Genomic-informed pathogen surveillance in Africa: opportunities and challenges

Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR

(2020) Victor M Corman et al.   Eurosurveillance

Preparedness and vulnerability of African countries against importations of COVID-19: a modelling study

(2020) Marius Gilbert et al.   LANCET

The African Genomic Medicine Training Initiative (AGMT): Showcasing a Community and Framework Driven Genomic Medicine Training for Nurses in Africa

(2020) Victoria Nembaware et al.   Frontiers in Genetics

Health security capacities in the context of COVID-19 outbreak: an analysis of International Health Regulations annual report data from 182 countries

(2020) Nirmal Kandel et al.   LANCET

Let Africa into the market for COVID-19 diagnostics

(2020) John Nkengasong   NATURE

External Quality Assessment for Next-Generation Sequencing-Based HIV Drug Resistance Testing: Unique Requirements and Challenges

(2020) Emma R. Lee et al.   Viruses-Basel

Early estimates of the indirect effects of the COVID-19 pandemic on maternal and child mortality in low-income and middle-income countries: a modelling study

(2020) Timothy Roberton et al.   Lancet Global Health

Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus

(2020) Bette Korber et al.   CELL

SARS-CoV-2 genomic variations associated with mortality rate of COVID-19

(2020) Yujiro Toyoshima et al.   JOURNAL OF HUMAN GENETICS

Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study

(2020) Luke W Meredith et al.   LANCET INFECTIOUS DISEASES

Need for sustainable biobanking networks for COVID-19 and other diseases of epidemic potential

(2020) Rosanna W Peeling et al.   LANCET INFECTIOUS DISEASES

Multi-Laboratory Comparison of Next-Generation to Sanger-Based Sequencing for HIV-1 Drug Resistance Genotyping

(2020) Neil T. Parkin et al.   Viruses-Basel

Potential impact of the COVID-19 pandemic on HIV, tuberculosis, and malaria in low-income and middle-income countries: a modelling study

(2020) Alexandra B Hogan et al.   Lancet Global Health

Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT–qPCR primer–probe sets

(2020) Chantal B. F. Vogels et al.   Nature Microbiology

Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study

(2020) Barnaby E Young et al.   LANCET

Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report

(2020) Jennifer Giandhari et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

PANGEA-HIV 2

(2019) Lucie Abeler-Dörner et al.   Current Opinion in HIV and AIDS

Expanding Research Capacity in Sub-Saharan Africa Through Informatics, Bioinformatics, and Data Science Training Programs in Mali

(2019) Jeffrey G. Shaffer et al.   Frontiers in Genetics

2018 Ebola virus disease outbreak in Équateur Province, Democratic Republic of the Congo: a retrospective genomic characterisation

(2019) Placide Mbala-Kingebeni et al.   LANCET INFECTIOUS DISEASES

Medical countermeasures during the 2018 Ebola virus disease outbreak in the North Kivu and Ituri Provinces of the Democratic Republic of the Congo: a rapid genomic assessment

(2019) Placide Mbala-Kingebeni et al.   LANCET INFECTIOUS DISEASES

Applying next-generation sequencing to track falciparum malaria in sub-Saharan Africa

(2019) Sofonias K. Tessema et al.   MALARIA JOURNAL

Pathogen Genomics in Public Health

(2019) Gregory L. Armstrong et al.   NEW ENGLAND JOURNAL OF MEDICINE

Next-Generation Sequencing: An Eye-Opener for the Surveillance of Antiviral Resistance in Influenza

(2019) Laura A.E. Van Poelvoorde et al.   TRENDS IN BIOTECHNOLOGY

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

Real-time analysis and visualization of pathogen sequence data

(2018) Richard A. Neher et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018

(2018) Katherine J. Siddle et al.   NEW ENGLAND JOURNAL OF MEDICINE

Expansion of Surveillance for Vaccine-preventable Diseases: Building on the Global Polio Laboratory Network and the Global Measles and Rubella Laboratory Network Platforms

(2017) Mick N. Mulders et al.   JOURNAL OF INFECTIOUS DISEASES

Virus genomes reveal factors that spread and sustained the Ebola epidemic

(2017) Gytis Dudas et al.   NATURE

Towards a genomics-informed, real-time, global pathogen surveillance system

(2017) Jennifer L. Gardy et al.   NATURE REVIEWS GENETICS

Establishing the Africa Centres for Disease Control and Prevention: responding to Africa's health threats

(2017) John N Nkengasong et al.   Lancet Global Health

Assuring the Quality of Next-Generation Sequencing in Clinical Microbiology and Public Health Laboratories

(2016) Amy S. Gargis et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Affordable HIV drug-resistance testing for monitoring of antiretroviral therapy in sub-Saharan Africa

(2016) Seth C Inzaule et al.   LANCET INFECTIOUS DISEASES

Cost-efficient HIV-1 drug resistance surveillance using multiplexed high-throughput amplicon sequencing: implications for use in low- and middle-income countries

(2014) H. Ekici et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Why are antiretroviral treatment patients lost to follow-up? A qualitative study from South Africa

(2010) Candace M. Miller et al.   TROPICAL MEDICINE & INTERNATIONAL HEALTH