Immunodominant antibody responses directed to SARS-CoV-2 hotspot mutation sites and risk of immune escape

Introduction

Considering the likely need for the development of novel effective vaccines adapted to emerging relevant CoV-2 variants, the increasing knowledge of epitope recognition profile among convalescents and afterwards vaccinated with identification of immunodominant regions may provide important information.

Methods

We used an RBD peptide microarray to identify IgG and IgA binding regions in serum of 71 COVID-19 convalescents and 18 vaccinated individuals.

Results

We found a set of immunodominant RBD antibody epitopes, each recognized by more than 30% of the tested cohort, that differ among the two different groups and are within conserved regions among betacoronavirus. Of those, only one peptide, P44 (S415-429), recognized by 68% of convalescents, presented IgG and IgA antibody reactivity that positively correlated with nAb titers, suggesting that this is a relevant RBD region and a potential target of IgG/IgA neutralizing activity.

Discussion

This peptide is localized within the area of contact with ACE-2 and harbors the mutation hotspot site K417 present in gamma (K417T), beta (K417N), and omicron (K417N) variants of concern. The epitope profile of vaccinated individuals differed from convalescents, with a more diverse repertoire of immunodominant peptides, recognized by more than 30% of the cohort. Noteworthy, immunodominant regions of recognition by vaccinated coincide with mutation sites at Omicron BA.1, an important variant emerging after massive vaccination. Together, our data show that immune pressure induced by dominant antibody responses may favor hotspot mutation sites and the selection of variants capable of evading humoral response.

Colonization by Streptococcus pneumoniae among children in Porto Velho, Rondônia, Western Brazilian Amazon

Streptococcus pneumoniae is one of the primary pathogens that are associated with acute respiratory infections (ARI) that cause high rates of morbidity and mortality among children under five years of age in developed and developing countries. This study aimed to determine the prevalence of nasopharyngeal colonization, the antimicrobial resistance profile, and the capacity for biofilm formation by S. pneumoniae isolated from children aged 0-6 years with ARI throughout the Porto Velho-RO. A total of 660 swabs were collected from children with ARI. Molecular and biochemical tests were performed to characterize the isolates. The disk-difusion method and the E-test were used for antimicrobial sensitivity testing (TSA). Biofilm formation capacity was assessed using microtiter plate assays, and serotype detection was acheived using polymerase chain reaction (PCR) analyses. The colonization rate for S. pneumoniae was 8.9% (59/660) and exhibited a high prevalence in children under 23 months of age 64.4% (38/59). The observed serotypes were 9V and 19F with frequencies of 1.7% (1/59) and 13.6% (8/59), respectively. The antimicrobial susceptibility test revealed 100% (59/59) sensitivity to vancomycin. In contrast, trimethoprim and oxacillin exhibited high resistance rates of 76.3% (45/59) and 52.5% (31/59), respectively. Of the biofilm-forming isolates, 54.8% (23/42) possessed resistance to some antimicrobials. In this study, S. pneumoniae showed high rates of antimicrobial resistance and the ability to form biofilms, as these are factors that favor bacterial persistence and can cause serious damage to the host.

Selenium and mercury in Brazilian Cerrado soils and their relationships with physical and chemical soil characteristics

The objective of this study was to determine the natural concentrations of Hg and Se in 45 representative soil profiles from the Cerrado biome in central Brazil, and to correlate their concentrations with soil chemical and physical characteristics. The study area was composed of three sub-regions: Goiás, Northwest of Minas Gerais, and Minas Gerais Triangle. Selenium and Hg concentrations were determined by acid digestion and atomic absorption spectroscopy. Data were subjected to analysis of variance on the means of the Hg and Se variables within each soil class at two depths, followed by multivariate statistical methods. The Hg concentrations ranged from 15 to 182 μg kg^-1 and the Se concentrations ranged from 22 to 72 μg kg^-1. The soil characteristics that most contributed to Hg concentrations in the soils, according to principal component analysis, were Fe₂O₃, FeO, TiO₂, pH, P₂O₅, and effective CEC. In general, the soils of the Cerrado biome have deficient Se concentrations. The Humic Rhodic Acrustoxes have Hg concentrations above the prevention reference value for soils of Minas Gerais.

