Current and emerging technology approaches in genomics

African Swine Fever Virus (ASFV): Biology, Genomics and Genotypes Circulating in Sub-Saharan Africa

African swine fever (ASF) is a highly infectious and fatal haemorrhagic disease of pigs that is caused by a complex DNA virus of the genus Asfivirus and Asfarviridae African suids family. The disease is among the most devastating pig diseases worldwide including Africa. Although the disease was first reported in the 19th century, it has continued to spread in Africa and other parts of the world. Globally, the rising demand for pork and concomitant increase in transboundary movements of pigs and pork products is likely to increase the risk of transmission and spread of ASF and pose a major challenge to the pig industry. Different genotypes of the ASF virus (ASFV) with varying virulence have been associated with different outbreaks in several countries in sub-Saharan Africa (SSA) and worldwide, and understanding genotype circulation will be important for ASF prevention and control strategies. ASFV genotypes unique to Africa have also been reported in SSA. This review briefly recounts the biology, genomics and genotyping of ASFV and provides an account of the different genotypes circulating in SSA. The review also highlights prevention, control and progress on vaccine development and identifies gaps in knowledge of ASFV genotype circulation in SSA that need to be addressed.

The first genotype II African swine fever virus isolated in Africa provides insight into the current Eurasian pandemic

African swine fever (ASF) caused by the African swine fever virus (ASFV) is ranked by OIE as the most important source of mortality in domestic pigs globally and is indigenous to African wild suids and soft ticks. Despite two ASFV genotypes causing economically devastating epidemics outside the continent since 1961, there have been no genome-level analyses of virus evolution in Africa. The virus was recently transported from south-eastern Africa to Georgia in 2007 and has subsequently spread to Russia, eastern Europe, China, and south-east Asia with devastating socioeconomic consequences. To date, two of the 24 currently described ASFV genotypes defined by sequencing of the p72 gene, namely genotype I and II, have been reported outside Africa, with genotype II being responsible for the ongoing pig pandemic. Multiple complete genotype II genome sequences have been reported from European, Russian and Chinese virus isolates but no complete genome sequences have yet been reported from Africa. We report herein the complete genome of a Tanzanian genotype II isolate, Tanzania/Rukwa/2017/1, collected in 2017 and determined using an Illumina short read strategy. The Tanzania/Rukwa/2017/1 sequence is 183,186 bp in length (in a single contig) and contains 188 open reading frames. Considering only un-gapped sites in the pairwise alignments, the new sequence has 99.961% identity with the updated Georgia 2007/1 reference isolate (FR682468.2), 99.960% identity with Polish isolate Pol16_29413_o23 (MG939586) and 99.957% identity with Chinese isolate ASFV-wbBS01 (MK645909.1). This represents 73 single nucleotide polymorphisms (SNPs) relative to the Polish isolate and 78 SNPs with the Chinese genome. Phylogenetic analysis indicated that Tanzania/Rukwa/2017/1 clusters most closely with Georgia 2007/1. The majority of the differences between Tanzania/Rukwa/2017/1 and Georgia 2007/1 genotype II genomes are insertions/deletions (indels) as is typical for ASFV. The indels included differences in the length and copy number of the terminal multicopy gene families, MGF 360 and 110. The Rukwa2017/1 sequence is the first complete genotype II genome from a precisely mapped locality in Africa, since the exact origin of Georgia2007/1 is unknown. It therefore provides baseline information for future analyses of the diversity and phylogeography of this globally important genetic sub-group of ASF viruses.

Pharmacogenomics and prescription opioid use

Genome-wide association studies and candidate gene findings suggest that genetic approaches may help in choosing the most appropriate drug and dosage, while preventing adverse drug reactions. This is the field that addresses precision medicine: to evaluate variations in the DNA sequence that could be responsible for different individual analgesic response. We review potential gene biomarkers with best overall convergent functional evidence, for opioid use, in pain management. Polymorphisms can modify pharmacodynamics (i.e., mu opioid receptor, OPRM1) and pharmacokinetics (i.e., CYP2D6 phenotypes) pathways altering opioid effectiveness, consumption, side effects or additionally, prescription opioid use dependence vulnerability. This review provides a summary of these candidate variants for the translation of genotype into clinically useful information in pain medicine.

