2020 in genomics: a global pandemic and groundbreaking scientific developments

As the world celebrated a new decade on Jan. 1, 2020, the World Health Organization (WHO) initiated an emergency response to a notification from the Wuhan Municipal Health Commission of a cluster of viral pneumonia of unknown cause. By March, we were in a global pandemic and for the first time in modern history the whole world was focused on solving a single problem.

The COVID-19 pandemic is a watershed event of our time, straining health systems, revealing unconscionable inequalities, and permanently changing the way we work and live. The pandemic has also deepened our capacity for connection and collaboration, and catalyzed amazing scientific breakthroughs including key developments in genomics. Here’s a look back at some of them, starting with the breakthroughs from the pandemic:

The pandemic showed the crucial role of genomics for pathogen outbreak surveillance

Rapidly identifying the causative pathogen and how it’s mutating, and spreading is critical in battling an outbreak – informing public policy decisions and the development of vaccines, diagnostics, and therapies.

Around 2 a.m. on Jan. 5, after working over 40 hours straight, Dr. Zhang and his team at the Shanghai Public Health Clinical Center sequenced the unknown virus on the NovaSeq™ 6000 System. They published its genome on Jan. 10, 10 days after the first case was reported to the WHO – a remarkable accomplishment. It took researchers 149 days to publish the viral genome of SARS in 2002 and 77 days for the swine flu in 2009.

Sequencing also emerged as a critical tool to track the spread of the virus, helping guide public policy decisions. In February, Dr. Bedford and the team at Fred Hutchinson Cancer Research Center used genomic data to show that the coronavirus had been spreading undetected in Seattle for weeks. This helped guide a speedy public health response in Washington state, averting a catastrophic spread like the one that occurred later in New York City. Dr Chiu, at UCSF, began sequencing the genomes of Bay Area COVID-19 patients to identify where outbreaks in the Bay Area came from and how quickly the disease was spreading. His work in tracking mutations and the spread of infection helped drive public health response in the early days of the pandemic. The New York Genome Center launched the COVID-19 Genomics Research Network, undertaking large-scale sequencing projects to understand how the virus spreads and develop strategies to help reduce the spread and alleviate symptoms.

Similar efforts emerged around the world. Australia created the first national COVID-19 tracking system using genomics to track the virus throughout the country. The Communicable Disease Genomics Network included real-time data sharing to understand the transmission and spread in Australia. The Africa Centers for Disease Control launched the Africa Pathogen Genomics Initiative to build a continent-wide disease surveillance network based on pathogen genomic sequencing, to inform research and public health responses to COVID-19 and other epidemic threats such as AIDS, tuberculosis, malaria, cholera, and other infectious diseases.

Looking forward, we need a global genomics surveillance network to identify and track outbreaks including novel coronaviruses, anti-microbial resistance, bioterrorism, and zoonotic transmission.

Breakthrough mRNA vaccines and a new era of genomic-driven vaccines

On Dec. 8 in the UK, Margaret Keenan, 90, became the first person to receive the Pfizer/BioNTech COVID-19 vaccine, just 272 days after the first case was reported to the WHO. Vaccine development is slow and complex, lasting 15+ years and, despite previous outbreaks – SARS in 2002 and MERS in 2012 – there has never been a coronavirus vaccine. Going from the discovery of the novel virus to the delivery of an effective vaccine in less than 1 year is unprecedented in scientific and medical history.

The exciting, emerging generation of nucleic-acid based vaccines, including mRNA (Pfizer/BioNTech, Moderna), ASO, siRNA, and CRISPR-Cas will revolutionize vaccine development.

Genomic research gives valuable insight into COVID-19 susceptibility and potential precision treatments.

For some people COVID-19 is severe, sometimes fatal, while others experience few, if any symptoms. Some of this difference is genetic, and understanding the genetic drivers is important to develop treatments and public health policy. There are several population scale research efforts ongoing worldwide and the results have already been valuable. A landmark study of 2,200 intensive care COVID-19 patients in the UK by the GenOMICC consortium identified five genes associated with the most severe form of the disease, opening the path for clinical trials for existing drugs that target these genes. A team of scientists at the New York Genome Center, New York University and Icahn School of Medicine at Mount Sinai used CRISPR to identify the genes that can protect human cells against COVID-19 and developed a series of human lung cell models for the coronavirus screening to better understand immune responses to the disease.

