Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes

Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely to monitor endemic disease transmission and control in low- and middle-income countries. Rabies is an almost invariably fatal viral disease that causes a large public health and economic burden in Asia and Africa, despite being entirely vaccine preventable. With policy efforts now directed towards achieving a global goal of zero dog-mediated human rabies deaths by 2030, establishing effective surveillance tools is critical. Genomic data can provide important and unique insights into rabies spread and persistence that can direct control efforts. However, capacity for genomic research in low- and middle-income countries is held back by limited laboratory infrastructure, cost, supply chains and other logistical challenges. Here we present and validate an end-to-end workflow to facilitate affordable whole genome sequencing for rabies surveillance utilising nanopore technology. We used this workflow in Kenya, Tanzania and the Philippines to generate rabies virus genomes in two to three days, reducing costs to approximately £60 per genome. This is over half the cost of metagenomic sequencing previously conducted for Tanzanian samples, which involved exporting samples to the UK and a three- to six-month lag time. Ongoing optimization of workflows are likely to reduce these costs further. We also present tools to support routine whole genome sequencing and interpretation for genomic surveillance. Moreover, combined with training workshops to empower scientists in-country, we show that local sequencing capacity can be readily established and sustainable, negating the common misperception that cutting-edge genomic research can only be conducted in high resource laboratories. More generally, we argue that the capacity to harness genomic data is a game-changer for endemic disease surveillance and should precipitate a new wave of researchers from low- and middle-income countries.

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Implementation of whole genome sequencing for tuberculosis diagnostics in a low-middle income, high MDR-TB burden country

Scientific Reports ◽

10.1038/s41598-021-94297-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Monica Vogel ◽

Christian Utpatel ◽

Caroline Corbett ◽

Thomas A. Kohl ◽

Altyn Iskakova ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Successful Implementation ◽

Whole Genome ◽

Kyrgyz Republic ◽

Middle Income ◽

External Assessment ◽

Middle Income Countries ◽

Mdr Tb ◽

Miseq Platform

AbstractWhole genome sequencing (WGS) is revolutionary for diagnostics of TB and its mutations associated with drug-resistances, but its uptake in low- and middle-income countries is hindered by concerns of implementation feasibility. Here, we provide a proof of concept for its successful implementation in such a setting. WGS was implemented in the Kyrgyz Republic. We estimated needs of up to 55 TB-WGS per week and chose the MiSeq platform (Illumina, USA) because of its capacity of up to 60 TB-WGS per week. The project’s timeline was completed in 93-weeks. Costs of large equipment and accompanying costs were 222,065 USD and 8462 USD, respectively. The first 174 WGS costed 277 USD per sequence, but this was skewed by training inefficiencies. Based on real prices and presuming optimal utilization of WGS capacities, WGS costs could drop to 167 and 141 USD per WGS using MiSeq Reagent Kits v2 (500-cycles) and v3 (600-cycles), respectively. Five trainings were required to prepare the staff for autonomous WGS which cost 48,250 USD. External assessment confirmed excellent performance of WGS by the Kyrgyz laboratory in an interlaboratory comparison of 30 M. tuberculosis genomes showing complete agreeance of results.

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Sequencing Using a Two-Step Strategy Reveals High Genetic Diversity in the S Gene of SARS-CoV-2 after a High-Transmission Period in Tunis, Tunisia

Microbiology Spectrum ◽

10.1128/spectrum.00639-21 ◽

2021 ◽

Author(s):

Wasfi Fares ◽

Kais Ghedira ◽

Mariem Gdoura ◽

Anissa Chouikha ◽

Sondes Haddad-Boubaker ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

High Genetic Diversity ◽

Middle Income ◽

Middle Income Countries ◽

Transmission Period ◽

Variant Detection ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

The method of choice for SARS-CoV-2 variant detection is whole-genome sequencing using next-generation sequencing (NGS) technologies. Resources for this technology remain limited in many low- and middle-income countries, where it is not possible to perform whole-genome sequencing for representative numbers of SARS-CoV-2-positive cases.

