Zika: Open genomic surveillance of Zika virus in Brazil using a novel portable real-time sequencing device
Lead Research Organisation:
University of Birmingham
Department Name: UNLISTED
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
A major epidemic of Zika virus (ZIKV) is ongoing in Latin America. Critically, there is
evidence for an association between infection with ZIKV and both microcephaly in newborns
and Guillain-Barré syndrome. Currently there is a paucity of complete genome sequences for
this virus, in part due to difficulties in transporting material outside of Brazil for sequencing,
hindering attempts to determine virus origins, epidemiology and any genomic basis to
microcephaly. We have recently established real-time portable genome sequencing using the
Oxford Nanopore MinION device, and successfully used this to characterize Ebola virus
genetic diversity in Guinea during the 2014-2015 outbreak [1]. We propose to extend this
ground-breaking achievement to ZIKV by establishing two portable genome sequencing
laboratories in Brazil. Through collaboration with the Oswaldo Cruz Foundation (FIOCRUZ)
and the Instituto Evandro Chagas public health laboratory in Brazil we will sequence 750
complete genomes of ZIKV, covering a broad geographical region including historical
samples, and from patients with a range of clinical presentations. These novel genomic data
will provide key information on how and when ZIKV was introduced to Brazil, the pattern and
determinants of spread through the country and to neighbouring localities, the extent of
genetic diversity (of importance to vaccine and diagnostic design), and whether there are any
associations between changes in the virus genome and the likelihood of ZIKV complications
such as microcephaly. Crucially these data will provide a surveillance framework for tracking
further spread into other geographic regions. In common with our previous efforts, this effort
will serve as a beacon for open science during a public health emergency [1-4]. Data will be
subject to open release as it is generated.
evidence for an association between infection with ZIKV and both microcephaly in newborns
and Guillain-Barré syndrome. Currently there is a paucity of complete genome sequences for
this virus, in part due to difficulties in transporting material outside of Brazil for sequencing,
hindering attempts to determine virus origins, epidemiology and any genomic basis to
microcephaly. We have recently established real-time portable genome sequencing using the
Oxford Nanopore MinION device, and successfully used this to characterize Ebola virus
genetic diversity in Guinea during the 2014-2015 outbreak [1]. We propose to extend this
ground-breaking achievement to ZIKV by establishing two portable genome sequencing
laboratories in Brazil. Through collaboration with the Oswaldo Cruz Foundation (FIOCRUZ)
and the Instituto Evandro Chagas public health laboratory in Brazil we will sequence 750
complete genomes of ZIKV, covering a broad geographical region including historical
samples, and from patients with a range of clinical presentations. These novel genomic data
will provide key information on how and when ZIKV was introduced to Brazil, the pattern and
determinants of spread through the country and to neighbouring localities, the extent of
genetic diversity (of importance to vaccine and diagnostic design), and whether there are any
associations between changes in the virus genome and the likelihood of ZIKV complications
such as microcephaly. Crucially these data will provide a surveillance framework for tracking
further spread into other geographic regions. In common with our previous efforts, this effort
will serve as a beacon for open science during a public health emergency [1-4]. Data will be
subject to open release as it is generated.
Publications
Faria NR
(2017)
Establishment and cryptic transmission of Zika virus in Brazil and the Americas.
in Nature
Faria NR
(2018)
Genomic and epidemiological monitoring of yellow fever virus transmission potential.
in Science (New York, N.Y.)
Faria NR
(2016)
Mobile real-time surveillance of Zika virus in Brazil.
in Genome medicine
Forato J
(2024)
Molecular Epidemiology of Mayaro Virus among Febrile Patients, Roraima State, Brazil, 2018-2021.
in Emerging infectious diseases
Gardy JL
(2018)
Towards a genomics-informed, real-time, global pathogen surveillance system.
in Nature reviews. Genetics
Giovanetti M
(2020)
Genomic and Epidemiological Surveillance of Zika Virus in the Amazon Region.
in Cell reports
Grubaugh ND
(2017)
Genomic epidemiology reveals multiple introductions of Zika virus into the United States.
in Nature
Grubaugh ND
(2019)
An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar.
in Genome biology
Harish V
(2024)
Human movement and environmental barriers shape the emergence of dengue
in Nature Communications
Hill V
(2024)
A new lineage nomenclature to aid genomic surveillance of dengue virus.