CRISPR enters the clinic

The 2020 Nobel Prize in Chemistry was awarded to Emmanuelle Charpentier and Jennifer Doudna for pioneering the revolutionary gene-editing technology. 2020 was also the year we saw the first clinical applications of CRISPR.

In May, the FDA granted the first-ever Emergency Use Authorization for CRISPR for Sherlock Biosciences’ CRISPR SARS-CoV-2 detection kit. The kit detects SARS-CoV-2 in the upper respiratory tract and provides results in less than an hour. Beyond COVID-19, Locus Biosciences is developing antibacterial products based on CRISPR-Cas3 to pursue indications against bacterial pathogens and microbiome applications by targeting the bacterial genome. And Scribe engineered CasX enzyme to develop therapeutics for ALS.

Liquid biopsy builds momentum

A set of key FDA approvals has given momentum to liquid biopsy for use in molecular profiling of solid tumors and as companion diagnostics for targeted cancer therapies. In August, Guardant Health received FDA approval for its Guardant360 CDx cancer test as the first liquid biopsy able to genetically profile solid tumors anywhere in the body through a single blood draw. The test provides biomarker and mutation information across 55 genes linked to multiple cancers without needing to remove samples of the tumor tissue—but the test has not yet been approved to direct patients toward a particular treatment. Foundation Medicine’s FoundationOne Liquid CDx received FDA approval to analyze 300+ genes and genomic signatures in solid cancers, and for use in matching targeted therapies to patients with advanced or metastatic breast cancer, advanced ovarian cancer and certain metastatic non-small cell lung cancers.

A blood test to find early stage cancer signals a new era for cancer detection

Most cancers today are detected too late, when chances of survival are much lower, because the majority of deadly cancers still do not have a screening test available. In April, Grail published validation data from one of the largest clinical study programs ever conducted in genomic medicine for its multi-cancer early detection blood test, Galleri™, demonstrating that the test can detect more than 50 cancer types across all stages, with 99+ percent accuracy through a single blood draw. When a cancer signal is detected, the test also identifies where the cancer is located in the body with 93 percent accuracy. GRAIL announced that the UK's National Health Service will pilot Galleri in 2021 with 165,000 patients, who will get annual blood tests over three years.

Genomic testing advances to standard of care for genetic disease and noninvasive prenatal testing

More than 3,000 Australian families in will benefit each year from the Australian Federal Government’s listing of genetic testing for childhood syndromes and intellectual disability on the Medicare Benefits Schedule. Whole-exome or genome sequencing to identify the genetic cause of intellectual disability will be fully reimbursed, an important milestone for the genetic disease community.

Noninvasive prenatal testing (NIPT) analyzes DNA from an expecting mother’s blood to screen for chromosomal conditions in a baby. It’s the most sensitive and specific screening test for chromosomal changes and could prevent the need for more invasive procedures. In August, the American College of Obstetricians and Gynecologists (ACOG) recommended NIPT be made available to all pregnant women, regardless of maternal age or baseline risk. ACOG’s endorsement helped expand insurance coverage and broaden access to NIPT. This year some of the largest U.S. insurance providers, including UnitedHealthcare, Aetna, Humana and Centene expanded coverage for NIPT to all pregnant women, instead of only pregnant women at risk or over the age of 35 – a big win for expectant parents.

Looking ahead

The pandemic has brought suffering and trauma around the globe and exposed major global healthcare issues – from lack of preparedness to inequities in impact and access. But we have also seen the selfless dedication of healthcare professionals, frontline essential workers, scientists, and researchers around the world. We have seen how much stronger we are when we collaborate across borders and industries. We witnessed the radically accelerated adoption of science and technologies — from years, to months and weeks. As we head into 2021, we have ushered in new eras of science and medicine, from mRNA vaccines to cancer detection from a simple blood test, that will benefit humanity into the future.