Quality Statement

Pacific Biosciences is committed to providing high-quality products that meet customer expectations and comply with regulations. We will achieve these goals by adhering to and maintaining an effective quality-management system designed to ensure product quality, performance, and safety.


Image Use Agreement

By downloading, copying, or making any use of the images located on this website (“Site”) you acknowledge that you have read and understand, and agree to, the terms of this Image Usage Agreement, as well as the terms provided on the Legal Notices webpage, which together govern your use of the images as provided below. If you do not agree to such terms, do not download, copy or use the images in any way, unless you have written permission signed by an authorized Pacific Biosciences representative.

Subject to the terms of this Agreement and the terms provided on the Legal Notices webpage (to the extent they do not conflict with the terms of this Agreement), you may use the images on the Site solely for (a) editorial use by press and/or industry analysts, (b) in connection with a normal, peer-reviewed, scientific publication, book or presentation, or the like. You may not alter or modify any image, in whole or in part, for any reason. You may not use any image in a manner that misrepresents the associated Pacific Biosciences product, service or technology or any associated characteristics, data, or properties thereof. You also may not use any image in a manner that denotes some representation or warranty (express, implied or statutory) from Pacific Biosciences of the product, service or technology. The rights granted by this Agreement are personal to you and are not transferable by you to another party.

You, and not Pacific Biosciences, are responsible for your use of the images. You acknowledge and agree that any misuse of the images or breach of this Agreement will cause Pacific Biosciences irreparable harm. Pacific Biosciences is either an owner or licensee of the image, and not an agent for the owner. You agree to give Pacific Biosciences a credit line as follows: "Courtesy of Pacific Biosciences of California, Inc., Menlo Park, CA, USA" and also include any other credits or acknowledgments noted by Pacific Biosciences. You must include any copyright notice originally included with the images on all copies.


You agree that Pacific Biosciences may terminate your access to and use of the images located on the PacificBiosciences.com website at any time and without prior notice, if it considers you to have violated any of the terms of this Image Use Agreement. You agree to indemnify, defend and hold harmless Pacific Biosciences, its officers, directors, employees, agents, licensors, suppliers and any third party information providers to the Site from and against all losses, expenses, damages and costs, including reasonable attorneys' fees, resulting from any violation by you of the terms of this Image Use Agreement or Pacific Biosciences' termination of your access to or use of the Site. Termination will not affect Pacific Biosciences' rights or your obligations which accrued before the termination.

I have read and understand, and agree to, the Image Usage Agreement.

I disagree and would like to return to the Pacific Biosciences home page.

Pacific Biosciences

NIH Scientists Chart SARS-CoV-2 Evolution Within an Individual Over Time

Tuesday, June 8, 2021

An exciting new paper from scientists at the National Institute of Allergy and Infectious Diseases and the NIH Clinical Center reports on the evolution of the SARS-CoV-2 virus within individuals. The team used HiFi sequencing to make this work possible.

The paper, which was published in PLoS Pathogens, comes from lead authors Sung Hee Ko, Elham Bayat Mokhtari, Prakriti Mudvari, senior author Eli Boritz, and collaborators. They conceived the project to overcome a key challenge in tracking viral adaptation. “An important obstacle to understanding intra-individual evolution of SARS-CoV-2 is that standard sequencing and analytical procedures yield a single consensus sequence for each sample, rather than multiple sequences representing virus quasispecies diversity,” they write.

SARS-CoV-2 Assay Design

Figure 1. The SARS-CoV-2 sequencing assay relies on a 6.1 kb amplicon, UMIs, and HiFi sequencing to phase all mutations in the S, E, and M genes with high reproducibility.

To address the issue, they developed a new method based on HiFi sequencing to focus on the 6.1 kb region of the SARS-CoV-2 genome encoding its surface proteins. They then conducted deep sequencing of eight individuals, yielding large numbers of fully phased S, E, and M gene sequences from each person. In one individual, the availability of four samples collected over time allowed for a longitudinal analysis of viral response to host immune pressure. The scientists had previously used HiFi sequencing to study the intra-individual evolution of HIV, and believed that the same approach could be useful during the COVID-19 pandemic.

The choice of HiFi sequencing, which builds a highly accurate sequence based on consensus calls from covering the same molecule over and over, gave the team an excellent view of viral evolution. When we asked senior author Eli Boritz about his choice of technology, he shared that “By early 2020, we had been working for several years to use HiFi sequencing for high-throughput, single-copy, long-read HIV genetic analysis. Our approach in the HIV studies used unique molecular identifiers (UMIs) for error correction and drew on a short-read approach from Ron Swanstrom’s group and a PacBio approach from Jim Mullins’s group. As the pandemic took off around the world, we decided to adapt our approach to SARS-CoV-2. We didn’t know if this new virus would generate enough diversity to warrant our detailed sequence analysis, but we decided that it would be important to look.”

Time course data correlation between the appearance of minor variants.

Figure 2. In one patient, time course data showed a correlation between the appearance of minor variants with NTD mutations, a change in relative epitope binding in host serum, and a transient increase in viral load.

The longitudinal analysis yielded results highly suggestive of natural selection, revealing four viral haplotypes harboring three mutations that arose independently in a single epitope. “These mutations arose coincident with a 6.2-fold rise in serum binding to spike and a transient increase in virus burden,” the scientists note. “We conclude that SARS-CoV-2 exhibits a capacity for rapid genetic adaptation that becomes detectable in vivo with the onset of humoral immunity, with the potential to contribute to delayed virologic clearance in the acute setting.”

In the other study participants for whom repeated sampling was not possible, the team found lower genetic diversity in the viruses sequenced. They hypothesize that this is likely the result of analyzing samples collected early in the infection process rather than after the host’s immune response has had time to select variants with mutated spike proteins.

We asked Eli Boritz about what’s next for his team. For future longitudinal studies, he told us, “it will be important … to sequence additional regions of the virus and to perform a comprehensive analysis of antiviral host responses, including neutralizing antibodies, T cells, and other mechanisms.” He also hopes to analyze viral samples from more complex cases, such as reinfections. “We hope these studies can teach us about the virus’s capacity for additional waves of escape variants in the future,” he said.

The team’s insights into viral evolution in a single person have important implications for COVID-19 treatment. “Our results also emphasize that early antiviral therapy or combinations of antivirals with distinct targets could have markedly higher virologic efficacy than monotherapy administered later in the disease course,” the scientists conclude.

Visit our Coronavirus Sequencing page to learn how HiFi reads from the Sequel IIe System provide a reliable, cost effective, high-throughput solution for sequencing SARS-CoV-2 quickly and easily.

Subscribe for blog updates: