ; 20, 2022.
Article in English | EuropePMC | ID: covidwho-1738042

ABSTRACT

Objective: To describe the first COVID-19 pandemic at Casa Ondina Lobo, a philanthropic nursing home in São Paulo city, and the containment measures against the pandemic that proved to be effective. Methods: Several preventive measures were taken before and during the pandemic, with emphasis on universal testing by reverse transcription polymerase chain reaction for COVID-19. All residents and employees were tested twice in a D9 period. Results: Among the 62 residents and 55 employees, in both testing, eight residents and nine employees tested positive for COVID-19. Of 22% of employees and 75% of residents evolved asymptomatic, emphasizing the importance of universal testing for the detection and isolation of these cases. A quarter of residents evolved without any symptoms, however, with COVID-19 signs, reinforcing the importance of monitoring vital signs. The second testing did not detect any new cases among residents, demonstrating the effectiveness of the containment measures, however, it found four new cases among employees. This emphasized their role in COVID-19 outbreaks in nursing homes. Only one patient died, a 12.5% lethality among those known to be infected and a 1.6% mortality in the total population of residents were seen. Conclusion: The adoption of appropriate containment measures enabled to contain an COVID-19 pandemic in studied nursing home. Universal reverse transcription polymerase chain reaction testing for COVID-19 has proved to be particularly important and effective.

5.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-307760

ABSTRACT

The current outbreak of severe acute respiratory syndrome associated with coronavirus 2 (SARS-CoV-2) is pressing public health systems around the world, and large population testing is a key step to control this pandemic disease. Real-time reverse-transcription PCR (real-time RT-PCR) is the gold standard test for virus detection but the soaring demand for this test resulted in shortage of reagents and instruments, severely limiting its applicability to large-scale screening. To be used either as an alternative, or as a complement, to real-time RT-PCR testing, we developed a high-throughput targeted proteomics assay to detect SARS-CoV-2 proteins directly from clinical respiratory tract samples. Sample preparation was fully automated by using a modified magnetic particle-based proteomics approach implemented on a robotic liquid handler, enabling a fast processing of samples. The use of turbulent flow chromatography included four times multiplexed on-line sample cleanup and UPLC separation. MS/MS detection of three peptides from SARS-CoV-2 nucleoprotein and a 15 N-labeled internal global standard was achieved within 2.5 min, enabling the analysis of more than 500 samples per day. The method was validated using 562 specimens previously analyzed by real-time RT-PCR and was able to detect over 83% of positive cases. No interference was found with samples from common respiratory viruses, including other coronaviruses (NL63, OC43, HKU1, and 229E). The strategy here presented has high sample stability and low cost and should be considered as an option to large population testing.

6.
Braz J Infect Dis ; 25(4): 101604, 2021.
Article in English | MEDLINE | ID: covidwho-1397193

ABSTRACT

BACKGROUND: São Paulo city has been one of the regions most affected by the COVID-19 pandemic in Brazil. Frequent asymptomatic and oligosymptomatic infections and poor access to diagnostic tests make serosurveys crucial to monitor the magnitude of the epidemic and to inform public health policies, such as vaccination plans. OBJECTIVES: To estimate, early in the epidemic, the seroprevalence of antibodies to SARS-CoV-2 in adults living in the six most affected districts in São Paulo city, and to assess potential associated risk factors. METHODS: This was a cross-sectional population-based survey of 1,152 households randomly selected from 72 census tracts. During the period May 4-12, 2020, 463 participants completed a questionnaire on sociodemographic characteristics and history of symptoms in the past two weeks, and provided a blood sample. Prevalence of SARS-CoV-2 antibodies was the outcome of interest and was estimated based on results of two immunoassays, Maglumi SARS-CoV-2 chemiluminescence assay Immunoglobulin (Ig) M (IgM) and IgG, and Roche electrochemiluminescence assay total Ig. Serum samples reactive to either assay were considered positive. RESULTS: Weighted overall seroprevalence was 6% (95%CI 3.9-8.3%). No association was observed between seropositivity and sex, age group or education level. Participants who reported black and brown skin color showed a 2.7 fold higher prevalence than people with white skin (p = 0.007). Among the 30 seropositive individuals, 14 (46.6%) reported no COVID-19 compatible symptoms in the past two weeks. CONCLUSION: This study represents the first assessment of SARS-CoV-2 seroprevalence in the city of São Paulo and 6% is the baseline estimate of a series of population-based seroprevalence surveys. Serological screening using sound serological assays is the key tool to monitoring temporal and geographic changes in the spread of the virus through an important epicenter of the COVID-19 pandemic in Brazil. Ultimately, it may inform prevention and control efforts.