First Report of Enterobacter cowanii Causing Bacterial Spot on Mabea fistulifera, a Native Forest Species in Brazil

In the summer of 2011, in a nursery located in Viçosa City, Minas Gerais State, brownish, necrotic, irregular spots were observed on leaves of Mabea fistulifera Mart. (Euphorbiaceae), an indigenous forest species commonly found in Brazil. Around 6,300 seedlings were evaluated and as many as 60% of them showed disease symptoms, including severe defoliation and plant death. Leaves with coalescing lesions turned papery in texture and had a blighted appearance. Bacterial colonies were isolated from these symptomatic leaves on King B's medium and identified based on biochemical and molecular analysis, as a member of the Enterobacteriaceae family. Like other members of the Enterobacteriaceae family, the bacteria were facultative anaerobic, gram-negative, cream-colored on YDC medium, urease and oxidase negative, as well as catalase and asparagine positive. Bacterial DNA was extracted from pure culture grown overnight in liquid 523 medium at 28°C using the Wizard Genomic DNA Purification kit (Promega) and conserved sequences in 16S rDNA (3) and rpoB (1) were amplified by PCR. The sequence of the 1,300-bp 16S rDNA fragment and the 750-bp rpoB gene were analyzed by NCBI BLAST. Related sequences were aligned and analyzed by ClustalW in MEGA 5 software. Phylogenetic analysis by maximum likelihood, using PAUP version 4.0 and TBR algorithm with 1,000 bootstrap replications, grouped the isolate in a clade with Enterobacter cowanii and the result showed 99% and 98% identity to the 16s rDNA and rpoB, respectively. The isolate clustered closely with the type strain of E. cowanii in both phylogenetic trees constructed. Pathogenicity tests were carried out by inoculating leaves of healthy seedlings either by spraying or cutting with a scissor previously dipped into a 10⁸ CFU/ml bacterial suspension. The experiment was in a completely randomized design, with six replications. A pot with one plant was considered one experimental unit. Control seedlings were sprayed or cut with a scissor treated with saline solution. Prior to and after inoculation, plants were kept in a humid chamber for 24 h at 26°C in the dark and at room temperature. Subsequently, plants were transferred to growth chamber at 26°C, under a 12-h photoperiod (40 μmol/s/m²). Consistent with the symptoms observed originally, 7 days after inoculation, all seedlings developed leaf spots. No characteristic symptoms could be observed in the negative control. Furthermore, Koch's postulates were confirmed by reisolation of the bacterium from symptomatic tissues. In summary, the phenotypic, biochemical, and molecular tests identified the pathogen as E. cowanii. Recently, E. cowanii was isolated from Eucalyptus trees with symptoms of bacterial blight, although its pathogenicity was not demonstrated (2). To the best of our knowledge, this is the first report of a member of the Enterobacteriaceae family causing disease in M. fistulifera. The result has a great importance to better understand the role of E. cowanii as a pathogen-causing disease on a forest species. References: (1) C. L. Brady et al. Syst. Appl. Microbiol. 31:447, 2008. (2) C. L. Brady et al. Lett. Appl. Microbiol. 49:461, 2009. (3) W. G. Weisburg et al. J. Bacteriol. 173:697, 1991.

No evidence of association between the D10S1423 locus and Alzheimer disease in Brazilian patients

In a genome survey for Alzheimer's disease (AD), Zubenko et al. (1998) reported that the 234bp allele of the D10S1423 locus was more frequent among AD cases than in controls. We have analyzed this polymorphic locus in patients and healthy controls and observed that the 226bp allele is the most frequent allele in the D10S1423 locus in Brazilian AD patients. However, no statistically significant association between any D10S1423 allele was observed in AD patients as well as in controls.

