An Efficient Extraction Method Allowing the Genetic Evaluation of Host DNA from Samples Collected for Virus Infection Diagnosis in Viral Transport Medium

Introduction: During the COVID-19 pandemic, an extraordinary number of nasopharyngeal secretion samples inoculated in viral transport medium (VTM) were collected and analyzed to detect SARS-CoV-2 infection. In addition to viral detection, those samples can also be a source of host genomic material, providing excellent opportunities for biobanking and research. Objective: To describe a simple, in-house-developed DNA extraction method to obtain high yield and quality genomic DNA from VTM samples for host genetic analysis and assess its relative efficiency by comparing its yield and suitability to downstream applications to two different commercial DNA extraction kits. Methods: In this study, 13 VTM samples were processed by two commercial silica-based kits and compared with an in-House-developed protocol for host DNA extraction. An additional 452 samples were processed by the in-House method. The quantity and quality of the differentially extracted DNA samples were assessed by Qubit and spectrophotometric measurements. The suitability of extracted samples for downstream applications was tested by polymerase chain reaction (PCR) amplification followed by amplicon sequencing and allelic discrimination in real-time PCR. Results: The in-House method provided greater median DNA yield (0.81 μg), being significantly different from the PureLink® method (0.14 μg, p < 0.001), but not from the QIAamp® method (0.47 μg, p = 0.980). Overall satisfactory results in DNA concentrations and purity, in addition to cost, were observed using the in-House method, whose samples were able to produce clear amplification in PCR and sequencing reads, as well as effective allelic discrimination in real-time PCR TaqMan® assay. Conclusion: The described in-House method proved to be suitable and economically viable for genomic DNA extraction from VTM samples for biobanking purposes. These results are extremely valuable for the study of the COVID-19 pandemic and other emergent infectious diseases, allowing host genetic studies to be performed in samples initially collected for diagnosis.

HLA haplotypes and differential regional mortality caused by COVID-19 in Brazil: an ecological study based on a large bone marrow donor bank dataset

The coronavirus disease 2019 (COVID-19) mortality rates varied among the states of Brazil during the course of the pandemics. The human leukocyte antigen (HLA) is a critical component of the antigen presentation pathway. Individuals with different HLA genotypes may trigger different immune responses against pathogens, which could culminate in different COVID-19 responses. HLA genotypes are variable, especially in the highly admixed Brazilian population. In this ecological study, we aimed to investigate the correlation between HLA haplotypes and the different regional distribution of COVID-19 mortality in Brazil. HLA data was obtained from 4,148,713 individuals registered in The Brazilian Voluntary Bone Marrow Donors Registry. COVID-19 data was retrieved from epidemiological bulletins issued by State Health Secretariats via Brazil's Ministry of Health from February/2020 to July/2022. We found a positive significant correlation between the HLA-A*01~B*08~DRB1*03 haplotype and COVID-19 mortality rates when we analyzed data from 26 states and the Federal District. This result indicates that the HLA-A*01~B*08~DRB1*03 haplotype may represent an additional risk factor for dying due to COVID-19. This haplotype should be further studied in other populations for a better understanding of the variation in COVID-19 outcomes across the world.

Investigation of the impact of AXL, TLR3, and STAT2 in congenital Zika syndrome through genetic polymorphisms and protein-protein interaction network analyses

INTRODUCTION

Zika virus (ZIKV) is a human teratogen that causes congenital Zika syndrome (CZS). AXL, TLR3, and STAT2 are proteins involved in the ZIKV's entry into cells (AXL) and host's immune response (TLR3 and STAT2). In this study, we evaluated the role of genetic polymorphisms in these three genes as risk factors to CZS, and highlighted which proteins that interact with them could be important for ZIKV infection and teratogenesis.

MATERIALS AND METHODS

We evaluate eighty-eight children exposed to ZIKV during the pregnancy, 40 with CZS and 48 without congenital anomalies. The evaluated polymorphisms in AXL (rs1051008), TLR3 (rs3775291), and STAT2 (rs2066811) were genotyped using TaqMan® Genotyping Assays. A protein-protein interaction network was created in STRING database and analyzed in Cytoscape software.

