SARS-CoV-2 intra-host diversity, antibody response, and disease severity after reinfection by the variant of concern Gamma in Brazil

The rapid spread of the SARS-CoV-2 Variant of Concern (VOC) Gamma in Amazonas during early 2021 fueled a second large COVID-19 epidemic wave and raised concern about the potential role of reinfections. Very few cases of reinfection associated with the VOC Gamma have been reported to date, and their potential impact on clinical, immunological, and virological parameters remains largely unexplored. Here we describe 25 cases of SARS-CoV-2 reinfection in Brazil. SARS-CoV-2 genomic analysis confirmed that individuals were primo-infected with distinct viral lineages between March and December 2020 (B.1.1, B.1.1.28, B.1.1.33, B.1.195, and P.2) and reinfected with the VOC Gamma between 3 to 12 months after primo-infection. We found a similar mean cycle threshold (Ct) value and limited intra-host viral diversity in both primo-infection and reinfection samples. Sera of 14 patients tested 10-75 days after reinfection displayed detectable neutralizing antibodies (NAb) titers against SARS-CoV-2 variants that circulated before (B.1.*), during (Gamma), and after (Delta and Omicron) the second epidemic wave in Brazil. All individuals had milder or no symptoms after reinfection, and none required hospitalization. These findings demonstrate that individuals reinfected with the VOC Gamma may display relatively high RNA viral loads at the upper respiratory tract after reinfection, thus contributing to onward viral transmissions. Despite this, our study points to a low overall risk of severe Gamma reinfections, supporting that the abrupt increase in hospital admissions and deaths observed in Amazonas and other Brazilian states during the Gamma wave was mostly driven by primary infections. Our findings also indicate that most individuals analyzed developed a high anti-SARS-CoV-2 NAb response after reinfection that may provide some protection against reinfection or disease by different SARS-CoV-2 variants.

Low prevalence of influenza A strains with resistance markers in Brazil during 2017-2019 seasons

The influenza A virus (IAV) is of a major public health concern as it causes annual epidemics and has the potential to cause pandemics. At present, the neuraminidase inhibitors (NAIs) are the most widely used anti-influenza drugs, but, more recently, the drug baloxavir marboxil (BXM), a polymerase inhibitor, has also been licensed in some countries. Mutations in the viral genes that encode the antiviral targets can lead to treatment resistance. Worldwide, a low prevalence of antiviral resistant strains has been reported. Despite that, this situation can change rapidly, and resistant strain surveillance is a priority. Thus, the aim of this was to evaluate Brazilian IAVs antiviral resistance from 2017 to 2019 through the identification of viral mutations associated with reduced inhibition of the drugs and by testing the susceptibility of IAV isolates to oseltamivir (OST), the most widely used NAI drug in the country. Initially, we analyzed 282 influenza A(H1N1)pdm09 and 455 A(H3N2) genetic sequences available on GISAID. The amino acid substitution (AAS) NA:S247N was detected in one A(H1N1)pdm09 strain. We also identified NA:I222V (n = 6) and NA:N329K (n = 1) in A(H3N2) strains. In addition, we performed a molecular screening for NA:H275Y in 437 A(H1N1)pdm09 samples, by pyrosequencing, which revealed a single virus harboring this mutation. Furthermore, the determination of OST IC₅₀ values for 222 A(H1N1)pdm09 and 83 A(H3N2) isolates revealed that all isolates presented a normal susceptibility profile to the drug. Interestingly, we detected one A(H3N2) virus presenting with PA:E119D AAS. Moreover, the majority of the IAV sequences had the M2:S31N adamantanes resistant marker. In conclusion, we show a low prevalence of Brazilian IAV strains with NAI resistance markers, in accordance with what is reported worldwide, indicating that NAIs still remain an option for the treatment of influenza infections in Brazil. However, surveillance of influenza resistance should be strengthened in the country for improving the representativeness of investigated viruses and the robustness of the analysis.