Community acquired pneumonia among pediatric outpatients in Salvador, Northeast Brazil, with emphasis on the role of pneumococcus

Pneumonia is one of the leading causes of hospitalization and death among children in developing countries, and mortality due to pneumonia has been associated with S. pneumoniae infection. This investigation was designed to describe the antimicrobial susceptibility and serotype patterns of pneumococcal strains recovered from the blood of children with community-acquired pneumonia (CAP) and to assess the clinical findings of pneumococcal bacteremic patients with pneumonia. In a 26 month prospective study, blood cultures were obtained as often as possible from children (<16 years of age) diagnosed with CAP in two emergency rooms. Antimicrobial drug susceptibility tests and serotyping were performed when pneumococcus was identified. We studied 3,431 cases and cultured blood samples from 65.5% of those. Pneumococcus was recovered from 0.8% of the blood samples. The differences in age, somnolence, wheezing and hospitalization among children with and without pneumococcal bacteremia were statistically significant. Pneumococcal bacteremia was age-related (mean 1.63 +/- 1.55; median 0.92) and associated with somnolence and hospitalization among children with CAP. One strain was recovered from pleural fluid. Penicillin resistance was detected in 21.0% (4/19) of the strains at an intermediate level, whereas 63.0% of the strains were resistant to trimethoprim-sulfamethoxazole. The most common serotypes were 14 and 6B, and these serotypes included the resistant strains. Eight of our 18 isolates from blood were of types included in the heptavalent conjugate pneumococcal vaccine, recently licensed in the USA.

Analysis of the disease risk locus DXS1047 polymorphism in Brazilian Alzheimer patients

Alzheimer's disease (AD) is a disorder characterized by a progressive deterioration in memory and other cognitive functions. Four genes associated with early onset AD have been identified but familial AD is rare. The majority of late onset AD (LOAD) is caused by a complex inheritance with several genes interacting with environmental factors. The epsilon4 allele of the apolipoprotein E (APOE) gene has been reported worldwide as a risk factor associated with LOAD. The short variant of a polymorphism in the transcriptional region of the serotonin transporter gene (5-HTTLPR) was analyzed in several psychiatric conditions and found to be more frequently associated with European and Brazilian LOAD patients. Recently, allelic associations with LOAD were reported for five other loci, the most significant for one X-linked 202-bp allele, at the DXS1047 locus. We have analyzed this locus in Brazilian LOAD patients and observed that the 202-bp allele was not significantly more frequent among patients. In contrast, two other alleles (200 bp and 208 bp) were less frequent among AD male patients than in controls, confirming the importance of replicating association studies in different populations.

Medical students at risk of nosocomial transmission of Mycobacterium tuberculosis

SETTING

University and teaching hospital in Rio de Janeiro, Brazil, a city with a high prevalence of tuberculosis (TB).

OBJECTIVE

To determine whether medical students are at increased risk of nosocomial transmission of Mycobacterium tuberculosis relative to other university students.

DESIGN

A cross-sectional study of medical and chemical engineering students in different levels of their training programmes. Information about socio-demographic characteristics, BCG vaccination history, and potential exposures to TB were obtained using a standardised questionnaire. Tuberculin skin testing (TST) was used to determine the prevalence of infection with TB.

RESULTS

Medical students have an increasing prevalence of TST positivity as they advance in their training programme to increasing levels of study (4.6%, 7.8%, 16.2%, respectively, P < 0.001), but chemical engineering students do not (4.2%, 4.3%, 4.4%, respectively, P = 0.913). The risks are greatest during the years of clinical training, when medical students have increased contact with patients.

CONCLUSIONS

Medical students in this setting may be at increased risk of M. tuberculosis infection, relative to chemical engineering students. A programme of routine tuberculin skin testing is needed, combined with interventions to reduce the risk of nosocomial transmission in the workplace.

The study of genetic polymorphisms related to serotonin in Alzheimer's disease: a new perspective in a heterogenic disorder

Genetic and environmental factors have been implicated in the development of Alzheimer's disease (AD), the most common form of dementia in the elderly. Mutations in 3 genes mapped on chromosomes 21, 14 and 1 are related to the rare early onset forms of AD while the epsilon 4 allele of the apolipoprotein E (APOE) gene (on chromosome 19) is the major susceptibility locus for the most common late onset AD (LOAD). Serotonin (5-hydroxytryptamine or 5-HT) is a key neurotransmitter implicated in the control of mood, sleep, appetite and a variety of traits and behaviors. Recently, a polymorphism in the transcriptional control region upstream of the 5-HT transporter (5-HTT) gene has been studied in several psychiatric diseases and personality traits. It has been demonstrated that the short variant(s) of this 5-HTT gene-linked polymorphic region (5-HTTLPR) is associated with a different transcriptional efficiency of the 5-HTT gene promoter resulting in decreased 5-HTT expression and 5-HT uptake in lymphocytes. An increased frequency of this 5-HTTLPR short variant polymorphism in LOAD was recently reported. In addition, another common polymorphic variation in the 5-HT2A and 5-HT2C serotonin receptor genes previously analyzed in schizophrenic patients was associated with auditory and visual hallucinations in AD. These observations suggest that the involvement of the serotonin pathway might provide an explanation for some aspects of the affective symptoms commonly observed in AD patients. In summary, research on genetic polymorphisms related to AD and involved in receptors, transporter proteins and the enzymatic machinery of serotonin might enhance our understanding of this devastating neurodegenerative disorder.