Subject(s)
COVID-19 , SARS-CoV-2 , Adult , Antibodies, Viral , Brazil/epidemiology , Cross-Sectional Studies , Humans , Immunoglobulin G , Pandemics , Seroepidemiologic Studies
7.
Transpl Infect Dis ; 23(5): e13706, 2021 Oct.
Article in English | MEDLINE | ID: covidwho-1331786

ABSTRACT

BACKGROUND: Kidney transplant recipients have higher COVID-19 associated mortality compared to the general population. However, as only symptomatic patients seek medical attention, the current level of exposure, the main sources of acquisition, and the behavior of humoral immunity over time are poorly understood. METHODS: This cross-sectional prospective single-center study recruited kidney transplant recipients of any age living in Sao Paulo. A sample size of 401 patients was calculated considering the 17.2% seroprevalence in the municipality population from a published survey, a 95% confidence interval and an absolute error of 2%. RESULTS: Of the 2636 eligible patients, 416 were included. The seroprevalence for IgG anti-SARS-CoV-2 was 8.2%. Seroconversion rate decreased with increasing age, from 15.7% (18-35 years) to 8.3% (36-60 years) and 4.2% (>60 years, p = 0.042). Seropositivity among previously confirmed COVID-19 patients was 68.4%, followed by 9.4% in those with flu-like symptoms and only 4.6% among asymptomatic patients (p < 0.0001). Seroprevalence was significantly higher among patients reporting household contact (p = 0.018). Twenty-seven from the 34 IgG+ patients had a second test after 59 (IQR 50-63) days, and, in 33%, the IgG index became below the positivity threshold. CONCLUSIONS: In this cohort of kidney transplant recipients, the seroprevalence for IgG anti-SARS-CoV-2 was lower than that of the general population, decreased with ageing, and was associated with household contacts. In a considerable proportion of the patients, there was a significant decay in the IgG levels in a short period of time. Therefore, preventive strategies, such as prioritization for vaccination, should be urgently considered.


Subject(s)
COVID-19 , Kidney Transplantation , Adolescent , Adult , Antibodies, Viral , Brazil/epidemiology , Cross-Sectional Studies , Humans , Kidney Transplantation/adverse effects , Prospective Studies , SARS-CoV-2 , Seroepidemiologic Studies , Transplant Recipients , Young Adult
8.
Medicine (Baltimore) ; 100(15): e25495, 2021 Apr 16.
Article in English | MEDLINE | ID: covidwho-1180673

ABSTRACT

ABSTRACT: While the new Coronavirus Disease 2019 (COVID-19) pandemic rapidly spread across the world, South America was reached later in relation to Asia, Europe and the United States of America (USA). Brazil concentrates now the largest number of cases in the continent and, as the disease speedily progressed throughout the country, prompt and challenging operational strategies had to be taken by institutions caring for COVID-19 and non-COVID-19 patients in order to assure optimal workflows, triage, and management. Although hospitals in the USA, Europe and Asia have shared their experience on this subject, little has been discussed about such strategies in South America or by the perspective of outpatient centers, which are paramount in the radiology field. This article shares the guidelines adopted early in the pandemic by a nationwide outpatient healthcare center composed by a network of more than 200 patient service centers and nearly 2,000 radiologists in Brazil, discussing operational and patient management strategies, staff protection, changes adopted in the fellowship program, and the effectiveness of such measures.


Subject(s)
Ambulatory Care , COVID-19 , Change Management , Civil Defense , Critical Pathways , Strategic Planning , Technology, Radiologic , Ambulatory Care/methods , Ambulatory Care/organization & administration , Ambulatory Care/statistics & numerical data , Brazil/epidemiology , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19/prevention & control , Civil Defense/organization & administration , Civil Defense/statistics & numerical data , Critical Pathways/organization & administration , Critical Pathways/trends , Humans , Organizational Innovation , Practice Guidelines as Topic , SARS-CoV-2 , Strategic Planning/standards , Strategic Planning/statistics & numerical data , Technology, Radiologic/methods , Technology, Radiologic/organization & administration , Technology, Radiologic/statistics & numerical data
9.
Arch Endocrinol Metab ; 65(3): 381-385, 2021 Nov 03.
Article in English | MEDLINE | ID: covidwho-1145747