Multifunctional cytokine and T cell memory phenotype profiles differ in active versus cured tuberculosis

Tuberculosis, one of the most prevalent and deadliest infectious diseases worldwide, requires long-term multidrug treatment regimens for curing active clinical disease. However, a diagnostic method for identifying successful cure from TB disease following anti-TB chemotherapy remains elusive. The overall goal of this study was to assess differential patterns of cytokine production and memory T cell phenotypes to distinguish between active TB subjects and remotely cured TB individuals. Using peripheral blood mononuclear cells from subjects enrolled in a TB household contact study established in Vitória, Brazil, cells were stimulated ex vivo with TB antigens and evaluated using multi-parametric flow cytometry. Total cytokine and multifunctional cytokine analyses revealed an increase in the proportion of IL-17 producing CD4+ T cells in active TB subjects, while cured TB subjects showed a clear dominance of cells producing IFNγ and IL-2 or TNFα. Comparison of memory phenotypes revealed differences between proportions of several CD4+ T cell memory subsets, with an effector memory dominance in cured TB compared to an increased stem cell memory representation in active TB. Increased expression of exhaustion marker PD-1 in advanced stages of memory cell differentiation suggested its possible use as a surrogate indicator of memory subset fluxes, with possible application as a biomarker for distinguishing differences between cured TB and active TB individuals.

Strains of Mycobacterium tuberculosis transmitting infection in Brazilian households and those associated with community transmission of tuberculosis

Molecular epidemiologic studies have shown that the dynamics of tuberculosis transmission varies geographically. We sought to determine which strains of Mycobacterium tuberculosis (MTB) were infecting household contacts (HHC), and which were causing clusters of tuberculosis (TB) disease in Vitoria-ES, Brazil. A total of 741 households contacts (445 TST +) and 139 index cases were characterized according to the proportion of contacts in each household that had a tuberculin skin test positive: low (LT) (≤40% TST+), high (HT) (≥70% TST+) and (40-70% TST+) intermediate (IT) transmission. IS6110-RFLP and spoligotyping analysis were performed only 139 MTB isolates from index cases and 841 community isolates. Clustering occurred in 45% of the entire study population. There was no statistically significant association between MTB household transmission category and clustering. Within the household study population, the proportion of clusters in HT and LT groups was similar (31% and 36%, respectively; p = 0.82). Among index cases isolates associated with households demonstrating TST conversion, the frequency of unique pattern genotypes was higher for index cases of the LT compared to HT households (p = 0.03). We concluded that clusters and lineages associated with MTB infection in HT households had no proclivity for increased transmission of TB in the community.

Epidemiologically characterized high and low transmission isolates of Mycobacterium tuberculosis induce distinct infection outcomes in mice

In a study of household contacts of infectious TB cases (HHC) conducted by us in Brazil, “index” cases were categorized into High (HT) and Low (LT) transmission groups based on the proportion of household contacts with a positive tuberculin skin test. In this study we wanted to determine whether Mycobacterium tuberculosis (Mtb) isolates with different transmission phenotypes diverged in their interaction with the host immune system. Initial in vitro analysis of 15 isolates from each group revealed significantly higher levels of TNF produced by macrophages infected with HT isolates. Two each of the HT and LT isolates were further characterized in vivo in the C3HeB/FeJ mice which develop lesions characteristic of human TB. Through the course of these infections, both the LT isolates exhibited a significantly higher bacterial burden and enhanced cellular recruitment to the lungs. Mice infected with the LT isolates exhibited early pulmonary inflammation that rapidly progressed to widespread consolidation of the granulomatous lesions. In contrast, mice infected with the two HT isolates formed organized cellular aggregates that contained abundant lymphocytes and foamy macrophages. Interestingly, pathological progression of the cellular aggregates into caseous fibrotic lesions, with abundant extracellular bacilli, was observed with one of the HT isolates. Furthermore, elevated levels of the pro-inflammatory cytokines IL-1β, IL-6 and IL-17 were found in the lungs of mice infected with the LT isolates. These results suggest that distinct interactions between microbe and host immunity might lead to differential trajectory in intracellular growth pattern and lung pathology that underlie differences in transmission potential.

