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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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, NigeriaSlide2
By establishing a continental consortium of key national laboratories, academic and public health institutions to advance outbreak surveillance and research in Africa
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.
We want to understand and control transmission of infectious
in Africa to save lives and protect an already fragile health systemSlide3
Rapid 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 populationSlide4
10 days from sample to Genbank
The data were generated super quickly!Slide5
We Developed the First EBOLA RDT
Generation Ebola Virus RDT Approved for EU by WHO and US FDA
Next Generation Sequencing Capacity
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 populationSlide6
Next Generation Sequencing of Lassa Virus Genomes
00 patient samples• 22 Rodents
• Unbiased sequencing - no specific amplification
• Average 1,000X coverage of Lassa genomeSlide7
Real-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 transmissionSlide8
analysis of blood samples obtained from Lassa Fever patients in Nigeria
Oguzie et al 2019Slide9
Lassa virus validation of Rapid Diagnostic Test Kit
Sensitivity = 85%Specificity = 90% Also validated for testing of urine and saliva samples.Slide10
2018 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 sequencesSlide11
Next Generation Sequencing of COVID-19 Samples:
SARS-CoV-2 Genome analysis from Nigeria
OVER 70,000 COVID-19 SUSPECTED SAMPLES
Boost testing capacity from 300 to over 5000 per day at ACEGID
First African SARS-CoV-2 genome sequenced was in ACEGID,
, Nigeria in 48 hours.
Announced in March 06, 2020Slide12
The 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).
: Maximum likelihood tree of SARS-CoV-2 including Nigeria’s index caseSlide13
SARS-CoV-2 Genomes from Nigeria
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.Slide14
SARS-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.
Detection 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.Slide16
Discovery 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.Slide17
B.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.1.525Slide18
Discovery 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.Slide19
Second 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, 2021Slide20
Metagenomics 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 sampleSlide21
Summary: 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.1.1.7Slide22
SARS-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.Slide23
SARS-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 usingSlide24
Lineage 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.1Slide25
EMPOWERING 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
-informed clinical toolsSlide28
SHINE (Streamlined Highlighting of Infections to Navigate Epidemics)
Ambient-temperature, no equipment required, higher throughput
Ambient-temperature, no equipment requiredSlide29
Validated 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
Rapid assay development
Design crRNAs & RPA primers
crRNAs, primer, target synthesis
All human-associated viruses with ≥10
primers and crRNAs
(8 chips; 28,561 tests)
Extensive test of cross-reactivity (169
169), using synthetic targets at 10
CARMEN - CRISPR-Cas13 in massive multiplexSlide31
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).Slide32
Dr. 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 InstituteSlide33
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.Slide34
Specialist Teaching Hospital
Viral Hemorrhagic Fever Consortium
Broad Institute of Harvard and MIT
KGH, Sierra Leone
University of Cambridge
outbreaks genomic response team