in PLoS biology
Lackritz E
(2025)
Zika virus: advancing a priority research agenda for preparedness and response
in The Lancet Infectious Diseases
Li A
(2025)
Role of non-human primate models in accelerating research and developing countermeasures against Zika virus infection
in The Lancet Microbe
Mendes-Correa MC
(2024)
SARS-CoV-2 shedding, infectivity, and evolution in an immunocompromised adult patient.
in Revista do Instituto de Medicina Tropical de Sao Paulo
Mirza JD
(2024)
Tracking arboviruses, their transmission vectors and potential hosts by nanopore sequencing of mosquitoes.
in Microbial genomics
Márquez S
(2017)
First Complete Genome Sequences of Zika Virus Isolated from Febrile Patient Sera in Ecuador.
in Genome announcements
Naveca FG
(2019)
Genomic, epidemiological and digital surveillance of Chikungunya virus in the Brazilian Amazon.
in PLoS neglected tropical diseases
Ostrowsky J
(2025)
Zika virus vaccines and monoclonal antibodies: a priority agenda for research and development
in The Lancet Infectious Diseases
Quick J
(2017)
Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples.
in Nature protocols
Rivera LF
(2024)
Characteristics of Madariaga and Venezuelan Equine Encephalitis Virus Infections, Panama.
in Emerging infectious diseases
| Description | In 2016 the world urgently needed to understand the origins of Zika virus with was associated with cases of newborn microcephaly in the Americas. To do this we worked with Brazilian colleagues to develop an entirely new method of sequencing virus genomes rapidly. We were able to show that Zika had been circulating in Brazil for a full year before it was detected, and demonstrated how it had spread from Asia across the Pacific. We continue to work closely with our Brazilian colleagues using our methods to understand new and emerging mosquito-transmitted viruses. Our new method became ultimately famous globally, as it set the standard for how the SARS-CoV-2 virus was sequenced during the COVID-19 pandemic. |
| Exploitation Route | This project has formed the basis of a global standard for sequencing viruses and other microbial pathogens and is available as a freely available open source toolkit for that purpose. It will be of use for future pathogen surveillance projects and pandemic preparedness. |
| Sectors | Environment Healthcare Pharmaceuticals and Medical Biotechnology |
| URL | http://www.zibraproject.org |
| Description | ZIBRA 2 - ZIKV in Brazil Real-Time Analysis - Second Round |
| Amount | R$ 1,100,000 (BRL) |
| Funding ID | MCTIC/FNDCT-CNPq/MEC-CAPES/MS-Decit/No.14/2016 - Preventing and Combating Zika Virus |
| Organisation | National Council for Scientific and Technological Development (CNPq) |
| Sector | Public |
| Country | Brazil |
| Start | 03/2017 |
| End | 03/2019 |
| Title | ARTIC mpox sequencing primers and protocol |
| Description | We developed an end-to-end sequencing protocol and primer scheme initially for Mpox clade 2, then extended this to cover both clades 1 and 2 and released as an open source protocol (https://artic.network/mpxv/resources). We made sequencing reagents (primer schemes) broadly available including numerous countries in Africa currrently experiencing a clade 1b epidemic (e.g. DRC). These resources extend work previously used for Ebola and Zika viruses and latterly SARS-CoV-2. We included bioinformatics pipelines that can be run easily through a graphical interface on the Oxford Nanopore platform, and quality control software (Squirrel) for robust phylogenetic inference in the hard-to-sequence MPXV genome. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | These resources have been used in a number of rapid outbreak reports particularly e.g. reporting the presence of human-to-human transmission of MPXV in DRC of clade 1b: - https://virological.org/t/clade-ib-mpox-in-the-democratic-republic-of-the-congo-drc-clinical-and-virological-report-of-the-first-case-in-kinshasa-the-capital-city/978 - https://virological.org/t/mpox-clade-ib-cases-in-goma/962 |
| URL | https://artic.network/mpxv/resources |
| Title | Virus genome sequencing infrastructure - Ministry of Health Angola |
| Description | Our team introduced portable Oxford Nanopore Technology sequencers, including the Mk1D MinION and sequencing laptops, at the Health Institute Research, Ministry of Health Angola. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2025 |
| Provided To Others? | Yes |
| Impact | First in-country generation of mpox, measles and dengue 3 viral genomes using targeted sequencing protocols. In-country improvement in Pathogen X detection through training in untargeted metagenomic sequencing protocols. |
| Title | Brazilian municipal health policies during the COVID-19 pandemic |