Intranasal vaccination with adjuvant-free S. aureus antigens effectively protects mice against experimental sepsis

Staphylococcus aureus (S. aureus) is a Gram-positive coccal bacterium comprising part of the human skin, nares and gastrointestinal tract normal microbiota. It is also an important cause of nosocomial/community-acquired infections in humans and animals, which can cause a diverse array of infections, including sepsis, which is a progressive systemic inflammation response syndrome that is frequently fatal. The emergence of drug-resistant strains and the high toxicity of the treatments used for these infections point out the need to develop an effective, inexpensive and safe vaccine that can be used prophylactically. In this work, we used an experimental sepsis model to evaluate the effectiveness of whole antigens from S. aureus (SaAg) given by the intranasal route to induce protective immunity against S. aureus infection in mice. BALB/c mice were vaccinated via intranasal or intramuscular route with two doses of SaAg, followed by biocompatibility and immunogenicity evaluations. Vaccinated animals did not show any adverse effects associated with the vaccine, as determined by transaminase and creatinine measurements. Intranasal, but not intramuscular vaccination with SaAg led to a significant reduction in IL-10 production and was associated with increased level of IFN-γ and NO. SaAg intranasal vaccination was able to prime cellular and humoral immune responses and inducing a higher proliferation index and increased production of specific IgG1/IgG2, which contributed to decrease the bacterial load in both liver and the spleen and improve survival during sepsis. These findings present the first evidence of the effectiveness of whole Ag intranasal-based vaccine administration, which expands the vaccination possibilities against S. aureus infection.

Comparison of interferon-γ release assay to two cut-off points of tuberculin skin test to detect latent Mycobacterium tuberculosis infection in primary health care workers

BACKGROUND

An interferon-γ release assay, QuantiFERON-TB (QFT) test, has been introduced an alternative test for the diagnosis of latent Mycobacterium tuberculosis infection (LTBI). Here, we compared the performance of QFT with tuberculin skin test (TST) measured at two different cut-off points among primary health care work (HCW) in Brazil.

METHODS

A cross-sectional study was carried out among HCWs in four Brazilian cities with a known history of high incidence of TB. Results of the QFT were compared to TST results based on both ≥5 mm and ≥10 mm as cut-off points.

RESULTS

We enrolled 632 HCWs. When the cut-off value of ≥10 mm was used, agreement between QFT and TST was 69% (k = 0.31), and when the cut-off of ≥5 mm was chosen, the agreement was 57% (k = 0.22). We investigated possible factors of discordance of TST vs QFT. Compared to the TST-/QFT- group, risk factors for discordance in the TST+/QFT- group with TST cut-off of ≥5 mm included age between 41-45 years [OR = 2.70; CI 95%: 1.32-5.51] and 46-64 years [OR = 2.04; CI 95%: 1.05-3.93], BCG scar [OR = 2.72; CI 95%: 1.40-5.25], and having worked only in primary health care [OR = 2.30; CI 95%: 1.09-4.86]. On the other hand, for the cut-off of ≥10 mm, BCG scar [OR = 2.26; CI 95%: 1.03-4.91], being a household contact of a TB patient [OR = 1.72; CI 95%: 1.01-2.92] and having had a previous TST [OR = 1.66; CI 95%: 1.05-2.62], were significantly associated with the TST+/QFT- group. No statistically significant associations were found among the TST-/QFT+ discordant group with either TST cut-off value.

CONCLUSIONS

Although we identified BCG vaccination to contribute to the discordance at both TST cut-off measures, the current Brazilian recommendation for the initiation of LTBI treatment, based on information gathered from medical history, TST, chest radiograph and physical examination, should not be changed.

Microsatellite markers for the Cabreúva tree, Myroxylon peruiferum (Fabaceae), an endangered medicinal species from the Brazilian Atlantic Forest

The Cabreúva tree, Myroxylon peruiferum, is an endangered tropical species from Brazil used in forest restoration projects. It is known for its medicinal properties. Eleven microsatellite markers were developed for this species, from a microsatellite-enriched library. Nine of these markers, characterized in 30 individuals from a semideciduous forest remnant population in southeast Brazil, were polymorphic, with allele numbers ranging from 2 to 8 per locus; expected and observed heterozygosities ranged from 0.103 to 0.757 and 0.107 to 0.704, respectively. One locus (Mpe-C04) showed significant deviation from Hardy-Weinberg equilibrium, probably due to null alleles. Two other loci (Mpe-E09 and Mpe-H07) were monomorphic in this population. These microsatellite loci should be useful for future population genetic studies of this species.

