BioNTech and InstaDeep Developed and Successfully Tested Early
Warning System to Detect Potential High-Risk SARS-CoV-2 Variants
- Early Warning System combines Spike protein structural modeling
with artificial intelligence (AI) to detect and monitor high-risk
SARS-CoV-2 variants, identifying >90% of WHO-designated variants
on average two months prior to officially receiving the
designation
- Study introduces a new method of combining publicly available
SARS-CoV-2 sequence information with predictive analytics to
effectively detect and monitor potential high-risk variants which
could help increase preparedness against future variants of
concern
- Early Warning System is fully scalable as new variant data
become available
- Study is available on the pre-print server BioRxiv and has been
submitted to a peer-reviewed journal
MAINZ, Germany and LONDON, United
Kingdom, January 11, 2022 — BioNTech SE (Nasdaq: BNTX,
“BioNTech”) and InstaDeep Ltd (“InstaDeep”) today announced the
development of a new computational method that analyses worldwide
available sequencing data and predicts high-risk variants of
SARS-CoV-2. The Early Warning System (EWS) developed in
collaboration by BioNTech and InstaDeep is based on artificial
intelligence (AI) calculated immune escape and fitness metrics.
The new method combines structural modeling of
the viral Spike protein and AI algorithms to quickly flag potential
high-risk variants entered into SARS-CoV-2 sequence data
repositories within less than a day based on metrics scoring their
fitness (e.g. ACE2 and variant Spike protein interaction) as well
as their immune escape properties. The companies validated these
predictions using experimental data generated in-house and publicly
available data.
During the trial period, the system has
identified >90% of the World Health Organization
(WHO)-designated variants (Variants of Concern, VOC; Variants of
Interest, VOI; Variants Under Monitoring,VUM) on average two months
in advance. WHO-designated variants Alpha, Beta, Gamma, Theta, Eta
and Omicron were detected by the EWS in the same week its sequence
was first uploaded. The Omicron variant was ranked as a high-risk
variant the same day its sequence became available. The IHU variant
observed in France has also been evaluated by the EWS, which
highlighted immune escape properties that are relatively similar to
Omicron but with significantly lower fitness, making it less of a
concern given current data.
The results from the study underline that the
EWS is capable of evaluating new variants in minutes and risk
monitoring variant lineages nearly in real-time. It is also fully
scalable as new variant data becomes available.
“With the advanced computational methods we have
been developing over the past months we can analyse sequence
information of the Spike protein and rank new variants according to
their predicted immune escape and ACE2 binding score,” said
Ugur Sahin, M.D., Chief Executive Officer and Co-Founder of
BioNTech. “Early flagging of potential high-risk variants
could be an effective tool to alert researchers, vaccine
developers, health authorities and policy makers, thereby providing
more time to respond to new variants of concern.”
“More than 10,000 novel variant sequences are
currently discovered every week and human experts simply cannot
cope with complex data at this scale. We’ve addressed this
challenge by deploying the powerful AI capabilities of InstaDeep’s
DeepChain platform combined with BioNTech’s SARS-CoV-2 know-how and
technology. For the first time, high-risk variants could be
detected on the spot, potentially saving months of precious time.
We are happy to make our research work publicly available and, most
importantly, look forward to its continued real-world impact,”
added Karim Beguir, Co-Founder and CEO of
InstaDeep.
The Early Warning System (EWS) relies on two
approaches: (1) structural modeling of the interaction of the viral
Spike protein receptor-binding domain (RBD) with the host cell
receptor and scoring the impact of the virus variant in escaping
the immune response, and (2) AI-based predictive modeling to
extract information from hundreds of thousands of registered virus
variants from global sequence repositories. The EWS computes an
immune escape score and a fitness (transmissibility potential)
prior score. While the immune escape score alone was already highly
predictive of the risk, combining these two metrics into a Pareto
score provided the best assessment of the risk posed by a given
virus variant. The higher the score, the higher the risk of the
variant impacting global health. The EWS approach ranks SARS-CoV-2
variants for immune escape and fitness potential based solely on
existing data, and therefore is not dependent on a “wait-and-watch”
approach.
The EWS was able to distinguish the
WHO-designated variants from those that had no designation during a
11-month period, underlining the viable computational model ability
to determine variant lineage. An analysis conducted every week
between September 16th, 2020 and November 23rd, 2021 flagged 12 out
of 13 WHO-designated variants with an average of 58 days of lead
time (i.e. two months) before the variants were given their
designation. For variants Alpha to Mu, only around 25 cases on
average were recorded at the time of them being flagged by the EWS.
This is in contrast with the WHO announcements that happened on
average when more than 1,500 cases were recorded. The EWS detected
Omicron on the day its sequence was first uploaded as the highest
immune escaping variant from over more than 70,000 variants that
were discovered between early October 2021 and late November 2021
while also assigning it a high fitness score.
The data published as a pre-print is the result
of a collaboration established between BioNTech and InstaDeep in
November 2020 to coalesce AI and immunology. As part of the
collaboration, the companies formed a joint AI Innovation Lab in
London, UK, and Mainz, Germany, to advance novel drug discovery and
design, protein engineering, manufacturing and supply chain
optimization.