RESULTS

We did not find any statistical significant association among the polymorphisms and the occurrence of CZS. Through the analyses of the network composed by AXL, TLR3, STAT2 and their interactions targets, we found that EGFR and SRC could be important proteins for the ZIKV infection and its teratogenesis.

CONCLUSION

In summary, our results demonstrated that the evaluated polymorphisms do not seem to represent risk factors for CZS; however, EGFR and SRC appear to be important proteins that should be investigated in future studies.

Downregulation of Microcephaly-Causing Genes as a Mechanism for ZIKV Teratogenesis: A Meta-analysis of RNA-Seq Studies

Zika virus (ZIKV) is a neurotropic teratogen that causes congenital Zika syndrome (CZS), characterized by brain and eye anomalies. Impaired gene expression in neural cells after ZIKV infection has been demonstrated; however, there is a gap in the literature of studies comparing whether the differentially expressed genes in such cells are similar and how it can cause CZS. Therefore, the aim of this study was to compare the differential gene expression (DGE) after ZIKV infection in neural cells through a meta-analysis approach. Through the GEO database, studies that evaluated DGE in cells exposed to the Asian lineage of ZIKV versus cells, of the same type, not exposed were searched. From the 119 studies found, five meet our inclusion criteria. Raw data of them were retrieved, pre-processed, and evaluated. The meta-analysis was carried out by comparing seven datasets, from these five studies. We found 125 upregulated genes in neural cells, mainly interferon-stimulated genes, such as IFI6, ISG15, and OAS2, involved in the antiviral response. Furthermore, 167 downregulated, involved with cellular division. Among these downregulated genes, classic microcephaly-causing genes stood out, such as CENPJ, ASPM, CENPE, and CEP152, demonstrating a possible mechanism by which ZIKV impairs brain development and causes CZS.

Increasing taxon sampling suggests a complete taxonomic rearrangement in Echinantherini (Serpentes: Dipsadidae)

Although the recent advances on the relationship of its major groups, the systematics of the rich fauna of Neotropical snakes is far from being a consensus. In this sense, derived groups presenting continental distributions have represented a main challenge. The taxonomy of the snake tribe Echinantherini is one of the most contentious among the diverse family known as Dipsadidae. The tribe is poorly sampled in phylogenetic studies, resulting in conflicting hypotheses of relationships among its taxa. Moreover, several rare and micro endemic species of Echinantherini have never been evaluated within a comprehensive phylogenetic framework. Here, we assess for the first time the phylogenetic position of the rare Echinanthera amoena within Echinantherini. We based our analyses on a comprehensive multilocus dataset including 14 of the 16 species described for the tribe. Our results support the monophyly of Echinantherini and strongly indicate E. amoena as a unique lineage, phylogenetically positioned apart from all other congeners. From the three current genera (Echinanthera, Taeniophallus, and Sordellina) our results indicate that Echinanthera and Taeniophallus are paraphyletic, since the T. affinis species group is positioned as sister to Echinanthera (except E. amoena) clustering apart from the clade formed by the T. brevirostris and T. occipitalis groups. We describe new genera for the T. affinis and T. occipitalis species groups and an additional monospecific genus for E. amoena. Although we did not evaluate the phylogenetic position of T. nebularis, we described a new genus and removed it from Echinantherini since its morphology strikingly departs from all species now included in the tribe. Finally, we redefine the genera Echinanthera and Taeniophallus and we provide comments about further directions to study the biogeography and the evolution of morphological traits in Echinantherini.

Molecular Mechanisms of ZIKV-Induced Teratogenesis: A Systematic Review of Studies in Animal Models