The short variant of the polymorphism within the promoter region of the serotonin transporter gene is a risk factor for late onset Alzheimer's disease

We analyzed a deletion/insertion polymorphism within the promoter region of the serotonin transporter gene (5-HTTPLR) in 81 patients with late onset Alzheimer's (AD) disease (mean age 70.02 +/- 8.13 years). Control groups included 81 normal subjects with comparable age (mean age 75.6 +/- 10.2) and 82 younger normal subjects (mean age 37.4 +/- 9.1). Statistical analysis showed a significant difference in the genotype and gene frequencies between the AD group and normal controls (chi 2 = 9.021; 2 d.f. and chi 2 = 5.59, 1 d.f., respectively, P < 0.05) due to the higher frequency of the L allele and the lower frequency of the s allele in controls than among AD patients. However, no differences were found in the genotype frequencies in older as compared to younger normal control groups (chi 2 = 0.337, 2 d.f. and P > 0.05). The present study confirms, in a different population, that the short variant of the 5-HTTPLR polymorphism may be a risk factor for late onset AD.

The receiver operating characteristics curve in the evaluation of a random urine specimen as a screening test for diabetic nephropathy

OBJECTIVE

To assess the performance of measurements of urinary albumin concentration (UAC) and urinary albumin:creatinine ratio (UACR) in a diurnal random urine specimen (RUS) for the screening of diabetic nephropathy.

RESEARCH DESIGN AND METHODS

A total of 95 ambulatory NIDDM patients (49 women, ages 40-75 years) collected 123 RUSs during the morning after completing a timed 24-h urine collection. Albumin was measured by immunoturbidimetry. According to timed urinary albumin excretion rate (UAER) measured in the 24-h collection (criterion standard), samples were classified as normoalbuminuric (UAER < 20 micrograms/min; n = 54), microalbuminuric (UAER 20-200 micrograms/min; n = 44), and macroalbuminuric (UAER > 200 micrograms/min; n = 25). The receiver operating characteristics (ROC) curve approach was used. The ROC curves of UAC and UACR in RUS for screening of microalbuminuria (normo- and microalbuminuric samples; n = 98) and macroalbuminuria (micro- and macroalbuminuric samples; n = 69) were plotted.

RESULTS

Spearman's coefficients of correlation of 24-h UAER vs. UAC and UACR were 0.91 and 0.92, respectively (P < 0.001). The calculated areas (+/- SE) under the ROC curves to screen microalbuminuria for UAC (0.9766 +/- 0.015) and UACR (0.9689 +/- 0.014) were similar (P > 0.05) as were the corresponding areas for macroalbuminuria (0.9868 +/- 0.0094 and 0.9614 +/- 0.0241, respectively; P > 0.05). The first point with 100% sensitivity and the point of intersection with a 100%-to-100% diagonal for microalbuminuria were as follows: 16.9 and 33.6 mg/l for UAC and 15.0 and 26.8 mg/g for UACR; for macroalbuminuria 174.0 and 296.2 mg/l for UAC and 116.0 and 334.3 mg/g for UACR, respectively.

CONCLUSIONS

Albumin measurements (UAC and UACR) in an RUS presented almost perfect accuracy for the screening of micro- and macroalbuminuria and UAC measured in an RUS is simpler and less expensive than UACR and UAER. It is suggested as a valid test for use in screening for diabetic nephropathy.