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Identifying Aspects of Public Attitudes Toward Whole Genome Sequencing to Inform the Integration of Genomics into Care

Public Health Genomics ◽

10.1159/000515952 ◽

2021 ◽

pp. 1-12

Author(s):

Holly Etchegary ◽

Daryl Pullman ◽

Charlene Simmonds ◽

Zoha Rabie ◽

Proton Rahman

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Online Survey ◽

Public Attitudes ◽

Genetic Counselor ◽

Genomic Medicine ◽

Genomic Data ◽

Whole Genome ◽

The Public ◽

Genomic Test

Introduction: The growth of global sequencing initiatives and commercial genomic test offerings suggests the public will increasingly be confronted with decisions about sequencing. Understanding public attitudes can assist efforts to integrate sequencing into care and inform the development of public education and outreach strategies. Methods: A 48-item online survey was advertised on Facebook in Eastern Canada and hosted on SurveyMonkey in late 2018. The survey measured public interest in whole genome sequencing and attitudes toward various aspects of sequencing using vignettes, scaled, and open-ended items. Results: While interest in sequencing was high, critical attitudes were observed. In particular, items measuring features of patient control and choice regarding genomic data were strongly endorsed by respondents. Majority wanted to specify upfront how their data could be used, retain the ability to withdraw their sample at a later date, sign a written consent form, and speak to a genetic counselor prior to sequencing. Concerns about privacy and unauthorized access to data were frequently observed. Education level was the sociodemographic variable most often related to attitude statements such that those with higher levels of education generally displayed more critical attitudes. Conclusions: Attitudes identified here could be used to inform the development of implementation strategies for genomic medicine. Findings suggest health systems must address patient concerns about privacy, consent practices, and the strong desire to control what happens to their genomic data through public outreach and education. Specific oversight procedures and policies that are clearly communicated to the public will be required.

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Management of germline findings revealed throughout the course of tumor-normal whole genome sequencing in oncology.

Journal of Clinical Oncology ◽

10.1200/jco.2017.35.15_suppl.e13113 ◽

2017 ◽

Vol 35 (15_suppl) ◽

pp. e13113-e13113

Author(s):

Howard John Lim ◽

Kasmintan A Schrader ◽

Sean Young ◽

Jessica Nelson ◽

Alexandra Fok ◽

...

Keyword(s):

Genetic Counseling ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Cancer Susceptibility ◽

Susceptibility Gene ◽

Susceptibility Genes ◽

Genomic Research ◽

Whole Genome ◽

Pathogenic Variants ◽

Cancer Susceptibility Genes

e13113 Background: The Personalized OncoGenomics (POG) project at the BC Cancer Agency utilizes tumor-normal whole genome sequencing (WGS) to understand key driver pathways and guide personalized treatment decisions. Analysis of the germline data can reveal variants; these may be presumed pathogenic, presumed benign or of unknown significance (VUS). We have developed a process for evaluating and returning presumed pathogenic variants in known cancer susceptibility genes to patients, for counseling and validation in a clinical-accredited laboratory. Methods: Patients receive germline cancer related information as part of the consent process for participation in the POG program. A sub-committee comprised of medical geneticists, bioinformaticians, pathologists, oncologists and an ethicist review the germline results. Any variants suspicious of being an artifact undergo a technical validation step. Presumed pathogenic findings of known cancer susceptibility genes are returned to the patient by their treating oncologist and patients are referred to the Hereditary Cancer Program (HCP), for genetic counseling and clinical confirmation. Results: From June 2012 - January 2017 – 466 patients have consented to the project. To date, 39 cases (8.4%) had at least one variant that was deemed pathogenic, 86 cases had at least one VUS in a known cancer susceptibility gene. 11 out of 23 cases (47.8%) with high penetrance mutations were already known to HCP. All VUS were reviewed by the sub-committee taking in to consideration the VUS and clinical context. 8 of the subjects with pathogenic results and 3 with VUS were known to HCP before POG data was generated. A VUS in 7 cases (1.5%) was returned after review. Conclusions: The number of pathogenic variants in known cancer susceptibility genes is consistent with published oncology results. We created a process to manage clinically relevant germline findings discovered during the course of genomic research to ensure appropriate care for patients. Genetic counseling within HCP and validation of variants in the clinically accredited Cancer Genetics Laboratory enables seamless return of research generated clinically relevant germline results to affected subjects. Clinical trial information: NCT02155621.

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Whole Genome Sequencing Analysis of Salmonella enterica Serovar Typhi: History and Current Approaches

Microorganisms ◽

10.3390/microorganisms9102155 ◽

2021 ◽

Vol 9 (10) ◽

pp. 2155

Author(s):

Wan Ratmaazila Wan Makhtar ◽

Izwan Bharudin ◽

Nurul Hidayah Samsulrizal ◽

Nik Yusnoraini Yusof

Keyword(s):

Infectious Diseases ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Salmonella Enterica ◽

