Judith U Oguzie DVM PhD Research Fellow World BankAfrican Center of Excellence for Genomics of Infectious Diseases ACEGID Redeemers University Ede Nigeri a How By establishing a continental consortium of key national laboratories academic and public health institutions to ad ID: 935107 Download Presentation
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Presentation on theme: "Highlighting Excellent Research at ACEGID"— Presentation transcript
Slide1
Highlighting Excellent Research at ACEGID
Judith U. Oguzie, DVMPhD Research Fellow, World Bank-African Center of Excellence for Genomics of Infectious Diseases (ACEGID)Redeemer’s University, Ede, Nigeria
Slide2How?
By establishing a continental consortium of key national laboratories, academic and public health institutions to advance outbreak surveillance and research in Africa
What?
Generate and analyze the genomic diversity of Pathogens in real-time to map the spread of the disease and characterize its pathogenicity, virulence and to inform public health preventive and control measures. real-time to map the spread of the disease and characterize its pathogenicity, virulence and to inform public health preventive and control measures.
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Why?
We want to understand and control transmission of infectious
diseases
in Africa to save lives and protect an already fragile health system
Slide3Rapid sequencing of Ebola Virus-Summer 2014: Data made public immediately.
New deep Sequencing Methods for Lassa and Ebola viruses developed and published immediately for the benefit of the community (
Matranga CB et al. Genome Biol. 15 (2014)
June 2014: 99 genomes publicly availableAnother 150 genomes released between March 2014 and August 2015
First large-scale genome sequence-based analysis of the circulating Ebola viral population
Slide410 days from sample to Genbank
The data were generated super quickly!
Slide5We Developed the First EBOLA RDT
1st
Generation Ebola Virus RDT Approved for EU by WHO and US FDA
Next Generation Sequencing Capacity
Real-time PCR
Real-time Diagnosis: Key to West Africa Successful Containment of the 2014 Ebola Outbreak.
June 2014: 99 genomes publicly available
Another 150 genomes released between March 2014 and August 2015
First large-scale genome sequence-based analysis of the circulating Ebola viral population
Slide6Next Generation Sequencing of Lassa Virus Genomes
• ~
4
00 patient samples• 22 Rodents
• Unbiased sequencing - no specific amplification
• Average 1,000X coverage of Lassa genome
Slide7Real-time Genome Sequencing of Outbreak samples
Whole Genome sequencing of 90% of 2018 outbreak samples.
Lassa virus extensive genetic diversityTransmission pattern of Lassa virus clustered by Geography. Rodents to human transmission
Slide8Metagenomic
analysis of blood samples obtained from Lassa Fever patients in Nigeria
Oguzie et al 2019
Slide9Control
Test Line
Lassa virus validation of Rapid Diagnostic Test Kit
Sensitivity = 85%Specificity = 90% Also validated for testing of urine and saliva samples.
Slide102018 YFV sequences formed a tightly clustered clade.
The 2018 clade was more closely related to sequences from other West African countries than to earlier (1946–1991) Nigerian sequences
Slide11Next Generation Sequencing of COVID-19 Samples:
SARS-CoV-2 Genome analysis from Nigeria
OVER 70,000 COVID-19 SUSPECTED SAMPLES
TESTING
METAGENOMIC SEQUENCING
Boost testing capacity from 300 to over 5000 per day at ACEGID
First African SARS-CoV-2 genome sequenced was in ACEGID,
RUN,Ede
, Nigeria in 48 hours.
Announced in March 06, 2020
Slide12The sample of the index case was sent to the ACEGID lab for
sequencing on 1st March, 2020.
Using one of the two Illumina MiSeqs in the sequencing platform
of ACEGID, we sequenced the sample and obtained a full genome of SARS-CoV-2 within 48 hours.
We obtained all HCoV
whole genome sequences obtained from
human hosts with geographical annotations from GISAID
and aligned with the index genome sequence from Nigeria.
The genome clusters with a European clade, consistent with the
known travel history of this case (Figure 1).
Figure 1
: Maximum likelihood tree of SARS-CoV-2 including Nigeria’s index case
Slide13SARS-CoV-2 Genomes from Nigeria
We have
screened over twenty thousand (20,000) samples for SARS-COV-2 by rt-qPCR.
Currently, we have sequenced over 1300 SARS-CoV-2 samples across the country and have assembled 623 genomes so far from twenty-six (26) states of the country.
Slide14SARS-CoV-2 PANGO Lineages in Nigeria
At the moment, there are about 37 different lineages of SARS-CoV-2 circulating in Nigeria and they are changing at a very fast speed. Currently, B.1.525 accounts for the largest after taking over the B.1.1.7 (second largest) PANGO lineage in Nigeria.
