Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative

Host genetics is a key determinant of COVID-19 outcomes. Previously, the COVID-19 Host Genetics Initiative genome-wide association study used common variants to identify multiple loci associated with COVID-19 outcomes. However, variants with the largest impact on COVID-19 outcomes are expected to be rare in the population. Hence, studying rare variants may provide additional insights into disease susceptibility and pathogenesis, thereby informing therapeutics development. Here, we combined whole-exome and whole-genome sequencing from 21 cohorts across 12 countries and performed rare variant exome-wide burden analyses for COVID-19 outcomes. In an analysis of 5,085 severe disease cases and 571,737 controls, we observed that carrying a rare deleterious variant in the SARS-CoV-2 sensor toll-like receptor TLR7 (on chromosome X) was associated with a 5.3-fold increase in severe disease (95% CI: 2.75-10.05, p=5.41x10-7). This association was consistent across sexes. These results further support TLR7 as a genetic determinant of severe disease and suggest that larger studies on rare variants influencing COVID-19 outcomes could provide additional insights. Author SummaryCOVID-19 clinical outcomes vary immensely, but a patients genetic make-up is an important determinant of how they will fare against the virus. While many genetic variants commonly found in the populations were previously found to be contributing to more severe disease by the COVID-19 Host Genetics Initiative, it isnt clear if more rare variants found in less individuals could also play a role. This is important because genetic variants with the largest impact on COVID-19 severity are expected to be rarely found in the population, and these rare variants require different technologies to be studies (usually whole-exome or whole-genome sequencing). Here, we combined sequencing results from 21 cohorts across 12 countries to perform a rare variant association study. In an analysis comprising 5,085 participants with severe COVID-19 and 571,737 controls, we found that the gene for toll-like receptor 7 (TLR7) on chromosome X was an important determinant of severe COVID-19. Importantly, despite being found on a sex chromosome, this observation was consistent across both sexes.

Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination

Between November 2021 and February 2022, SARS-CoV-2 Delta and Omicron variants co-circulated in the United States, allowing for co-infections and possible recombination events. We sequenced 29,719 positive samples during this period and analyzed the presence and fraction of reads supporting mutations specific to either the Delta or Omicron variant. We identified 18 co-infections, one of which displayed evidence of a low Delta-Omicron recombinant viral population. We also identified two independent cases of infection by a Delta-Omicron recombinant virus, where 100% of the viral RNA came from one clonal recombinant. In the three cases, the 5-end of the viral genome was from the Delta genome, and the 3-end from Omicron including the majority of the spike protein gene, though the breakpoints were different. Delta-Omicron recombinant viruses were rare, and there is currently no evidence that Delta-Omicron recombinant viruses are more transmissible between hosts compared to the circulating Omicron lineages.

A method for variant agnostic detection of SARS-CoV-2, rapid monitoring of circulating variants, detection of mutations of biological significance, and early detection of emergent variants such as Omicron

The rapid emergence of new SARS-CoV-2 variants raises a number of public health questions including the capability of diagnostic tests to detect new strains, the efficacy of vaccines, and how to map the geographical distribution of variants to better understand patterns of transmission and possible load on healthcare resources. Next-Generation Sequencing (NGS) is the primary method for detecting and tracing the emergence of new variants, but it is expensive, and it can take weeks before sequence data is available in public repositories. Here, we describe a Polymerase Chain Reaction (PCR)-based genotyping approach that is significantly less expensive, accelerates reporting on SARS-CoV-2 variants, and can be implemented in any testing lab performing PCR. Specific Single Nucleotide Polymorphisms (SNPs) and indels are identified that have high positive percent agreement (PPA) and negative percent agreement (NPA) compared to NGS for the major genotypes that circulated in 2021. Using a 48-marker panel, testing on 1,128 retrospective samples yielded a PPA and NPA in the 96.3 to 100% and 99.2 to 100% range, respectively, for the top 10 most prevalent lineages. The effect on PPA and NPA of reducing the number of panel markers was also explored. In addition, with the emergence of Omicron, we also developed an Omicron genotyping panel that distinguishes the Delta and Omicron variants using four (4) highly specific SNPs. Data from testing demonstrates the capability to use the panel to rapidly track the growing prevalence of the Omicron variant in the United States in December 2021.

Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission

As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also introduce biases. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here, we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We develop and deploy improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detect emerging variants of concern up to 14 days earlier in wastewater samples, and identify multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.