| Description | This dataset deals with the need to monitor and share information about fragmented policies designed to tackle health crises like the COVID-19 pandemic. Quantifying these initiatives and how they varied across municipalities can help us to understand the effectiveness of interventions in reducing virus transmission. We offer information over time on a series of measures to encourage social distancing, implement the vaccination programme, provide infrastructure to treat infected people, and facilitate how local governments would eventually ease these measures. This information can contribute to the institutional learning of health systems worldwide, assisting in future situations where a highly contagious virus challenges society. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | Dataset was already useful for investigate severity of the SARS-CoV-2 P.1/Gamma Variant of Concern (https://www.nature.com/articles/s41591-022-01807-1). |
| URL | https://doi.org/10.5061/dryad.v6wwpzh5h |
| Title | CADDE Workshop on Portable Metagenomics for Pathogen Surveillance |
| Description | This is the official repository of CADDE Workshop on Portable Metagenomics for Pathogen Surveillance. Here you will find extra material about the presentations and activities of the workshop. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | Used to train >50 early career researchers in metagenomics for public health (Brazil, 2023). |
| URL | https://github.com/CADDE-CENTRE/MetagenomicWorkshop |
| Title | Cross-Sectional Seroprevalence Dengue Data from Angola |
| Description | This repository contains the code used to implement the analyses presented in "Dengue transmission dynamics and spread in Angola: a phylogenetic and cross-sectional seroprevalence study." |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | This dataset was used to investigate transmission dynamics of dengue in Angola. |
| URL | https://github.com/mrc-ide/dengue_dynamics_angola |
| Title | Fatal outcome of chikungunya virus infection in Brazil |
| Description | Abstract Background Chikungunya virus (CHIKV) emerged in the Americas in 2013 and has caused ~2.1 million cases and over 600 deaths. A retrospective investigation was undertaken to describe clinical, epidemiological and virus genomic features associated with deaths caused by CHIKV in Ceará state, northeast Brazil. Methods Sera, cerebrospinal fluid (CSF) and tissue samples from 100 fatal cases with suspected arbovirus infection were tested for CHIKV, dengue (DENV) and Zika virus (ZIKV). Clinical, epidemiological and death reports were obtained for patients with confirmed CHIKV infection. Logistic regression analysis was undertaken to identify independent factors associated with risk of death during CHIKV infection. Phylogenetic analysis was conducted using whole genomes from a subset of cases. Results 68 fatal cases had CHIKV infection confirmed by RT-qPCR (52.9%), viral antigen (41.1%), and/or specific-IgM (63.2%). Co-detection of CHIKV with DENV were found in 22% of fatal cases, ZIKV in 2.9%, and DENV and ZIKV in 1.5%. A total of 39 CHIKV-deaths presented with neurological signs and symptoms, and CHIKV-RNA was found in the CSF of 92.3% of these patients. Fatal outcomes were associated with irreversible multiple organ dysfunction syndrome. Patients with diabetes appear to die at a higher frequency during the sub-acute phase. Genetic analysis showed circulation of two CHIKV-East Central South African (ECSA) lineages in Ceará and revealed no unique virus genomic mutation associated with fatal outcome. Conclusion The investigation of the largest cross-sectional cohort of CHIKV-deaths to date reveals that CHIKV-ECSA strains can cause death in individuals from both risk and non-risk groups, including young adults. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | This dataset formed the basis for subsequent studies investigating the pathophysiology of chikungunya virus infection with fatal outcomes. |
| URL | https://datadryad.org/dataset/doi:10.5061/dryad.7d7wm37sm |
| Title | SARS-CoV-2 sequencing data for the eight cities |
| Description | This repository contains fasta and metadata files for sequences obtained from samples from PCR+ patients. Samples were collected between March 2020 and December 2022 in the eight Brazilian capitals participating of the COVID-IgG project (Belo Horizonte, Curitiba, Fortaleza, Manaus, Recife, Rio de Janeiro, Salvador, São Paulo). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | This dataset contributed to SARS-CoV-2 genomic surveillance efforts in Brazil. A publication is currently being prepared addressing the importance of representativity in pathogen sequencing strategies. |