AIDS-associated paracoccidioidomycosis in a patient with a CD4+ T-cell count of 4 cells/mm³

We describe a case of a patient presenting with HIV and paracoccidioidomycosis co-infection. At the time of diagnosis total CD4+ T-cell count was 4 cells/mm3. Histopathology revealed tuberculoid granulomas, scarce CD4+ T cells, a moderate number of CD8+ cells and the absence of Foxp3+ cells. Most of the cutaneous lesions healed after two weeks of treatment with amphotericin B. After 14 months the patient is still under antiretroviral therapy and no clinical evidence of recurrence of the mycosis has been observed.

Computed tomography assessment of lung structure in patients undergoing cardiac surgery with cardiopulmonary bypass

Hypoxemia is a frequent complication after coronary artery bypass graft (CABG) with cardiopulmonary bypass (CPB), usually attributed to atelectasis. Using computed tomography (CT), we investigated postoperative pulmonary alterations and their impact on blood oxygenation. Eighteen non-hypoxemic patients (15 men and 3 women) with normal cardiac function scheduled for CABG under CPB were studied. Hemodynamic measurements and blood samples were obtained before surgery, after intubation, after CPB, at admission to the intensive care unit, and 12, 24, and 48 h after surgery. Pre- and postoperative volumetric thoracic CT scans were acquired under apnea conditions after a spontaneous expiration. Data were analyzed by the paired Student t-test and one-way repeated measures analysis of variance. Mean age was 63 ± 9 years. The PaO2/FiO2 ratio was significantly reduced after anesthesia induction, reaching its nadir after CPB and partially improving 12 h after surgery. Compared to preoperative CT, there was a 31% postoperative reduction in pulmonary gas volume (P < 0.001) while tissue volume increased by 19% (P < 0.001). Non-aerated lung increased by 253 ± 97 g (P < 0.001), from 3 to 27%, after surgery and poorly aerated lung by 72 ± 68 g (P < 0.001), from 24 to 27%, while normally aerated lung was reduced by 147 ± 119 g (P < 0.001), from 72 to 46%. No correlations (Pearson) were observed between PaO2/FiO2 ratio or shunt fraction at 24 h postoperatively and postoperative lung alterations. The data show that lung structure is profoundly modified after CABG with CPB. Taken together, multiple changes occurring in the lungs contribute to postoperative hypoxemia rather than atelectasis alone.

Spatial patterns of pulmonary tuberculosis incidence and their relationship to socio-economic status in Vitoria, Brazil

OBJECTIVE

To investigate spatial patterns of the incidence of pulmonary tuberculosis (TB) and its relationship with socio-economic status in Vitoria, Espirito Santo, Brazil.

DESIGN

In a 4-year, retrospective, territory-based surveillance study of all new pulmonary TB cases conducted in Vitoria between 2002 and 2006, spatial patterns of disease incidence were compared using spatial clustering statistics (Anselin's local indicators of spatial association [LISA] and Getis-Ord Gi* statistics), smoothed empirical Bayes estimates and model-predicted incidence rates. Spatial Poisson models were fit to examine the relationship between socio-economic status and TB incidence.

RESULTS

A total of 651 TB cases were reported across 78 neighborhoods, with rates ranging from 0 to 129 cases per 100,000 population. Moran's I indicated strong spatial autocorrelation among incidence rates (0.399, P < 0.0001), and four areas of high incidence were identified by LISA and Gi* statistics. Smoothed spatial empirical Bayes estimates demonstrate that two of these areas range from 70 to 90 cases/100,000, while the other two range from 40 to 70 cases/100,000. TB incidence and socio-economic status had a significant curvilinear relationship (P = 0.02).

CONCLUSIONS

Data derived from these spatial statistical tools will help TB control programs to allocate TB resources to those populations most at risk of increasing TB rates and to target areas where TB control efforts need to be concentrated.