Zika virus (ZIKV) is a teratogen that causes congenital anomalies, being linked to microcephaly in children exposed during pregnancy. Animal studies have been conducted to investigate the molecular mechanisms related to ZIKV teratogenesis. Although animal models can mimic the effects of ZIKV in human embryo development, few in vivo studies have addressed molecular changes following ZIKV infection in embryos. Moreover, few literature reviews have been conducted with these studies. The aim of this systematic review is to evaluate the molecular mechanisms of ZIKV teratogenesis determined from studies in animal models. PubMed/MEDLINE, EMBASE, Web of Science, and Scopus as well as grey literature were searched for studies that evaluated molecular alterations related to ZIKV teratogenesis which occurred during embryonic development. Nine studies were included: six with mice, one with mice and guinea pigs, one with pigs and one with chickens. In general, studies presented an unclear or high risk of bias for methodological criteria. Most of studies reported embryos exposed to ZIKV presenting microcephaly, reduced cortex thickness, and growth restriction. Different techniques were used to evaluated molecular changes in the animals following ZIKV infection: RNA sequencing, RT-qPCR, and in situ hybridization. It was found that common pathways are changed in most studies, being pathways related to immune response upregulated and those involved to neurodevelopment downregulated.

Functional Polymorphisms in the p53 Pathway Genes on the Genetic Susceptibility to Zika Virus Teratogenesis

Congenital Zika Syndrome (CZS) occurs in up to 42% of individuals exposed to ZIKV prenatally. Deregulation in gene expression and protein levels of components of the p53 signaling pathway, such as p53 and MDM2, due to ZIKV infection has been reported. Here, we evaluate functional polymorphisms in genes of the p53 signaling pathway as risk factors to CZS. Forty children born with CZS and forty-eight children exposed to ZIKV, but born without congenital anomalies were included in this study. Gestational and sociodemographic information as well as the genotypic and allelic frequencies of functional polymorphisms in TP53, MDM2, MIR605 and LIF genes were compared between the two groups. We found children with CZS exposed predominantly in the first trimester and controls in the third trimester (p<0.001). Moreover, children with CZS were predominantly from families with a lower socioeconomic level (p=0.008). We did not find a statistically significant association between the investigated polymorphisms and development of CZS; however, by comparing individuals with CZS and lissencephaly or without lissencephaly, we found a significative difference in the allelic frequencies of the TP53 rs1042522, which is associated with a more potent p53-induced apoptosis (p=0.007). Our findings suggest that the TP53 rs1042522 polymorphism should be better investigate as a genetic risk factor for the development of lissencephaly in children with CZS.

Skin pigmentation polymorphisms associated with increased risk of melanoma in a case-control sample from southern Brazil

BACKGROUND

Melanoma is the most aggressive type of skin cancer and is associated with environmental and genetic risk factors. It originates in melanocytes, the pigment-producing cells. Single nucleotide polymorphisms (SNPs) in pigmentation genes have been described in melanoma risk modulation, but knowledge in the field is still limited.

METHODS

In a case-control approach (107 cases and 119 controls), we investigated the effect of four pigmentation gene SNPs (TYR rs1126809, HERC2 rs1129038, SLC24A5 rs1426654, and SLC45A2 rs16891982) on melanoma risk in individuals from southern Brazil using a multivariate logistic regression model and multifactor dimensionality reduction (MDR) analysis.

RESULTS

Two SNPs were associated with an increased risk of melanoma in a dominant model: rs1129038AA and rs1426654AA [OR = 2.094 (95% CI: 1.106-3.966), P = 2.3 10^- 2 and OR = 7.126 (95% CI: 1.873-27.110), P = 4.0 10^- 3, respectively]. SNP rs16891982CC was associated with a lower risk to melanoma development in a log-additive model when the allele C was inherited [OR = 0.081 (95% CI: 0.008-0.782), P = 3 10^- 2]. In addition, MDR analysis showed that the combination of the rs1426654AA and rs16891982GG genotypes was associated with a higher risk for melanoma (P = 3 10^- 3), with a redundant effect.

CONCLUSIONS

These results contribute to the current knowledge and indicate that epistatic interaction of these SNPs, with an additive or correlational effect, may be involved in modulating the risk of melanoma in individuals from a geographic region with a high incidence of the disease.