Point Of Care ◽

Genomic Research ◽

Whole Genome ◽

Sequencing Analysis ◽

Significant Information ◽

Salmonella Enterica Serovar Typhi

In recent years, the advance in whole-genome sequencing technology has changed the study of infectious diseases. The emergence of genome sequencing has improved the understanding of infectious diseases, which has revamped many fields, such as molecular microbiology, epidemiology, infection control, and vaccine production. In this review we discuss the findings of Salmonella enterica serovar Typhi genomes, publicly accessible from the initial complete genome to the recent update of Salmonella enterica serovar Typhi genomes, which has greatly improved Salmonella enterica serovar Typhi and other pathogen genomic research. Significant information on genetic changes, evolution, antimicrobial resistance, virulence, pathogenesis, and investigation from the genome sequencing of S. Typhi is also addressed. This review will gather information on the variation of the Salmonella enterica serovar Typhi genomes and hopefully facilitate our understanding of their genome evolution, dynamics of adaptation, and pathogenesis for the development of the typhoid point-of-care diagnostics, medications, and vaccines.

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Annotated Genome Sequences of 16 Lineage 4 Mycobacterium tuberculosis Strains from Guatemala

Genome Announcements ◽

10.1128/genomea.00024-18 ◽

2018 ◽

Vol 6 (7) ◽

Cited By ~ 1

Author(s):

Joseph W. Saelens ◽

Dalia Lau-Bonilla ◽

Anneliese Moller ◽

Ana M. Xet-Mull ◽

Narda Medina ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Whole Genome Sequencing ◽

Central America ◽

Genome Sequencing ◽

Genomic Data ◽

Whole Genome ◽

Genome Sequences ◽

Clinical Strains ◽

Complete Genomes

ABSTRACT Whole-genome sequencing has resulted in new insights into the phylogeography of Mycobacterium tuberculosis . However, only limited genomic data are available from M. tuberculosis strains in Guatemala. Here we report 16 complete genomes of clinical strains belonging to the Euro-American lineage 4, the most common lineage found in Guatemala and Central America.

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Broad Consent for Genomic Research and Biobanking: Perspectives from Low- and Middle-Income Countries

Annual Review of Genomics and Human Genetics ◽

10.1146/annurev-genom-083115-022456 ◽

2016 ◽

Vol 17 (1) ◽

pp. 375-393 ◽

Cited By ~ 24

Author(s):

Paulina Tindana ◽

Jantina de Vries

Keyword(s):

Genomic Research ◽

Broad Consent ◽

Middle Income ◽

Middle Income Countries ◽

Low And Middle Income

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Human whole genome sequencing in South Africa

Scientific Reports ◽

10.1038/s41598-020-79794-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Brigitte Glanzmann ◽

Tracey Jooste ◽

Samira Ghoor ◽

Richard Gordon ◽

Rizwana Mia ◽

...

Keyword(s):

Whole Genome Sequencing ◽

South African ◽

Genome Sequencing ◽

Genomic Research ◽

Whole Genome ◽

Human Dna ◽

Whole Genomes ◽

World Class ◽

Average Sequencing Depth ◽

Generation Sequencing

AbstractThe advent and evolution of next generation sequencing has considerably impacted genomic research. Until recently, South African researchers were unable to access affordable platforms capable of human whole genome sequencing locally and DNA samples had to be exported. Here we report the whole genome sequences of the first six human DNA samples sequenced and analysed at the South African Medical Research Council’s Genomics Centre. We demonstrate that the data obtained is of high quality, with an average sequencing depth of 36.41, and that the output is comparable to data generated internationally on a similar platform. The Genomics Centre creates an environment where African researchers are able to access world class facilities, increasing local capacity to sequence whole genomes as well as store and analyse the data.

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Draft genome of tule elk Cervus elaphus nannodes

F1000Research ◽

10.12688/f1000research.12636.1 ◽

2017 ◽

Vol 6 ◽

pp. 1691

Author(s):

Jessica E. Mizzi ◽

Zachary T. Lounsberry ◽

C. Titus Brown ◽

Benjamin N. Sacks

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Cervus Elaphus ◽

Draft Genome ◽

Genetic Bottleneck ◽

Genomic Research ◽

Whole Genome ◽

Base Pairs ◽

Illumina Hiseq ◽

Tule Elk

This paper presents the first draft genome of the tule elk (Cervus elaphus nannodes), a subspecies native to California that underwent an extreme genetic bottleneck in the late 1800s. The genome was generated from Illumina HiSeq 3000 whole genome sequencing of four individuals, resulting in the assembly of 2.395 billion base pairs (Gbp) over 602,862 contigs over 500 bp and N50 = 6,885 bp. This genome provides a resource to facilitate future genomic research on elk and other cervids.

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