HLA-A*03:01 is associated with increased risk of fever, chills, and more severe reaction to Pfizer-BioNTech COVID-19 vaccination

COVID-19 vaccines are safe and highly effective, but some individuals experience unpleasant reactions to vaccination. As the majority of adults in the US have received a COVID-19 vaccine this year, there is an unprecedented opportunity to study the genetics of reactions to vaccination via surveys of individuals who are already part of genetic research studies. Here, we have queried 17,440 participants in the Helix DNA Discovery Project and Healthy Nevada Project about their reactions to COVID-19 vaccination. Our GWAS identifies an association between severe difficulties with daily routine after vaccination and HLA-A*03:01. This association was statistically significant only for those who received the Pfizer-BioNTech vaccine (BNT162b2; p=4.70E-11), but showed a trending association in those who received the Moderna vaccine (mRNA-1273; p=0.005) despite similar sample sizes for study. In Pfizer-BioNTech recipients, HLA-A*03:01 was associated with a two-fold increase in risk of severe vaccine reactions. The effect was consistent across ages, sexes, and whether the person had previously had a COVID-19 infection. The reactions experienced by HLA-A*03:01 carriers were driven by associations with chills, fever, fatigue, and in general feeling unwell.

Rapid displacement of SARS-CoV-2 variant B.1.1.7 by B.1.617.2 and P.1 in the United States

This study reports on the displacement of Alpha (B.1.1.7) by Delta (B.1.617.2 and its substrains AY.1, AY.2, and AY.3) in the United States. By analyzing RT-qPCR testing results and viral sequencing results of samples collected across the United States, we show that the percentage of SARS-CoV-2 positive cases caused by Alpha dropped from 67% in May 2021 to less than 3.0% in just 10 weeks. We also show that the Delta variant has outcompeted the Iota (B.1.526) variant of interest and Gamma (P.1) variant of concern. An analysis of the mean quantification cycles (Cq) values in positive tests over time also reveal that Delta infections lead to a higher viral load on average compared to Alpha infections, but this increase is only 2 to 3x on average for our study design. Our results are consistent with the hypothesis that the Delta variant is more transmissible than the Alpha variant, and that this could be due to the Delta variants ability to establish a higher viral load earlier in the infection compared to the Alpha variant.

Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States

As of January of 2021, the highly transmissible B.1.1.7 variant of SARS-CoV-2, which was first identified in the United Kingdom (U.K.), has gained a strong foothold across the world. Because of the sudden and rapid rise of B.1.1.7, we investigated the prevalence and growth dynamics of this variant in the United States (U.S.), tracking it back to its early emergence and onward local transmission. We found that the RT-qPCR testing anomaly of S gene target failure (SGTF), first observed in the U.K., was a reliable proxy for B.1.1.7 detection. We sequenced 212 B.1.1.7 SARS-CoV-2 genomes collected from testing facilities in the U.S. from December 2020 to January 2021. We found that while the fraction of B.1.1.7 among SGTF samples varied by state, detection of the variant increased at a logistic rate similar to those observed elsewhere, with a doubling rate of a little over a week and an increased transmission rate of 35-45%. By performing time-aware Bayesian phylodynamic analyses, we revealed several independent introductions of B.1.1.7 into the U.S. as early as late November 2020, with onward community transmission enabling the variant to spread to at least 30 states as of January 2021. Our study shows that the U.S. is on a similar trajectory as other countries where B.1.1.7 rapidly became the dominant SARS-CoV-2 variant, requiring immediate and decisive action to minimize COVID-19 morbidity and mortality.

Drug Contamination of U.S. Paper Currency and Forensic Relevance of Canine Alert to Paper Currency: A Critical Review of the Scientific Literature.

Several studies have reported on wide-spread contamination of U.S. paper currency with cocaine and to a lesser extent other illicit drugs. Canines are trained and employed to search for and alert to drugs. Canine alert to currency has been used as evidence that currency has been directly involved in illicit drug trafficking to justify currency seizure and forfeiture. This assertion, particularly when the only evidence is based upon canine alert, has been challenged in the courts considering that most currency in circulation is contaminated with cocaine. Comprehensive review of the scientific literature establishes that (i) 67-100% of circulated U.S. currency is contaminated with cocaine ranging from a few nanograms to over one milligram/bill (ii) various biological and environmental parameters impact canine alert to drugs. It is concluded that canine alert to U.S. currency is not sufficiently reliable to determine that currency was directly used in an illicit drug transaction.