Prevalence of the most common pathogenic variants in three genes for inborn errors of metabolism associated with sudden unexpected death in infancy: a population-based study in south Brazil

Citrullinemia type 1 (CTLNI), long-chain 3-hydroxyacyl-CoA dehydrogenase deficiency (LCHADD), and mut⁰ methylmalonic acidemia (mut⁰ MMA) are inborn errors of metabolism (IEMs) associated with sudden unexpected death in infancy (SUDI). Its most common pathogenic variants are: c.1168G&gt;A (CTLNI, ASS1 gene), c.1528G&gt;C (LCHADD, HADHA gene), c.655A&gt;T and c.1106G&gt;A (mut⁰ MMA, MUT gene). Considering the absence of estimates regarding the incidence of these diseases in Brazil, this study sought to investigate the prevalence of its main pathogenic variants in a healthy population in the southern region of the country. A total of 1,000 healthy subjects from Rio Grande do Sul were included. Genotyping was performed by real-time PCR. Individuals found to be heterozygous for c.1528G&gt;C underwent further acylcarnitine profile analysis by tandem mass spectrophotometry. Allele and genotype frequencies were calculated considering Hardy-Weinberg equilibrium. The c.1528G&gt;C variant was detected in heterozygosity in two subjects (carrier frequency = 1:500; allele frequency = 0.001; minimum prevalence of LCHADD = 1: 1,000,000), whose acylcarnitine profiles were normal. Variants c.1168G&gt;A, c.655A&gt;T, and c.1106G&gt;A were not identified. These results denote the rarity of these IEMs in Southern Brazil, highlighting the need to expand the investigation of IEMs in relation to infant morbidity and mortality within the country.

Infant mortality in Brazil attributable to inborn errors of metabolism associated with sudden death: a time-series study (2002-2014)

Background

The literature suggests that 0.9 to 6% of infants who die unexpectedly may have had a metabolic disorder. At least 43 different inborn errors of metabolism (IEMs) have been associated with sudden death (SUDI). To date, the frequency of IEM-associated SUDI has not been studied in Brazil. The present study sought to characterize infant mortality related to IEMs known to cause SUDI disaggregated by each of the regions of Brazil.

Methods

This was a descriptive, cross-sectional, population-based study of data obtained from the Brazilian Ministry of Health Mortality Information System (SIM). Death records were obtained for all infants (age < 1 year) who died in Brazil in 2002–2014 in whom the underlying cause of death was listed as ICD-10 codes E70 (Disorders of aromatic amino-acid metabolism), E71 (Disorders of branched-chain amino-acid metabolism and fatty-acid metabolism), E72 (Other disorders of amino-acid metabolism), or E74 (Other disorders of carbohydrate metabolism), which are known to be associated with SUDI.

Results

From 2002 to 2014, 199 deaths of infants aged < 1 year were recorded in the SIM with an underlying cause corresponding to one of the IEMs of interest. The prevalence of IEM-related deaths was 0.67 per 10,000 live births (0.58–0.77). Of these 199 deaths, 18 (9.0%) occurred in the North of Brazil, 43 (21.6%) in the Northeast, 80 (40.2%) in the Southeast, 46 (23.1%) in the South, and 12 (6.0%) in the Center-West region. Across all regions of the country, ICD10-E74 was predominant.

Conclusions

This 13-year time-series study provides the first analysis of the number of infant deaths in Brazil attributable to IEMs known to be associated with sudden death.

Electronic supplementary material

The online version of this article (10.1186/s12887-019-1421-y) contains supplementary material, which is available to authorized users.

The phenotypic spectrum of congenital Zika syndrome

In October 2015, Zika virus (ZIKV) outbreak the Brazilian Ministry of Health (MoH). In response, the Brazilian Society of Medical Genetics established a task force (SBGM-ZETF) to study the phenotype of infants born with microcephaly due to ZIKV congenital infection and delineate the phenotypic spectrum of this newly recognized teratogen. This study was based on the clinical evaluation and neuroimaging of 83 infants born during the period from July, 2015 to March, 2016 and registered by the SBGM-ZETF. All 83 infants had significant findings on neuroimaging consistent with ZIKV congenital infection and 12 had confirmed ZIKV IgM in CSF. A recognizable phenotype of microcephaly, anomalies of the shape of skull and redundancy of the scalp consistent with the Fetal Brain Disruption Sequence (FBDS) was present in 70% of infants, but was most often subtle. In addition, features consistent with fetal immobility, ranging from dimples (30.1%), distal hand/finger contractures (20.5%), and feet malpositions (15.7%), to generalized arthrogryposis (9.6%), were present in these infants. Some cases had milder microcephaly or even a normal head circumference (HC), and other less distinctive findings. The detailed observation of the dysmorphic and neurologic features in these infants provides insight into the mechanisms and timings of the brain disruption and the sequence of developmental anomalies that may occur after prenatal infection by the ZIKV.