Main clinical features of the three mapped autosomal recessive limb-girdle muscular dystrophies and estimated proportion of each form in 13 Brazilian families

Autosomal recessive limb-girdle muscular dystrophies (AR LGMD) represent a group of muscle diseases with a wide spectrum of clinical signs, varying from very severe to mild. Four different loci that when mutated cause the AR LGMD phenotype have been mapped or cloned or both: in two of them the linked families seem to have a relatively mild phenotype (LGMD2a and LGMD2b), in the third one the reported linked families show a more severe clinical course (LGMD2c), while mutations in the fourth locus may cause severe or mild phenotypes (LGMD2d). The relative proportion of each of these genetic forms among the LGMD families and whether there are other genes that when mutated cause this phenotype is unknown. The closest available informative markers for each of the mapped AR LGMD genes have been tested in 13 Brazilian families with at least three affected patients. The findings from the present report confirm non-allelic heterogeneity for LGMD and suggest that in our population about 33% of the LGMD families are caused by mutations in the 15q gene, 33% in the 2p gene, 17% by mutations in the adhalin gene, and less than 10% may be by mutations at the 13q locus. They also suggest that there is at least one other gene responsible for this phenotype. In addition, the main clinical features of the different forms are discussed.

Genetic heterogeneity for Duchenne-like muscular dystrophy (DLMD) based on linkage and 50 DAG analysis

Duchenne-like muscular dystrophy (DLMD) is an autosomal recessive (AR) muscular dystrophy which presents a clinical course indistinguishable from the Xp21 Duchenne muscular dystrophy or DMD. Recently, Othmane et al., based on a linkage study with 13q12 markers in 3 highly inbred DLMD families from Tunisia, suggested that the gene for this myopathy lies in the pericentromeric region of chromosome 13q. It is unknown if there is genetic heterogeneity causing the DLMD phenotype. Therefore, the aim of the present report is to describe the results of linkage analysis in 4 Brazilian DLMD families with 13q12 markers (D13S115 and D13S120), which were also tested for 50DAG. It was possible to exclude the 13q gene at theta = 0.10 as responsible for the DLMD phenotype in our families using both 13q12 markers, if the lod scores of each family were added up. Interestingly, 3 families were deficient for 50 DAG while one showed a positive pattern for this glycoprotein. Therefore, these results suggest: a) the DLMD phenotype is caused by more than one recessive gene; b) a gene, not located at 13q, causes deficiency of 50 DAG as a primary or secondary defect.

Evaluation of a program to overcome vitamin A and iron deficiencies in areas of poverty in Minas Gerais, Brazil

Randon samples of children from both sexes from Belo Horizonte, the capital City, and from Turmalina, Jequitinhonha Valley, Minas Gerais, Brazil, were submitted to nutritional evaluation before and after the intervention "Program to Overcome Vitamin A and Iron Deficiencies in Areas of Poverty in Minas Gerais, Brazil". After the first examination, all the children received, with an interval of 180 days, a single oral dose of vitamin A, oral iron sulfate during 50 days, and 200 mg of Mebendazol/day for three days. Thirty days after ending administration of the third dose of medicine, the children were subjected to a new evaluation. In Belo Horizonte, the first evaluation revealed a high prevalence of deficient and low values of vitamin A in preschool children (21.5%) and school children (21.7%). A small prevalence of low hematocrit values was also observed in both groups. Deficient and low values of hemoglobin were found as well in 21.5% of preschool children and in 17.5% of school children. The second evaluation, practiced 30 days after the third dose of medicine, showed a small incidence of low vitamin A values (4.3% in preschool children and 2.9% in school children) and low hemoglobin values (6.5% in preschool children and 2.9% in school children). No deficient values of hemoglobin and vitamin A were observed. Concerning the hematocrit value, only one school child presented a low value at the second evaluation. On the other hand, in Jequitinhonha Valley, five cases of Bitot spot with conjunctival xerosis, two cases of corneal xerosis, and one case of keratomalacia were detected at the first examination. Thirty days after ending the third dose of medicine, only one corneal scar was observed. Only a small number of children with deficient and low levels of vitamin A and hemoglobin was found in the final evaluation (less than 8%), while this number was high at the first evaluation (above 38 and 12%, respectively). These results show the efficiency of the intervention Program in relation to hypovitaminosis A and iron anemia prevention. The Program is now being implemented by the Brazilian Ministry of Health.