Bringing it all back home: Understanding the medical difficulties encountered by newly released prisoners in New Orleans, Louisiana - a qualitative study.

Formerly incarcerated persons (FIPs) face a disproportionate risk of death and serious illness in the immediate post-release period. Therefore, it is a critical time to initiate community-based care for chronic illnesses and behavioural disorders. Little is known about the unique transitional health and social support needs of FIPs in Louisiana, which has the highest incarceration rate in the world. As the average age of prisoners in the United States rises, the release of older prisoners with chronic conditions will become increasingly common. The aim of this study was to explore the healthcare experiences of FIPs in Louisiana in order to inform delivery of services tailored to this population. This research was done in partnership with a community organisation that advocates for restoration of voting rights to FIPs and helps newly released individuals transition back into society. This organisation identified FIPs in the Greater New Orleans area, and from January to May 2015, we conducted 24 semi-structured, in-person, audio-recorded interviews at the community organisation's transitional living facility. The interviews assessed FIPs' experiences with and barriers to receiving healthcare during and after incarceration. These discussions also explored FIPs' desires for services and attitudes towards health and healthcare. Interviews were transcribed and independently coded by two researchers. Interviewees reported negative experiences with healthcare during incarceration, and limited health guidance during the pre-release process. Post-release concerns included lack of insurance, difficulty accessing care and medication, and interest in learning about healthy lifestyles. Results suggest a need for a formalised system of transitional healthcare for FIPs. Findings are being used to inform a pilot transitional care clinic in New Orleans, Louisiana.

Severe Dengue Fever with Haemolytic Anaemia-A Case Study.

Dengue fever, the most common arthropod-borne viral infection in South East Asia, is increasing in prevalence due partially to increased awareness and better diagnostic methods. While haematologic complications, such as cytopeniae and bleeding, may occur in severe dengue infection due to a variety of aetiologies, reports of haemolytic anaemia in dengue fever are scant. We report a case of severe dengue fever with haemolytic anaemia following the critical phase of infection.

Validation of novel reference genes for reverse transcription quantitative real-time PCR in drought-stressed sugarcane.

One of the most challenging aspects of RT-qPCR data analysis is the identification of reliable reference genes. Ideally, they should be neither induced nor repressed under different experimental conditions. To date, few reference genes have been adequately studied for sugarcane (Saccharum spp.) using statistical approaches. In this work, six candidate genes ( αTUB, GAPDH, H1, SAMDC, UBQ, and 25S rRNA) were tested for gene expression normalization of sugarcane root tissues from drought-tolerant and -sensitive accessions after continuous dehydration (24 h). By undergoing different approaches (GeNorm, NormFinder, and BestKeeper), it was shown that most of them could be used in combinations for normalization purposes, with the exception of SAMDC. Nevertheless three of them (H1, αTUB, and GAPDH) were considered the most reliable reference genes. Their suitability as reference genes validated the expression profiles of two targets (AS and PFP α1), related to SuperSAGE unitags, in agreement with results revealed by previous in silico analysis. The other two sugarcane unitags (ACC oxidase and PIP1-1), after salt stress (100 mM NaCl), presented their expressions validated in the same way. In conclusion, these reference genes will be useful for dissecting gene expression in sugarcane roots under abiotic stress, especially in transcriptomic studies using SuperSAGE or RNAseq approaches.

Practicing Reiki does not appear to routinely produce high-intensity electromagnetic fields from the heart or hands of Reiki practitioners.