About SARS-CoV-2 MutationsThe
last two years have demonstrated how the frequent and wide
circulation of the SARS-CoV-2 virus increases its likelihood to
mutate in parts of its genetic make-up with the potential to change
its features. Current known variants harbor mutations that
distinguish them from the original strain identified in early 2020.
Over 13,400 individual missense mutations have been observed in the
Spike protein alone. Available data show that thousands of new
variants are emerging every week at an increasing rate, with a
weekly average of registered variants of about 300 in September
2020, 7,000 in August 2021 and 12,000 in December 2021.
While most mutations either reduce the overall
fitness of the virus, or bear no consequences to its features, some
individual or combinations of mutations lead to high-risk variants
(HRVs) with modified immune evasion capabilities and/or improved
transmissibility. A variant that can bypass neutralization by
antibodies is of particular importance and poses a risk to
individuals who previously had COVID-19 and those that are fully
vaccinated.
As new sequences continue to be detected in
infected individuals, foreseeing variants that have the potential
to become HRVs is critical for pandemic preparedness. Identifying
these variants creates a significant challenge for public health
authorities as detection by varied tests in the lab is very time
consuming. The EWS allows for early detection of these variants and
shortens the time that health authorities need to assess their
impact and respond in a timely manner.
About BioNTechBiopharmaceutical
New Technologies is a next generation immunotherapy company
pioneering novel therapies for cancer and other serious diseases.
The Company exploits a wide array of computational discovery and
therapeutic drug platforms for the rapid development of novel
biopharmaceuticals. Its broad portfolio of oncology product
candidates includes individualized and off-the-shelf mRNA-based
therapies, innovative chimeric antigen receptor T cells,
bi-specific checkpoint immuno-modulators, targeted cancer
antibodies and small molecules. Based on its deep expertise in mRNA
vaccine development and in-house manufacturing capabilities,
BioNTech and its collaborators are developing multiple mRNA vaccine
candidates for a range of infectious diseases alongside its diverse
oncology pipeline. BioNTech has established a broad set of
relationships with multiple global pharmaceutical collaborators,
including Genmab, Sanofi, Bayer Animal Health, Genentech, a member
of the Roche Group, Regeneron, Genevant, Fosun Pharma and Pfizer.
For more information, please visit www.BioNTech.de.
BioNTech Forward-looking
StatementsThis press release contains “forward-looking
statements” of BioNTech within the meaning of the Private
Securities Litigation Reform Act of 1995. These forward-looking
statements may include, but may not be limited to, statements
concerning: BioNTech’s efforts to combat COVID-19; its
collaboration with InstaDeep; capabilities of the Early Warning
System (EWS) to predict potential High-Risk Variants (HRV) and to
save time in HRV identification; and uncertainties regarding the
impact of COVID-19 on BioNTech’s trials, business and general
operations. Any forward-looking statements in this press release
are based on BioNTech current expectations and beliefs of future
events, and are subject to a number of risks and uncertainties that
could cause actual results to differ materially and adversely from
those set forth in or implied by such forward-looking statements.
These risks and uncertainties include, but are not limited to: the
ability to meet the pre-defined endpoints in clinical trials;
competition to create a vaccine for COVID-19; the ability to
produce comparable clinical or other results, including our stated
rate of vaccine effectiveness and safety and tolerability profile
observed to date, in the remainder of the trial or in larger, more
diverse populations upon commercialization; the ability to
effectively scale our productions capabilities; and other potential
difficulties.
For a discussion of these and other risks and
uncertainties, see the section entitled “Risk Factors” BioNTech’s
Annual Report as Form 20-F for the Year Ended December 31, 2020,
filed with the SEC on March 30, 2021, which is available on the
SEC’s website at www.sec.gov. All information in this press release
is as of the date of the release, and BioNTech undertakes no duty
to update this information unless required by law.
About InstaDeepFounded in 2014,
InstaDeep is today an EMEA leader in decision-making AI products
for the Enterprise, with headquarters in London and offices in
Paris, Tunis, Lagos, Dubai and Cape Town. With expertise in both
machine intelligence research and concrete business deployments,
the Company provides a competitive advantage to its partners in an
AI-first world. Leveraging its extensive know-how in
GPU-accelerated computing, deep learning and reinforcement
learning, InstaDeep has built products, such as its
novel DeepChainTM protein design platform, that tackle the
most complex challenges across a range of industries. InstaDeep has
also developed collaborations with global leaders in the Artificial
intelligence ecosystem, such as Google DeepMind, Nvidia and Intel.
The Company is part of Intel’s AI Builders program and was named an
Elite Partner by Nvidia. InstaDeep was recently selected by CB
Insights as one of the 100 most promising AI start-ups in the world
for the second year running. To learn more, please
visit www.instadeep.com.
CONTACTS
BioNTech: Media Relations Jasmina Alatovic +49
(0)6131 9084 1513 Media@biontech.de
Investor Relations Sylke Maas, Ph.D. +49 (0)6131 9084 1074
Investors@biontech.de
InstaDeep:Media RelationsLiz
Johns+44 (0)797 005 7603l.johns@instadeep.com
Investor RelationsLaurent Hiller+33 (0)6 22 91
94 71l.hiller@instadeep.com
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