Precision Health: Use of Omics to Optimize Self-Management of Chronic Pain in Aging

Chronic pain has become a public health epidemic based on the number of Americans affected and its associated health care costs. Unfortunately, there are few efficacious treatments to manage chronic pain and as the population of older adults and centenarians who are at high risk for chronic pain continues to grow, the chronic pain epidemic will continue to worsen unless new therapeutic strategies are discovered. In the current era of precision medicine, there is a major emphasis being placed on the use of self-management and omics to discover new therapeutic targets and design treatment strategies that are tailored to the individual patient. This commentary discusses the current state of the science related to omics and self-management of chronic pain in older adults, the role of gerontological nurses in this process, and future directions. [Res Gerontol Nurs. 2018; 11(1):7-13.].

Symptom Science: Repurposing Existing Omics Data

Omics approaches, including genomics, transcriptomics, proteomics, epigenomics, microbiomics, and metabolomics, generate large data sets. Once they have been used to address initial study aims, these large data sets are extremely valuable to the greater research community for ancillary investigations. Repurposing available omics data sets provides data to address research questions, generate and test hypotheses, replicate findings, and conduct mega-analyses. Many well-characterized, longitudinal, epidemiological studies collected extensive phenotype data related to symptom occurrence and severity. While the main phenotype of interest for many of these studies was often not symptom related, these data were collected to better understand the primary phenotype of interest. A search for symptom data (i.e., cognitive impairment, fatigue, gastrointestinal distress/nausea, sleep, and pain) in the database of genotypes and phenotypes (dbGaP) revealed many studies that collected symptom and omics data. There is thus a real possibility for nurse scientists to be able to look at symptom data over time from thousands of individuals and use omics data to identify key biological underpinnings that account for the development and severity of symptoms without recruiting participants or generating any new data. The purpose of this article is to introduce the reader to resources that provide omics data to the research community for repurposing, provide guidance on using these databases, and encourage the use of these data to move symptom science forward.

Increasing importance of genetics in nursing

OBJECTIVES

To examine the empirical literature related to the incorporation of genetic research and genetic competency needed by the nurse in practice.

DESIGN

Literature review.

DATA SOURCES

This article will explore published research within the past seven years of 2008-2015 that address the need for the increased incorporation of genetic content in nursing practice in addition to the need for the nurse to effectively screen the patient at risk of a genetic disorder. This literature review specifically focuses on the inadequacy of nurses in addressing genomic health compromise and serving as advocates for patients and families facing genetic disorders.

METHODS

A review of the literature published from 2008 to 2015 related to the incorporation of genetics in nursing practice and the role of the nurse as a patient advocate for families facing genetic disorders with resulting genomic health compromise.

RESULTS

The research exposes the lack of adequate preparation of nurses to incorporate and utilize the recent advances in genomic healthcare. Practicing nurses lack understating and skill in the application of genetics and genomic technologies to patient care. The nursing profession, including nursing academia, need to enhance the integration of genetic and genomic content into nursing curriculum and practice.

CONCLUSION

Practicing nurses are inadequately prepared to apply genetic advancements in screening at risk patients and addressing the needs of the patient or family facing a genomic health compromise.

Understanding Genomic Knowledge in Rural Appalachia: The West Virginia Genome Community Project

PURPOSE

Rural communities have limited knowledge about genetics and genomics and are also underrepresented in genomic education initiatives. The purpose of this project was to assess genomic and epigenetic knowledge and beliefs in rural West Virginia.

SAMPLE

A total of 93 participants from three communities participated in focus groups and 68 participants completed a demographic survey. The age of the respondents ranged from 21 to 81 years. Most respondents had a household income of less than $40,000, were female and most were married, completed at least a HS/GED or some college education working either part-time or full-time.

METHOD

A Community Based Participatory Research process with focus groups and demographic questionnaires was used.

FINDINGS

Most participants had a basic understanding of genetics and epigenetics, but not genomics. Participants reported not knowing much of their family history and that their elders did not discuss such information. If the conversations occurred, it was only during times of crisis or an illness event. Mental health and substance abuse are topics that are not discussed with family in this rural population.

CONCLUSIONS

Most of the efforts surrounding genetic/genomic understanding have focused on urban populations. This project is the first of its kind in West Virginia and has begun to lay the much needed infrastructure for developing educational initiatives and extending genomic research projects into our rural Appalachian communities. By empowering the public with education, regarding the influential role genetics, genomics, and epigenetics have on their health, we can begin to tackle the complex task of initiating behavior changes that will promote the health and well-being of individuals, families and communities.