OBJECTIVES: The study objective was to determine whether Reiki practice increases the electromagnetic field strength from the heart and hands of Reiki practitioners. RATIONALE: This study repeated experiments performed 20 years ago that detected exceptionally high-strength electromagnetic fields (100 nT) from the hands of several energy healers. The equipment used was far more sensitive than in the original studies. DESIGN: Using a Magnes 2500 WH SQUID, the electromagnetic field from the hands and heart of each of 3 Reiki masters was measured when they were (1) not practicing Reiki, (2) sending Reiki to a distant person, and (3) sending Reiki to a person in the room. Similar measurements were made on 4 Reiki-naïve volunteers before and after they received a Reiki training/attunement enabling them to self-administer Reiki. SETTING/LOCATION: The study setting was the Scripps Institute, San Diego, CA. OUTCOME MEASURES: Magnetic field intensity of hands and heart recorded over 5-minute sessions with corresponding frequency spectra. RESULTS: For all subjects, under all conditions, sensors closest to the heart and the hands produced spikes of 2 pT corresponding to the heartbeat. Recordings from 2 Masters and 1 volunteer showed a low-intensity sine wave oscillation of 0.25-0.3 Hz (intensity 0.1-0.5 pT) whether or not they were practicing Reiki. This oscillation probably reflected respiratory sinus arrhythmia, judged by comparison with recent previous studies. These signals were not detected in the original studies. In the current study, no electromagnetic field intensities greater than 3 pT were observed in any of the recordings. CONCLUSIONS: Practicing Reiki does not appear to routinely produce high-intensity electromagnetic fields from the heart or hands. Alternatively, it is possible that energy healing is stimulated by tuning into an external environmental radiation, such as the Schumann resonance, which was blocked in the present study by the strong magnetic shielding surrounding the SQUID.

Expression Analysis of Sugarcane Aquaporin Genes under Water Deficit.

The present work is a pioneer study specifically addressing the aquaporin transcripts in sugarcane transcriptomes. Representatives of the four aquaporin subfamilies (PIP, TIP, SIP, and NIP), already described for higher plants, were identified. Forty-two distinct aquaporin isoforms were expressed in four HT-SuperSAGE libraries from sugarcane roots of drought-tolerant and -sensitive genotypes, respectively. At least 10 different potential aquaporin isoform targets and their respective unitags were considered to be promising for future studies and especially for the development of molecular markers for plant breeding. From those 10 isoforms, four (SoPIP2-4, SoPIP2-6, OsPIP2-4, and SsPIP1-1) showed distinct responses towards drought, with divergent expressions between the bulks from tolerant and sensitive genotypes, when they were compared under normal and stress conditions. Two targets (SsPIP1-1 and SoPIP1-3/PIP1-4) were selected for validation via RT-qPCR and their expression patterns as detected by HT-SuperSAGE were confirmed. The employed validation strategy revealed that different genotypes share the same tolerant or sensitive phenotype, respectively, but may use different routes for stress acclimation, indicating the aquaporin transcription in sugarcane to be potentially genotype-specific.

Relação entre valores e o comportamento de motoristas no trânsito / The relationship between values and drivers' behavior in traffic

Para investigar o comportamento de motoristas, possivelmente correlacionado a valores e variáveis demográficas, foi aplicado a 505 motoristas de Belém e Curitiba o Questionário de Valores Pessoais (PVQ). Deste total de participantes, 372 eram homens e 133 mulheres, sendo que destes, 205 tiveram Carteira de Habilitação (CNH) suspensa. Os resultados do PVQ foram confrontados com os dados demográficos, cidade de origem, condição de habilitação do motorista e algumas informações históricas sobre a idade em que aprendeu a dirigir e com quem aprendeu. Foram encontradas algumas correlações entre os fatores: 1) Autodireção: Cidade e Escolaridade; 2) Poder: Cidade e Situação da CNH; 3) Universalismo: Cidade, Situação da CNH e Idade; 4) Hedonismo: Idade; 5) Segurança: Cidade, Idade e Situação da CNH; 6) Estimulação: Idade; 7) Conformidade: Situação da CNH, Idade e Cidade; 8) Benevolência: Cidade, Situação da CNH, Sexo e Idade; 9) Realização: Idade; 10) Tradição: Idade. Alguns resultados mostraram diferenças entre motoristas suspensos e não suspensos e também entre motoristas das cidades pesquisadas, como por exemplo, um maior percentual de suspensos aprendeu a dirigir com a família e os fatores Benevolência e Conformidade foram mais valorizados pelos motoristas de Belém.(AU)

In order to investigate drivers' behavior possibly correlated with values and demographic variables, 505 drivers from the cities of Belém and Curitiba completed the Personal Values Questionnaire (PVQ). 372 were men and 133 were women, and the driver's license of 205 had been suspended. Results of the PVQ were related to demographic variables, age, birth place, the situation of the driver´s license, and to some background information, such as the age when the participant learned to drive and who taught him/her. Correlations between these data and independent variables were found for the following PVQ factors: 1) Self-direction: City and Educational Level; 2) Power: City and License Situation; 3) Universalism: City, License Situation and Age; 4) Hedonism: Age; 5) Security: City, Age and License Situation; 6) Stimulation: Age; 7) Conformity: Driver´s License Situation, Age and City; 8) Benevolence: City, Driver´s License Situation, Gender and Age; 9) Achievement: Age; 10) Tradition: Age. Responses from those with suspended licenses were different from those in the non-suspended sample. Some results of drivers from Belém and Curitiba were also different. For example, a larger percentage of suspended drivers were taught how to drive by family members and the factors Benevolence and Conformity were more valued by drivers from Belém.(AU)

