“When working with diverse samples, we do not know how many viruses we might expect and there are other environmental or host DNA/RNA molecules in the sample. We are basically looking for a needle from a huge haystack.” — Dr. Haiping Hao
Dr. Hao’s, work demonstrates how genomic sequencing — particularly RNA sequencing — is not just a diagnostic tool, but an early warning system to detect new global health threats that continue to emerge. "Advancements in sequencing technologies, particularly Nextgen sequencing and long read sequencing, have revolutionized viral sequencing.", he explains.
Dr. Hao is using RNA and DNA sequencing to track viral evolution and global health challenges; and has spent his career on the practical applications of sequence data in public health and infectious disease control.
“I have been working in genomics and deep sequencing for over 20 years, and I am always interested in using genomics to help solve human health problems,” says Dr. Hao. “During my time at Johns Hopkins, I worked with Drs. Steven Salzburg and Carlos A. Pardo-Villamizar, and we used sequencing to identify pathogens in undiagnosed infectious cases.”
During the COVID-19 pandemic, Dr. Hao’s team partnered with public health officials in New York City to sequence hundreds of thousands of SARS-CoV-2 genomes. Their work enabled near real-time variant tracking and early detection of emerging mutations. “This kind of work has a real-life impact on society and that’s why I pursued viral sequencing research,” he reflects. It shows the importance of DNA/RNA sequencing in understanding how viruses mutate and adapt.
“Are there new mutations in the virus that could affect transmission between humans, animals and the environment?” he ponders. “The avian flu virus infects birds, when it starts to infect other animals or humans, we want to know if the viral sequence has mutated so it can infect other animals or humans more easily.”
Dr. Hao’s lab continues to provide critical sequencing support for public health. One of Dr. Hao’s current collaborations at UTMB, with Dr. Gregory Gray’s One Health team, demonstrates the value of genomic surveillance at the animal-human interface. In this project, the Genomics Core processed samples from cattle affected by H5N1 avian influenza. Using established protocols, Dr. Hao’s team performed whole genome sequencing and assembled full viral genomes for phylogenetic analysis.
Genomic data such as this informs vaccine development and outbreak response. “Sequencing provides information on which mutation(s) will affect vaccine efficacy and guide the development of new vaccines for future outbreaks.” Globally this data is now the foundation of public health decision making. The CDC and GISAID use large scale sequencing data to monitor pathogen evolution, detect mutations and assess vaccine targets. “Genomic data allows us to track how viruses emerge and spread,” states Dr. Hao, leading to "informed public health responses and/or preparedness strategies".
UTMB’s sequencing capacity is part of a broader network of research that uses genomic surveillance to prepare for the next pandemic. "The Genomics Core is a very specialized core facility that provides expertise and collaborates with the wide research community. We provide consultations on all aspects of genomics sequencing research, such as sample collection, experimental design, sequencing approaches and data analysis and interpretation."
Definitions adapted from NHGRI, Medline Plus, and NCBI
Next Generation Sequencing (NGS): DNA and RNA sequencing technology to read DNA or RNA to study viruses and other organisms.
Genomics Core: A specialized facility within a research institution that provides sequencing services and bioinformatics support for DNA/RNA analysis.
References:
- Centers for Disease Control and Prevention (CDC) – Genomic Surveillance for SARS-CoV-2
- GISAID Initiative – Global database for sharing viral genomic data
- UTMB Genomics Core – Research infrastructure and sequencing services
https://www.utmb.edu/research/cores/genomics-core - World Health Organization (WHO) – Tracking SARS-CoV-2 variants
- Siddle, K.J., et al. (2020). Genomic epidemiology of early introductions of SARS-CoV-2 into the New York City area. Science, 369(6501), 297–301.
- One Health Commission – What is One Health?
- Smith, G.J.D., et al. (2009). Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature, 459, 1122–