.
Slide15Detection of B.1.1.7 lineages (UK Variant of Concern) in Nigeria
Since the first B.1.1.7 genome detected in Edo State, Nigeria, 14th December, 2020. 339 genomes have been assembled since then and 97 (28.6%) of them are B.1.1.7
As at 24th of May 2021, we have detected a total of 106 cases of the B.1.1.7 lineage across Nigeria
These samples were collected between 14th December, 2020 and 22nd of February, 2021.
Slide16Discovery of the Nigeria Lineage- B.1.525
On the 11th of February, some recent SARS-CoV-2 genomes from England (28), Nigeria (10), USA (7), France (5), Canada (4), Ghana (4), Japan (4), Jordan (2), Belgium (1), Italy (1) and Spain (1) were seen to have distinct mutations. These new cluster of viruses have characteristic Spike protein mutations: E484K, Q677H, F888L, 69 - 70 deletion, 144 deletion and 9 nucleotide mutations in the Non-structural protein 6 (nsp6) as seen in
B.1.1.7, B.1.351 and P.1. Origin of this new cluster so far is located in Nigeria.
Slide17B.1.525 lineage (Variant of interest) in Nigeria
Currently observed in 9 states across the country with a total of 147 genomes
1st B.1.525 was from an Edo State sample dated 20th December, 2020. Since the detection of B.1.525, 339 genomes have been assembled and (43%) were B.1.525
Slide18Discovery of a New variant B.1.1.318 (Variant under investigation) in Nigeria
The B.1.1.318 lineage has been discovered in samples from Lagos, Akwa-Ibom, Oyo and Ebonyi states through whole genome sequencing of COVID-19 positive samples, as far back as January 2021.
This new variant has spread within and outside AfricaThis variant has Spike mutations D614G, D796H, E484K, P681H, T95I and Y144 deletion
So far, 8 genomes have been sequenced and this lineage has the potential to spread rapidly like the B.1.1.7 and B.1.525 due to the E484K mutation in the Receptor binding domain and the P681H in the furin cleavage site of the virus.
Because of the E484K and other mutations in the RBD of the spike protein, there is a risk for immune escape for this variant just like the B.1.525 variant.
Slide19Second wave of SARS-CoV-2 in Nigeria
Epicurve of SARS-CoV-2 confirmed cases in Nigeria. States that contributed to the resurgence are highlighted in red (Lagos State, FCT Abuja and Kaduna State. Source: NCDC, 2021
Slide20Metagenomics of COVID samples
Assembled a partial genome of Morbillivirus measles virus (85% of viruses from Kraken2 hit) was assembled from a PCR SARS-CoV-2 positive sample
Slide21Summary: SARS-CoV-2 Sequencing in Nigeria
Multiple introductions into Nigeria from different parts of the world.
Detection of B.1.1.7 variant of concern in Nigeria
Evidence of community transmission in different states of Nigeria.
The two variants of concern (B.1.1.7 and B.1.525) now account for 80% of the genomes in the country since their detection in December 2020.
D614G mutation taking over in the country.
Emergence of B.1.525 variant under investigation in Nigeria which is spreading rapidly like the B.1.1.7
Slide22SARS-CoV-2 Genome Analysis from Somalia
So far we have generated 18 genomes from Somalia samples.Including A, B.1, B.31, and B.1.422 lineagesWith the B.1 being the most dominant.