Educating future nursing scientists: Recommendations for integrating omics content in PhD programs

Preparing the next generation of nursing scientists to conduct high-impact, competitive, sustainable, innovative, and interdisciplinary programs of research requires that the curricula for PhD programs keep pace with emerging areas of knowledge and health care/biomedical science. A field of inquiry that holds great potential to influence our understanding of the underlying biology and mechanisms of health and disease is omics. For the purpose of this article, omics refers to genomics, transcriptomics, proteomics, epigenomics, exposomics, microbiomics, and metabolomics. Traditionally, most PhD programs in schools of nursing do not incorporate this content into their core curricula. As part of the Council for the Advancement of Nursing Science's Idea Festival for Nursing Science Education, a work group charged with addressing omics preparation for the next generation of nursing scientists was convened. The purpose of this article is to describe key findings and recommendations from the work group that unanimously and enthusiastically support the incorporation of omics content into the curricula of PhD programs in nursing. The work group also calls to action faculty in schools of nursing to develop strategies to enable students needing immersion in omics science and methods to execute their research goals.

Proposed mechanisms for cancer- and treatment-related cognitive changes

OBJECTIVES

To review the proposed mechanisms of cognitive changes associated with non-central nervous system cancers and cancer treatment.

DATA SOURCES

Review and synthesis of databased publications and review articles.

CONCLUSION

Proposed mechanisms include cytokine upregulation, hormonal changes, neurotransmitter dysregulation, attentional fatigue, genetic predisposition, and comorbid symptoms.

IMPLICATIONS FOR NURSING PRACTICE

Oncology nurses need to understand the multiple mechanisms that may contribute to the development of cancer- and treatment-related cognitive changes so that they can identify patients at high risk and help patients understand why these changes occur.

Cancer genetics and genomics: essentials for oncology nurses

Cancer genetics and genomics are rapidly evolving, with new discoveries emerging in genetic mutations, variants, genomic sequencing, risk-reduction methods, and targeted therapies. To educate patients and families, state-of-the-art care requires nurses to understand terminology, scientific and technological advances, and pharmacogenomics. Clinical application of cancer genetics and genomics involves working in interdisciplinary teams to properly identify patient risk through assessing family history, facilitating genetic testing and counseling services, applying risk-reduction methods, and administering and monitoring targeted therapies.

An overview of epigenetics in nursing

Epigenetic changes to the genome are biochemical alterations to the DNA that do not change an individual's genome but do change and influence gene expression. The nursing profession is qualified to conduct and integrate epigenetic-focused nursing research into practice. This article discusses current epigenetic nursing research, provides an overview of how epigenetic research relates to nursing practice, makes recommendations, and provides epigenetic online resources for nursing research. An overview of major epigenetic studies in nursing (specific to childbirth studies, preeclampsia, metabolic syndrome, immunotherapy cancer, and pain) is provided, with recommendations on next steps.

An update of childhood genetic disorders

PURPOSE

Thousands of single gene, mitochondrial, and chromosomal disorders have been described in children. The purpose of this article is twofold. The first is to increase nurses' awareness of new developments in genetic disorders that are commonly seen in practice and taught in schools of nursing. The second is to illustrate important genetic concepts of relevance to nurses who care for infants, children, or adolescents.

ORGANIZING CONSTRUCT

This article is organized into four sections: one that describes new developments in a well-known disorder, a second that discusses the process and potential outcomes of diagnosing a very rare disorder, and the third and fourth sections that describe select conditions caused by single gene mutations.

METHODS

Clinical expertise was paired with literature review to present evidence-based current information. Implications for nursing practice are highlighted throughout the article. Citations of publicly available evidence-based online resources are used so nurses can continue to use these in their practices.

FINDINGS

Diagnosis and treatment strategies for children with genetic disorders are rapidly changing. While it is impossible to stay current in all disorders, resources are available to help nurses provide evidence-based care to children with genetic disorders.

CLINICAL RELEVANCE

Nurses have an important role in the early identification of children with genetic disorders and in facilitating their access to appropriate services and resources. Nurses can also help families understand why genetic testing may be necessary and assure families are informed throughout the process.