Abstract P1-07-19: Spatial analyses of breast cancer in women 15-49 years-old in Rio Grande do Sul, southern Brazil

Breast cancer (BC) rates under 50 years have been increasing over time in several countries. Although the exact impact of BC is not know in low and middle income countries, it's estimated that at least 20% of deaths caused by BC affect women under the ahe of 50 years. In Porto Alegre, the capital of Rio Grande do Sul (RS), Brazil's southernmost state, the incidence of BC in women aged 40-49 years is 165 cases per 100,000, while the mortality rate reaches 25 in 100,000 women. In order to understand BC profile in this age group in the entire state of RS, we established incidence, morbidity and mortality between 2002-2011 through crude and smoothed rates for each municipality. Furthermore, we perform the spatial analysis of these indicators. Incidence data were only available for the state capital, where the rate incidence was 19 and 160 cases per 100,000 women in the age groups of 15-39 and 40-49, respectively. Statewide mortality was 2 and 21 per 100,000 women in the age groups of 15-39 and 40-49, respectively. Hospitalar morbidity associated with BC was 0.6% and 2% in women 15-39 and 40-49 years, respectively. The distribution of morbidity and mortality showed regions with continuously high rates throughout this period with result above 3% and 20 deaths per 100,000 women. In the same areas we did not identified centers specialized in cancer treatment and care. Although there is specific epidemiological surveillance for cancer in Brazil, the coverage is insufficient, especially when it comes to incidence. Morbidity and mortality data showed regions continually affected by high rates, suggesting that specific measures as well as specialized care for women in these regions are necessary. This result is particularly important since current guidelines of the Ministry of Health in Brazil recommend mammographic screening starting at the age of 50 years. The expansion of coverage and access to appropriate treatment is essential for the recognition of risk factors, adoption of effective strategies and reduction of cases and deaths in this group of women. Knowledge of the age distribution of BC cases and BC related deaths is important for the definition of health care policies, which will likely be different in different regions of the world.

Citation Format: Vianna FSL, Vargas F, Gross LG, Nunes LN, Ashton-Prolla P, Camey SA. Spatial analyses of breast cancer in women 15-49 years-old in Rio Grande do Sul, southern Brazil. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P1-07-19.

p53 signaling pathway polymorphisms associated to recurrent pregnancy loss

The p53 protein is known for performing essential functions in the maintenance of genomic stability in somatic cells and prevention of tumor formation. Studies of the p53 signaling pathway have suggested associations between some polymorphisms and infertility, post-in vitro fertilization implantation failure and recurrent abortions. The TP53 Pro72Arg polymorphism has been implicated as a risk factor for recurrent pregnancy loss (RPL); however, the association is controversial. In this study, our objective was to evaluate selected polymorphisms in genes of the p53 signalling pathway [TP53 c.215G>C (Pro72Arg), MDM2 c.14+309T>G (SNP309) and LIF c.1414T>G in the region 3' UTR] and determine their effect as risk factors for RPL. In a case-control study, we investigated 120 women with two or more pregnancy losses and 143 fertile control women reporting at least two live births and no history of pregnancy loss. When analyzed separately, the allele and genotype distributions of the polymorphisms in the two groups were not different. However, in a multivariate analysis adjusted for alcohol consumption, smoking, ethnicity, and number of pregnancies, the interaction between the genotypes TP53 Arg/Arg (rs1042522) and MDM2 TT (rs2279744) showed to be associated to RPL, increasing the risk for this condition (OR = 2.58, 95% CI: 1.31-5.07, p = 0.006). In conclusion, our study indicates that the combination of TP53 Arg/Arg (rs1042522) and MDM2 TT (rs2279744) genotypes may be a risk factor for RPL.