Slide23SARS-CoV-2 LINEAGES IN CAMEROON
Thirty-nine (39) full SARS-CoV-2 genomes were assembled from sequenced Cameroon COVID-19 samples sent to the ACEGID lab using
Slide24Lineage in Cameroon: A.23.1, A.27 and W.1
All of these lineages have mutations with potential for increase transmission and evade the immune system.So far, only 2 genomes have been assembled which belongs to the A.23.1
lineage.Only 2 genomes have been assembled so far that belong to W.1
Slide25GGTGGAAAGTTGTTGGGCGGTATAGAGTTTGATGTGACTCACAAAGGATGGCCTATTGCATAGACTGAAAACTAATGACTTTGCCCCTGCATGGTCAATGACAGGAACCTATTTCCCATTTATTTCAAATCCGAATTCCACATTGAATCACCGCTGTGGGCACTGAGAGTCATCCTTGCTGCAGGGATACAGGACCAGTTAATTGACCAGTCTTTGATTGAACCCTTAGCAGGAGCCCTTGGTTGATCTCTGATTGGCTGCTAACAACCAACACTAACCATTCAACATACGAACACAACGTGTCAAGGAGCAATTGAGCCTAAAAATGCTGTCGTTGATTCGATCCAATATTCTCAAGTTTATTAACGAATTGGAGCTCTACATGTTGTGAACTATAATGGATTATTGAGCAGTATTGAAATTGGGACTCAAAATCATACAATCATCATAACTCGAACTAACATGGGTTTTCTGGTGGAGCTCCAAGAACCCGACAAATCGGCAATGAACCGCAAGAAGCCTGGGCCGGCGAAATTTTCCCTCCTTCATGAGTCCACACTGAAAGCATTTACACAAGGGTCCTCGACACGAATGCAAAGTTTAATTCTTGAATTCAATAGCTCTCTTGCTATCTAACTAAGATGGAGTACTTCATATTGGGCTAACTCATATATGCTGACTCAATAGTTAACTTGACATCTCTGCCTTCATAATCAGATATATAAGCATAATAAATAAATACTCATATTTCTTGATAATTTGTTTAACCACAGAGAAATCCTCACTGTAAGCCAGCTTCCAAGTTGACACCCTTACAAAAACCAGGACTCAGAATTCCTCAAATAAGAGATTCCAAGACAACATCATAGAATTGCTTTATTATATATTAATAAGCATTTTATCACTAGAAATCCAATATACGAAATGGTTAATTGTAACTAAACTCGCAGGTCATGTGTGTTAGGTTTCACAAATTATATATATTACTAACTCCATACTCATAACTAACATTAGATAAGTAGGTTAAGAAAAAAGCTTGAGGAAGATTAAGAAAAAACTGCTTATTGGGTCTTTCCGTGTTTTAGATGAAGCAGTTGACATTCTTCCTCTTGATGTTAAATGGCTACACAACATACCCAATACCCAGACGCCAGGTTATCATCACCAATTTATTGGACCAATGTGACCTTGTCACTAGAGCTTGCG
Slide26Slide27EMPOWERING LOCAL CLINICIANS
ENHANCING LOCAL VIRAL DIAGNOSTICS
Mobile platform for data collection
Designed in close collaboration with clinicians and staff
Streamline existing workflows
Audiovisual aids for patient enrollment
CRISPR-based SHERLOCK diagnostics
Low cost, deployable lateral flow assay
Highly sensitive and specific
Designed, tested and deployed RUO Lassa assay in 2 weeks
Our
A
pproach
:
G
enomics
-informed clinical tools
Slide28SHINE (Streamlined Highlighting of Infections to Navigate Epidemics)
Ambient-temperature, no equipment required, higher throughput
Ambient-temperature, no equipment required
Slide29Validated in Nigeria
Tested 500 Nigerian RNA samples extracted from clinical samples (saliva, nasal swabs)
Test performed well on samples with high viral load but needs improvement for samples with low viral load.
SHINE Assay Validation
Fully field deployable
Urine
Saliva
Control line
Test line
Dengue Patient
Healthy
Rapid assay development
Day 1:
Design crRNAs & RPA primers
Days 2-5:
crRNAs, primer, target synthesis
Day 6:
SNP testing
Slide30All human-associated viruses with ≥10
genomes
Design
and select
primers and crRNAs
CATCH-dx
Comprehensively
test
cross-reactivity
(8 chips; 28,561 tests)
Extensive test of cross-reactivity (169
×
169), using synthetic targets at 10
4
cp/ul
CARMEN - CRISPR-Cas13 in massive multiplex
Slide31Data Availability
Open protocols (data generation, assembly and analysis).Open data but FAIR research (involve, acknowledge and capacitate).Open updates to public health officials and general public (pandemic responsiveness before academic exercise).
Slide32Dr. Christian Happi
African Center of Excellence for Genomics of Infectious DiseaseRedeemer’s UniversityHarvard T.H. Chan School of Public Health
SENTINEL – Pandemic Preemption and Response
Dr. Pardis Sabeti
Broad Institute of MIT and Harvard
Harvard T.H. Chan School of Public Health
Howard Hughes Medical Institute
Slide33Conclusion
Genomic data generated are the bases for diagnostics development and improvement.Our research output has been instrumental in vaccine development for Lassa virus and SARS-COV-2.Several Public health interventions such as mass YFV vaccination in affected communities and lock down recommendations during SARS-COV2.
Genomic surveillance is an ongoing effort and we keep making our data publicly available to the scientific community.
Slide34Acknowledgements
Outstanding Partners
Redeemer’s University
Irrua
Specialist Teaching Hospital
NCDC
Viral Hemorrhagic Fever Consortium
Broad Institute of Harvard and MIT
Harvard University
Tulane University
UCAD, Senegal
KGH, Sierra Leone
NPHI, Liberia
Zalgen
University of Cambridge
FETHA
FMC-
Owo
Generous Funders
outbreaks genomic response team