Acurácia do lavado gástrico realizado em ambiente hospitalar e ambulatorial no diagnóstico da tuberculose pulmonar em crianças

OBJETIVO: Comparar a acurácia do lavado gástrico (LG) realizado em ambiente hospitalar e ambulatorial no diagnóstico da tuberculose (TB) pulmonar em crianças. MÉTODOS: Estudo prospectivo realizado no Estado do Espírito Santo, Brasil, de 1999 a 2003. Um total de 230 crianças com suspeita de TB foi selecionado para realizar exame de LG em ambiente hospitalar (n = 103) ou em ambiente ambulatorial (n = 127). Desse total, 53 foram diagnosticadas como casos de TB e divididas em dois grupos: LG hospitalar (n = 30) e LG ambulatorial (n = 23). Todas as 53 crianças foram monitoradas por 6 meses para avaliação da acurácia do diagnóstico. A acurácia foi determinada com base na mudança do diagnóstico, na taxa de cura e no percentual de culturas positivas nos dois grupos estudados. RESULTADOS: A taxa de cura foi de 100% nos dois grupos, e não houve mudança de diagnóstico nas 53 crianças estudadas. Nenhuma diferença significativa foi encontrada entre os dois grupos estudados em relação ao achado do Mycobacterium tuberculosis (RR = 1,47; IC95%: 0,95-2,27; p = 0,095), apesar de o grupo LG ambulatorial ter apresentado o maior índice de cultura positivas. CONCLUSÕES: Nossos resultados mostram que a acurácia do LG realizado em ambiente hospitalar é semelhante à do realizado em ambiente ambulatorial, o que indica que a internação é necessária apenas em casos mais graves nos quais não se pode realizar o procedimento em ambiente ambulatorial.

Histopathological changes during experimental infections of calves withCooperia punctata

Eleven male two-month-old Holstein calves were used to determine the pathological changes induced by aCooperia punctatainfection. After weaning, ten calves received a single oral dose of 45,000C. punctatainfective larvae. One calf remained as a non-infected control. Groups of two calves were killed on days 7, 14, 21, 28 and 35 post-infection (p.i.) for determination of worm burdens and histopathological evaluation. The small intestine was sub-divided into three sections of approximately equal length, and representative samples of mucosa were fixed in 10% formalin, cut, and stained with haematoxylin-eosin. Samples of intestinal contents and mucosal digests were taken and fixed in 10% formalin for an estimation of total worm burdens. An increase in the number of adult parasites and a decrease in the number of larvae were observed with time (P<0.001). A higher concentration of worms was found in the first segment of the small intestine during the five weeks of observation. Histology showed larvae in the intestinal mucosa on day 7 p.i., with a discrete increase in the cellular response. Adult worms and a marked cellular infiltrate with eosinophils and neutrophils were present on day 21 p.i., and these persisted until day 35 p.i. Microcysts resulting from worm destruction were observed from day 21 p.i.

Bacterial Diversity in Tree Canopies of the Atlantic Forest

We found an extraordinary level of bacterial biodiversity in the tree leaf canopy of a tropical Atlantic forest by using culture-independent molecular methods. Our survey suggests that each tree species selects for a distinct microbial community. Analysis of the bacterial 16S ribosomal RNA gene sequences revealed that about 97% of the bacteria were unknown species and that the phyllosphere of any one tree species carries at least 95 to 671 bacterial species. The tree canopies of tropical forests likely represent a large reservoir of unexplored microbial diversity.

Inorganic chemical composition of native trees of the Atlantic Forest

The Atlantic Forest with its exuberant vegetation of high level of biodiversity is classified as one hotspot of the world. Chemical composition of leaves from native trees and underlying soils was evaluated by INAA. The predominant species Euterpe edulis, Bathysa meridionalis, Hyeronima alchorneoides, Marlierea tomentosa, Gomidesia flagellaris, and Gomidesia spectabilis belonging to the diverse plant families were studied. Euterpe edulis, the most abundant understory specie, presented the lowest element concentrations except for Zn. Some variation in chemical composition was noted, however, the chemical specificity of tree species can be more predominant than the soil variability for the obtained leaf concentrations. Factor values obtained through the Monte-Carlo assisted factor analysis were used for species discrimination, The results indicate that chemical investigation of native trees is a quite promising tool for biodiversity studies in the Atlantic Forest.

Megaselia scalaris (Diptera: Phoridae) causing myiasis in Crotalus durissus terrificus (Serpentes: Viperidae) in Brazil

We describe a case of myiasis in Crotalus durissus terrificus (Laurenti) caused by Megaselia scalaris (Loew). The snake was found in Anhembi, Sao Paulo, Brazil, with a lesion measuring 25 mm in diameter where the larvae of M. scalaris had penetrated the ribs. The opportunistic behavior of the larvae of M. scalaris is discussed.