Sugarcane (Saccharum X officinarum): A Reference Study for the Regulation of Genetically Modified Cultivars in Brazil.

Global interest in sugarcane has increased significantly in recent years due to its economic impact on sustainable energy production. Sugarcane breeding and better agronomic practices have contributed to a huge increase in sugarcane yield in the last 30 years. Additional increases in sugarcane yield are expected to result from the use of biotechnology tools in the near future. Genetically modified (GM) sugarcane that incorporates genes to increase resistance to biotic and abiotic stresses could play a major role in achieving this goal. However, to bring GM sugarcane to the market, it is necessary to follow a regulatory process that will evaluate the environmental and health impacts of this crop. The regulatory review process is usually accomplished through a comparison of the biology and composition of the GM cultivar and a non-GM counterpart. This review intends to provide information on non-GM sugarcane biology, genetics, breeding, agronomic management, processing, products and byproducts, as well as the current technologies used to develop GM sugarcane, with the aim of assisting regulators in the decision-making process regarding the commercial release of GM sugarcane cultivars.

Characterizing phospholipase A2-induced spinal cord injury-a comparison with contusive spinal cord injury in adult rats.

To assess whether phospholipase A2 (PLA2) plays a role in the pathogenesis of spinal cord injury (SCI), we compared lesions either induced by PLA2 alone or by a contusive SCI. At 24-h post-injury, both methods induced a focal hemorrhagic pathology. The PLA2 injury was mainly confined within the ventrolateral white matter, whereas the contusion injury widely affected both the gray and white matter. A prominent difference between the two models was that PLA2 induced a massive demyelination with axons remaining in the lesion area, whereas the contusion injury induced axonal damage and myelin breakdown. At 4 weeks, no cavitation was found within the PLA2 lesion, and numerous axons were myelinated by host-migrated Schwann cells. Among them, 45% of animals had early transcranial magnetic motor-evoked potential (tcMMEP) responses. In contrast, the contusive SCI induced a typical centralized cavity with reactive astrocytes forming a glial border. Only 15% of rats had early tcMMEP responses after the contusion. BBB scores were similarly reduced in both models. Our study indicates that PLA2 may play a unique role in mediating secondary SCI likely by targeting glial cells, particularly those of oligodendrocytes. This lesion model could also be used for studying demyelination and remyelination in the injured spinal cord associated with PLA2-mediated secondary SCI.

O desenvolvimento de dominância manual e podálica em crianças destras e canhotas entre três a oito anos de idade / The development of handedness and footedness in right- and left-handed children between the age of three and eight

Essa pesquisa estudou padrões de desenvolvimento de dominância manual, podálica e assimetrias fenotípicas associadas, como dominância mista e a correspondência entre a mão e o pé dominante, em crianças. Pesquisas indicaram que os canhotos diferem dos destros: são mais mistos nas suas preferências manuais e apresentam uma taxa elevada de dominância podálica contralateral, particularmente para chutar bola. Investigou-se em qual faixa de idade a direção e o grau de dominância ficam estáveis; se a dominância podálica se desenvolve simultaneamente com dominância manual e a idade entre canhotos, em que os fenótipos mistos e consistentes emergiram. Crianças (N=120) de três a oito anos de idade (60 destros e 60 canhotos) foram avaliados em dez tarefas manuais e quatro podálicas. Em destros e canhotos a direção e o grau de dominância manual estavam estabelecidos aos três anos; em ambos os grupos dominância manual e podálica evoluiram simultâneamente estabelecendo-se na mesma idade, senão antes. Entre canhotos, nos mistos e consistentes, já estava presente aos três anos de idade. A frequência permaneceu uniforme através das demais faixas etárias. Conclui-se que o padrão de dominância neuromotor para tarefas primárias e para o ato de chutar foi invariante, sendo, provavelmente, lateralização antes de três anos (AU)