Baylor genomics teams partner to provide COVID-19 testing for Houston area

Baylor College of Medicine’s Human Genome Sequencing Center is a leader in large scale DNA sequencing research, and the Alkek Center for Metagenomics and Microbiome Research is leading research related to how bacteria and viruses impact human health. Since the outbreak of the COVID-19 pandemic, researchers at both centers have come together to serve the need for COVID-19 testing in the Houston area by combining the expertise of each group’s laboratories. Now, Baylor is partnering with local public health departments to provide polymerase chain reaction (PCR) testing for tens of thousands of COVID-19 samples.

“We are pleased to work with the outstanding local government groups in this critical public health effort,” said Dr. Richard Gibbs, director of the Human Genome Sequencing Center and Wofford Cain Chair and Professor of molecular and human genetics at Baylor. “We are proud of the tireless determination and expertise of our centers and college staff that enabled the rapid development of this robust testing capacity to serve the greater Houston community.”

Baylor is one of the testing providers for Harris County Public Health. Anyone who wants to be tested can complete a pre-screening questionnaire, either online or by phone. If the person qualifies for testing, they will be given a personalized code and directed to one of the mobile testing sites. Harris County Public Health also provides testing services to individuals living in traditionally high-risk congregate settings such as nursing homes.

“We are fortunate to have Baylor College of Medicine as a close partner during the COVID-19 pandemic,” said Dr. Umair Shah, executive director of Harris County Public Health. “This is a challenging time for our community and as the need for increased testing capacity and getting results to residents faster has grown, Baylor has risen to the occasion. There are countless unsung heroes across Harris County who have stepped up to the plate during this pandemic and Baylor College of Medicine is one of them.”

Samples collected at testing sites are sent to the Alkek Center for Metagenomics and Microbiome Research to be prepared for testing. After arriving at the lab, each sample is decontaminated and put in a liquid solution that helps isolate the virus. Technicians then extract the genomic material of the virus (RNA) from the sample. That RNA is then sent to the Human Genome Sequencing Center to undergo quantitative reverse transcription PCR (RT-qPCR) testing. This process works by looking for specific sequences that are unique to the virus’s genome. If the sample’s RNA sequence matches that of the virus, the sample is positive. Each sample must test positive three times to be considered a positive case of COVID-19. A trained interpreter will also provide a final review, confirming a positive or negative case. Each report is signed by respiratory virus expert and Medical Director of the Alkek Center for Metagenomics and Microbiome Research lab, Dr. Pedro Piedra.

On average, results are returned to the tested person within 48 hours. Each test kit is equipped with a bar code that allows the test to be tracked digitally, speeding up the process of informing the tested person and county health officials. If a person tests positive, the Harris County Public Health team will follow up with them for contact tracing.

“Widespread testing capacity is a critical component for this pandemic response.  Whether we are identifying new cases or are performing surveillance, the only way to effectively allocate resources is with a response that includes testing,” said Dr. Joseph Petrosino, chair of the department of molecular virology and microbiology and director of the Alkek Center for Metagenomics and Microbiome Research at Baylor.

Since beginning the partnership with the County in May, the group has tested more than 30,000 samples. The lab also provides COVID-19 testing for other groups in the area.

"We knew we had all the pieces to stand up a testing center fast – large scale clinical sequencing, experts in virology and molecular biology, and a secure way to return results to patients,” said Ginger Metcalf, Human Genome Sequencing Center Director of Project Development. "We are also fortunate to have such great partners at Harris County Public Health, who have done an amazing job of gathering, tracking and delivering samples, especially for the most at-risk members of our community."

The Baylor testing lab currently has a capacity of more than 1,000 samples a day. Leaders hope to hire more staff soon to increase testing capacity.