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The novel coronavirus (COVID-19) outbreak has been a huge topic of concern across the globe as infection and death tolls continue to grow daily. However, it’s inarguable that the healthcare and life science industries overall have made great strides over the years since the SARS coronavirus outbreak in 2003, culminating in a vastly different experience from the outset. Here we reflect on these advances over the past 17 years and provide thoughts on where current industry trends could take us in the future.
Accessibility of next-generation sequencing and the infrastructure to share data and collaborate has allowed us to analyze COVID-19 from the early outset of the outbreak
The pneumonia outbreak in Wuhan was first reported to the WHO Dec 31st, 2019 and within merely a couple of weeks, researchers had sequenced the viral genome through a combination of short and long read NGS and sanger sequencing and made it available online on January 10th 1. Subsequently, researchers, labs, diagnostics manufacturers and pharma could begin leveraging the sequence to develop diagnostics, vaccines, and therapies, as we will discuss below.
Additionally, infrastructure to share new research findings have allowed researchers to collaborate in nearly real-time. Founded in 2013, BioRxiv is a free online archive and distribution service for unpublished preprints in the life sciences that allows authors to make their findings immediately available to the scientific community before acceptance by journals, which typically takes months. A quick search for “coronavirus” or “2019-nCov” or “COVID-19” since December 31, 2019 brings up over 75 results.
In contrast, during the 2003 SARS outbreak, the entire scientific and healthcare community was overall much slower to and less well equipped to identify the cause of the outbreak (though the delay in reaction can be attributed to factors outside of technical capabilities as well), with the SARS genome sequence not published until 2 months after the first case was reported to the WHO2, 3.
Increasing decentralization of sequencing will enable us to better detect and monitor outbreaks in the future
Additionally, the decentralization of sequencing enabled through both lower cost of benchtop platforms (e.g., Illumina MiSeq) and the increasing accessibility of portable platforms (e.g., Oxford Nanopore MinION) have increased accessibility to monitoring the epidemiology and evolution of the outbreak. Of note, on January 31st, Oxford Nanopore announced shipments of 200 MinION sequencers and consumables to China “to support the ongoing surveillance of the current COVID-19 outbreak, adding to a large number of the devices already installed in the country”. Portable platforms such as the Oxford Nanopore MinION (consumables $1000 for MinION Mk1B, or $4,900 for Mk1C) are well-positioned to offer rapid turnaround, agile, in-field testing required to track an outbreak in real-time, and will likely become an increasingly integral part of identifying outbreaks in the future.
With the COVID-19 epidemic, early access to the viral genome sequence was instrumental in ensuring diagnostic protocols could be created and distributed in a timely manner
Rapid development of diagnostics is vital in the control of emerging disease epidemics and effective triage of patients; within days after the viral genome was first published, the WHO and governmental health organizations across the globe, including U.S., China, France, and Australia, had released PCR testing protocols and offered these assays through public health labs and/or qualified hospital labs to facilitate identification of infected patients. In contrast, during the 2003 SARS outbreak, serology assays (ELISA, immunofluorescent assays) played a much greater role; a network of 17 labs collaborated to develop the first nucleic acid-based diagnostic for SARS. Today, nucleic acid based assays for detecting respiratory pathogens are much more commonplace, with faster development and to-market time.
Multiple commercial manufacturers have already announced intent to develop and market COVID-19 diagnostic assays, which could alleviate testing backlogs and improve accessibility to screening assays
Of note, Roche and Tib-Molbiol partnered to develop assays for COVID-19 screening run on the Roche Lightcycler as an RUO assay, with 150 instruments already ordered in bulk by China. BGI has built a lab in Wuhan within the week to offer PCR- and sequencing-based COVID-19 testing with throughput capabilities of up to 10,000 tests / day. Co-diagnostics is developing an assay that can be run on most open PCR systems, which could greatly increase accessibility. Additionally, French company Novacyt and Korean company Seegene have both received CE-marks for their test.
In the past 17 years since the SARS outbreak, PCR assays with fast turnaround time (<1 hour) and automated point-of-care platforms have become more widely available, and have the potential to revolutionize the current model of testing during infectious disease outbreaks
Cepheid, one of the leading sample-to-answer players in infectious disease, has announced its intention to develop a single-pathogen COVID-19 assay for their GeneXpert System, with a turnaround time of under 30 minutes. QIAGEN announced an update to their respiratory panel to include the pathogen that causes COVID-19 on the QiaStat-Dx point-of-care platform, a completely automated system with hand-on time of <1 minute and turnaround time of ~1 hour. China-based Sansure Biotech developed the first COVID-19 diagnostic to be certified by the CFDA, with 30-minute turnaround time.