Inhibition of Trypanosoma cruzi epimastigotes in vitro by iron chelating agents

The relative effectiveness of 20 iron chelating agents in suppressing the growth and multiplication of Trypanosoma cruzi epimastigotes has been examined in vitro. 1,2-Dimethyl-3-hydroxypyrid-4-one (L1) and several of its newly synthesised N-substituted analogs containing hydrophobic substituents were significantly more effective than deferoxamine, even though they possess only two donor sites for iron(III) while deferoxamine has six. Analogs with hydrophilic substituents were uniformly less active than L1 itself. Variations in effectiveness as the polarity of the compound is varied indicate that the ability to cross the cellular membrane is of critical importance in the determination of the in vitro trypanocidal activity of iron(III) chelating agents. A group of four tris(2-aminoethyl)amine based tris-imines were also screened, all of which had poor activity (0-28% inhibition). Among the other iron(III) chelating agents which showed a relatively high level of activity at 50 and 100 micrograms/ml were salicylhydroxamic acid (70 and 73% inhibition) and hydroxyurea (42 and 52% inhibition). N,N'-Di(2-hydroxybenzyl)ethylenediamine-N,N'-diacetic acid and acetohydroxamic acid exhibited only slight activity at 50 and 100 micrograms/ml. The best of these iron(III) chelating agents were as effective against the epimastigote form at both 50 and 100 micrograms/ml (74-82% inhibition) as benznidazole (81% inhibition), the drug currently used in the clinic.

Chelating agent inhibition of Trypanosoma cruzi epimastigotes in vitro

A number of chelating agents and some of their derivatives are as effective as, or superior to, benznidazole, the compound currently in clinical use, in the suppression of the reproduction of epimastigotes of Trypanosoma cruzi, the protozoa that causes Chagas' disease. All compounds were examined at a culture concentration of 5 micrograms/mL. The most effective compounds included N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine, sodium diethylamine-N-carbodithioate, piperidine-N-carbodithioate and several of its analogs, a number of other carbodithioates with two nonpolar groups on the nitrogen, and tetraethylthiuram disulfide, a prodrug of sodium diethylamine-N-carbodithioate and widely used in the treatment of alcoholism. The introduction of additional ionic or nonionic polar groups on the chelating molecule generally results in a loss of tyrpanocidal activity. Common commercially available chelating agents which exhibited no activity included D-penicillamine, meso-2,3-dimercaptosuccinic acid, and triethylenetetramine tetrahydrochloride. Dose-response data on the culture indicated that some of these compounds exhibited inhibition of Trypanosoma cruzi epimastigotes at concentrations as low as 0.625 microgram/mL. It is proposed that the mechanism of action of these compounds is based on their ability to interfere with the essential metal metabolism at intracellular sites of the epimastigote involving iron, copper, or zinc. The results also indicate that a certain degree of hydrophobicity may be necessary for the groups attached to the literal metal-bonding structure if the compounds are to successfully inhibit the epimastigotes of Trypanosoma cruzi. The development of antiprotozoal drugs which are chelating agents specifically designed to selectively disrupt the essential metal metabolism of Trypanosoma cruzi should furnish a new generation of drugs which can be used in the treatment of Chagas' disease.

The importance of the opossum (Didelphis albiventris) as a reservoir for Trypanosoma cruzi in Bambuí, Minas Gerais State

In a survey realized on the sylvatic and peridomestic environments at Bambuí county, Minas Gerais State, 44 (37.9%) out of 116 opossums (Didelphis albiventris) captured were found to be naturally infected with Trypanosoma cruzi. One hundred and forty three parasite samples were obtained from 43 infected opossums using simultaneously hemoculture, xenodiagnosis (Triatoma infestans, Panstrongylus megistus and Rhodnius neglectus) and examination of anal glands contents. The parasite samples were characterized according to six isoenzyme patterns. All samples, independently of the method of isolation, presented an isoenzyme pattern similar to the standard T. cruzi Z1, showing that either xenodiagnosis or hemoculture can used without selecting parasite subpopulation from naturally infected opossums. Previous isoenzyme patterns reported for human T. cruzi isolates from the same region were completely different. This isoenzyme dissimilarity between sylvatic and domiciliar environments suggests the existence of two independent T. cruzi transmission cycles in Bambuí. The epidemiological implications of these results are discussed.