ABSTRACT

In recent years the immunomodulatory actions of vitamin D, a steroid hormone, have been extensively studied. In 2020, due to the COVID-19 pandemic, the question arose as to 25(OH)D status would be related to susceptibility to SARS-CoV-2 infection, since several studies pointed out a higher prevalence and severity of the disease in populations with low levels of 25(OH)D. Thus, we investigated the 25(OH)D levels in adults "Detected" positive for SARS CoV-2 by RT-PCR (reverse transcriptase polymerase chain reaction) test, and in negative controls, "not Detected", using the Fleury Group's examination database, in Sao Paulo, Brazil. Of a total of 14.692 people with recent assessments of 25(OH)D and RT-PCR tests for COVID-19, 2.345 were positive and 11.585 were negative for the infection. The groups did not differ in the percentage of men and women, or in the age distribution. There were no differences in the distribution of 25(OH)D between the two groups (p = 0.08); mean 25(OH)D of 28.8 ± 21.4 ng/mL and 29.6 ± 18.1 ng/mL, respectively. In the specific population studied, clinical, environmental, socioeconomic and cultural factors should have greater relevance than 25(OH)D in determining the susceptibility to COVID-19.


Subject(s)
COVID-19 , Vitamin D Deficiency , Adult , Brazil/epidemiology , Female , Humans , Male , Pandemics , SARS-CoV-2 , Vitamin D , Vitamin D Deficiency/epidemiology
10.
Nat Commun ; 11(1): 6201, 2020 12 03.
Article in English | MEDLINE | ID: covidwho-960315

ABSTRACT

The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is pressing public health systems around the world, and large population testing is a key step to control this pandemic disease. Here, we develop a high-throughput targeted proteomics assay to detect SARS-CoV-2 nucleoprotein peptides directly from nasopharyngeal and oropharyngeal swabs. A modified magnetic particle-based proteomics approach implemented on a robotic liquid handler enables fully automated preparation of 96 samples within 4 hours. A TFC-MS system allows multiplexed analysis of 4 samples within 10 min, enabling the processing of more than 500 samples per day. We validate this method qualitatively (Tier 3) and quantitatively (Tier 1) using 985 specimens previously analyzed by real-time RT-PCR, and detect up to 84% of the positive cases with up to 97% specificity. The presented strategy has high sample stability and should be considered as an option for SARS-CoV-2 testing in large populations.


Subject(s)
COVID-19 Testing/methods , Clinical Laboratory Techniques , Mass Spectrometry/methods , Humans , Nasopharynx/virology , Oropharynx/virology , Proteomics , SARS-CoV-2/isolation & purification , Sensitivity and Specificity , Viral Proteins
11.
Science ; 369(6508): 1255-1260, 2020 09 04.
Article in English | MEDLINE | ID: covidwho-675945

ABSTRACT

Brazil currently has one of the fastest-growing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemics in the world. Because of limited available data, assessments of the impact of nonpharmaceutical interventions (NPIs) on this virus spread remain challenging. Using a mobility-driven transmission model, we show that NPIs reduced the reproduction number from >3 to 1 to 1.6 in São Paulo and Rio de Janeiro. Sequencing of 427 new genomes and analysis of a geographically representative genomic dataset identified >100 international virus introductions in Brazil. We estimate that most (76%) of the Brazilian strains fell in three clades that were introduced from Europe between 22 February and 11 March 2020. During the early epidemic phase, we found that SARS-CoV-2 spread mostly locally and within state borders. After this period, despite sharp decreases in air travel, we estimated multiple exportations from large urban centers that coincided with a 25% increase in average traveled distances in national flights. This study sheds new light on the epidemic transmission and evolutionary trajectories of SARS-CoV-2 lineages in Brazil and provides evidence that current interventions remain insufficient to keep virus transmission under control in this country.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/epidemiology , Coronavirus Infections/transmission , Pneumonia, Viral/epidemiology , Pneumonia, Viral/transmission , Basic Reproduction Number , Bayes Theorem , Betacoronavirus/classification , Brazil/epidemiology , COVID-19 , COVID-19 Testing , Cities/epidemiology , Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Coronavirus Infections/prevention & control , Coronavirus Infections/virology , Europe , Evolution, Molecular , Genome, Viral , Humans , Models, Genetic , Models, Statistical , Pandemics/prevention & control , Phylogeny , Phylogeography , Pneumonia, Viral/prevention & control , Pneumonia, Viral/virology , SARS-CoV-2 , Spatio-Temporal Analysis , Travel , Urban Population
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