| URL | https://github.com/CADDE-CENTRE/genomics_eight_cities |
| Description | Foundation of Tropical Medicine Dr Heitor Vieira Dourado, Manaus, Amazonas |
| Organisation | Tropical Medicine Foundation Doctor Heitor Vieira Dourado |
| Country | Brazil |
| Sector | Hospitals |
| PI Contribution | Co-organised a workshop for 30 early career researchers (15 UK, 15 Brazil/Amazon) entitled "Bridging Communities and Research for a Healthier Amazon: A Workshop on Infectious Diseases, Climate, and Development" at the Tropical Medicine Foundation Doctor Heitor Vieira Dourado. |
| Collaborator Contribution | Provided local expertise and contributed discussions on community engagement around One Health in the Brazilian Amazon. |
| Impact | The Brazilian Amazon PI, Prof. Wuelton Monteiro, is now involved as a collaborator in a MRC/FAPESP grant application. New collaborative links with One Project Vivera led by Brazilian Amazon PI, Prof. Wuelton Monteiro. Policy document on One Health surveillance in the Amazon (under preparation). |
| Start Year | 2024 |
| Description | Instituto Nacional de Investigação em Saúde - Ministry of Health Angola |
| Organisation | Ministry of Health |
| Department | Health Research Centre of Angola |
| Country | Angola |
| Sector | Public |
| PI Contribution | Expertise in epidemiology, genomics, and capacity building. |
| Collaborator Contribution | Country and regional expertise on arbovirus and Pathogen X surveillance. |
| Impact | Pilot grant on arbovirus genomics attributed by the Research England Institutional Support Grant (ISPF) Global Development Hub ODA Project Accelerator, Imperial College London. Outputs include: - Policy workshop at the Ministry of Health Angola for 50 Angolan public health officials (Feb 2025) - 2-week hands-on laboratory training workshop for 15 early career researchers at MoH Angola (Feb 2025) - First detection of dengue virus serotype 3 in the country (manuscript in preparation) - Generation of the first mpox genome sequences from Angola (manuscript in preparation) - Generation of the first measles genome sequences in Angola (manuscript in preparation) - Preparation of new applications for research funding |
| Start Year | 2024 |
| Description | WHO Global Arbovirus Initiative Technical Advisory Group |
| Organisation | World Health Organization (WHO) |
| Country | Switzerland |
| Sector | Public |
| PI Contribution | Expertise in arbovirus genomic surveillance and epidemiology. Discussion on the implementation of genomic surveillance programmes for arboviruses globally. |
| Collaborator Contribution | Country and regional expertise in arbovirus epidemiology. |
| Impact | Report of the third meeting of the WHO Technical Advisory Group on Arboviruses (?TAG-Arbovirus)?: hybrid meeting, Accra, Ghana, 20-22 June 2023 https://www.who.int/publications/i/item/9789240095830 Additional policy documents (including diagnostic guidelines and an updated list of priority arboviruses) and group publications are currently under preparation. |
| Start Year | 2024 |
| Description | WHO Virus Evolution Technical Advisory Group |
| Organisation | World Health Organization (WHO) |
| Country | Switzerland |
| Sector | Public |
| PI Contribution | Expertise in virus genomic epidemiology. |
| Collaborator Contribution | Country and regional expertise in mpox epidemiology. |
| Impact | Outcomes include an updated dashboard (https://worldhealthorg.shinyapps.io/mpx_global/) and a document regarding naming of mpox (under preparation). |
| Start Year | 2024 |
| Description | WHO Zika Taskforce Technical Advisory Group |
| Organisation | World Health Organization (WHO) |
| Country | Switzerland |
| Sector | Public |
| PI Contribution | Expertise in Zika virus genomic surveillance and evolution. |
| Collaborator Contribution | Expertise in laboratory diagnostics for detecting Zika virus across different settings. |
| Impact | Zika virus: advancing a priority research agenda for preparedness and response Lancet Infectious Diseases DOI: 10.1016/S1473-3099(24)00794-1 Zika virus vaccines and monoclonal antibodies: a priority agenda for research and development Lancet Infectious Diseases DOI: 10.1016/S1473-3099(24)00750-3 Specimen and data sharing to advance research and development on Zika virus Lancet Microbe DOI: 10.1016/j.lanmic.2024.101057 Role of non-human primate models in accelerating research and developing countermeasures against Zika virus infection Lancet Microbe DOI: 10.1016/j.lanmic.2024.101030 |
| Start Year | 2023 |
| Description | World Health Organization Global Advisory Alert and Response Network - Technical Expert/Outbreak Response Participation |
| Organisation | World Health Organization (WHO) |