Novel technologies such as CRISPR are also valid alternative technologies that are well-suited to fast response and decentralized models
Mammoth Biosciences, in collaboration with UCSF, has announced intentions to develop a diagnostic test using their differentiated CRISPR technology. When asked about the potential for their technology in the space, Vikram Joshi, Head of Business Development at Mammoth Biosciences said, “When there is an emergence of a new pathogen, for example in an outbreak, CRISPR is imminently suitable to address diagnostic needs because one simply synthesizes the guide specifically directed towards the pathogen, e.g. coronavirus. Furthermore, the CRISPR biochemistry is low cost and lends itself to portable form factors”. Mammoth Bioscience recently published a white paper describing the test protocol, which can be read here.
Within the therapeutics landscape, a myriad of landmarks has accelerated the pace of development of drugs and vaccines for COVID-19
Just weeks after the viral genome was published, the Peter Doherty Institute in Australia released a lab-grown version of COVID-19 by, which enabled broader access to cultured viruses to aid in the design, manufacture, and testing of drugs and vaccines. By leveraging the published viral genome and lab-grown viruses via computer modeling, researchers identified existing drugs that are likely to bind to receptors found on the novel pathogen’ cell membrane. As an example, Gilead’s Remdesivir was originally developed to treat Ebola but was shown to treat the majority of COVID-19 symptoms when administered to the first U.S. COVID-19 patient. This drug is now in clinical trials in China that could have results published as soon as April. Johnson and Johnson and Abbvie also have HIV drugs that are being evaluated for use as a COVID-19 therapy.
Though not immediately serving to contain viral spread in the short term, some companies have invested in the development of vaccines, the process of which has been greatly accelerated over the years
Development of a vaccine took about 20 months for SARS in 2003 and 6 months for Zika in 2015. For COVID-19, within hours of gaining access to the viral genome, Inovio Pharmaceuticals was able to leverage an algorithm to design a vaccine based on the genetic sequence and enter pre-clinical testing. Other companies have developed methods to optimize production and manufacturing – Johnson and Johnson, partnered with the U.S. Department of Health and Human Services, is leveraging their internal PER.C6 human cell line and AdVac viral vector technology to facilitate cost-effective vaccine production; GSK has developed a vaccine adjuvant platform that reduces the amount of antigen that is needed per vaccine dose, hence increasing the number of people who can ultimately have access to the vaccine, and has made this platform available to researchers at the University of Queensland and CEPI-funded companies Inovio and Moderna.
For all we do know about the COVID genome, there is still much that is not understood about the disease epidemiology
How did it spread to humans? When are patients contagious? Looking ahead, researchers will have to dig into the information hidden in the viral genome, comparing it to similar strains, to better understand the specifics of the next emerging disease from the outset. And with the COVID outbreak still affecting tens of thousands, we may have a lot to learn from its genetic code yet.
As globalization and urbanization increase the risk of infectious disease outbreaks, having access to tools to detect, monitor, and address the outbreak, as well as collaborate across geographies and agencies will be increasingly important
“… To make the world safer, global health security depends crucially on much greater awareness, cooperation and collaboration between individual countries, agencies, organizations and communities. The continuing scientific uncertainty around disease emergence requires even more collaboration and global awareness than has previously existed, not least to improve early detection …”
– World Health Organization, Managing epidemics: key facts about major deadly diseases (2018), Version 1
Reporting, promptly and openly, cases of any disease with the potential for international spread, is critical and, as developments in the life science industry and experience improve our ability to handle outbreaks, we expect will become easier to do.
Susan is a Senior Associate at DeciBio with experience in a variety of consulting engagements in diagnostics, health IT and research tools. She has a particular interest in oncology precision medicine, novel diagnostics, and novel therapeutics, and is the curator of the liquid biopsy and immune cell therapy weekly newsletters. Connect with her on LinkedIn, or email her at [email protected]
Katie Gillette is a senior analyst at DeciBio with experience in Clinical Diagnostics, Health IT, and Novel Techs. At DeciBio, many of Katie’s projects are related to digital health and oncology. Connect with her on LinkedIn.
Disclaimer: Companies listed above may be DeciBio clients and/or customers