| Department | WHO Global Outbreak Alert and Response Network |
| Country | France |
| Sector | Charity/Non Profit |
| PI Contribution | We have been included as technical experts on next-generation molecular diagnostics (by sequencing) to assist the WHO in outbreak and epidemic response when required in-country. |
| Collaborator Contribution | WHO are the recognised international agency responsible for the management and containment of outbreaks and epidemics. |
| Impact | In the past weeks this has included serving in an advisory function to support an outbreak of necrotising cellulitis in Sao Tome. We provided rapid response sequencing facility, in collaboration with Ian Goodfellow (University of Cambridge) to the island and provided real-time pathogen diagnostics and epidemiology using nanopore sequencing. |
| Start Year | 2016 |
| Title | The Zibra Pipeline |
| Description | The Zibra Pipeline provides the bioinformatics component of the Zika real-time sequencing project. This open source package was designed to simplify the process of bioinformatics analysis using standard laptops when performing in-field sequencing. It supports both nanopore and Illumina platforms. It is packaged as a Docker container which means it can run on Windows, Linux and Mac computers. |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | This software was pivotal in the ability to give local stakeholders in Brazil the ability to generate their own sequences with limited bioinformatics support. |
| URL | https://github.com/zibraproject/zika-pipeline |
| Description | BBC Health Check - A step closer to a Chikungunya vaccine |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Invited to talk about chikungunya, its spread in the Americas, and the new promising Valneva vaccine, reaching an audience of thousands. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.bbc.co.uk/sounds/play/w3ct4pd1 |
| Description | Invited Talk - WHO Global Arbovirus Initiative |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | 50 WHO members and industry representatives attended a WHO meeting, which instigated questions around the importance of using genomic sequencing as a toolkit to improve preparedness against arboviral threats, and WHO reported increased interest in including genomic surveillance analytics in the WHO Global Arbovirus Initiative dashboard (https://worldhealthorg.shinyapps.io/dengue_global/). |
| Year(s) Of Engagement Activity | 2024 |
| Description | Panel Presentation - Forum on Microbial Threats, National Academies of Sciences, Engineering, and Medicine, USA |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | 80 policy makers and researchers attended a workshop entitled "Mitigating arboviral threats and strenghtening public health preparedness" at the National Academies of Sciences, Engineering and Medicine, USA, to explore the role of arbovirus mitigation within the context of public health preparedness and capacity building. Outcomes include the Meeting Proceedings published afterwards. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.nationalacademies.org/our-work/mitigating-arboviral-threats-and-strengthening-public-hea... |
| Description | Participation in an activity, workshop or similar - Academy of Medical Sciences (UK and Brazil) |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Abuot 70 policymakers participated in a workshop entitled "Advancing a One Health approach to support the challenge of infectious diseases in Brazil', between 28-29 March 2023, organised by the Brazilian Academy of Sciences, the National Academy of Medicine and the UK Academy of Medical Sciences. Outcomes included a workshop report. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://acmedsci.ac.uk/file-download/86263830 |
| Description | WHO EPI-WIN Webinar Pathogen Genomics in Health Emergencies: Spotlight Dengue |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | With 1233 unique attendees from 144 countries, this webinar sparked 63 questions and discussion. WHO EpiWin team reported it to be the second most viewed webinar to date. It was attended by > Ministry of Health members from 29 countries, CDC members from 11 countries, WHO members from 37 countries, and Universities from 49 countries. 95% found it very useful or quite useful. Attendees' feedback included "enhances my ability to contribute to surveillance efforts by keeping me informed", "every information acquired in the webinars was very relevant for my work", "the webinar has equipped me with knowledge and understanding of dengue surveillance and the need for collaboration across sectors". |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.youtube.com/watch?v=kKO19Rt8RoI&ab_channel=WHOEPI-WIN |