While standard PCR testing can determine whether a sample is positive or negative for SARS-CoV-2, it does not provide any information on the origin of the viral strain. Next-generation sequencing (NGS), however, now helps researchers around the world to track how the virus is spreading by providing additional information that is building a more robust picture of potential transmission patterns and clusters. This is especially important for considering disease control strategies and mitigating emerging hot spots.
Dr. Paraic A. Kenny, director of the Kabara Cancer Research Institute of the Gundersen Medical Foundation in La Crosse, WI., recently pivoted his research from cancer to sequence known SARS-CoV-2 positive samples from his region. Using the Ion AmpliSeq SARS-CoV-2 Research Panel, his team tracked the spread of one strain of SARS-CoV-2 from its origin at a meatpacking plant in northeast Iowa across three states over the course of six weeks. His research is the subject of a preprint recently published in medRxiv.
We spoke with Dr. Kenny to discuss his team’s research and how analyzing the spread of SARS-CoV-2 can help public health officials respond to the spread of the virus.
Thermo Fisher Scientific (TFS): How is next-generation sequencing different from other modalities used to analyze SARS-CoV-2?
Dr. Kenny: Standard PCR analysis does an excellent job of telling if a sample is positive [for SARS-CoV-2], which is straightforward and incredibly valuable. However, sequencing research can provide additional information.
The virus slowly accumulates mutations through each infection cycle, around two mutations per month, and these mutations are heritable, so the next person who is infected by the virus will also have this mutation. Through sequencing, we can move beyond figuring out who is positive or negative and instead use these molecular fingerprints to assign people to genetic clusters and start to build more definitive transmission chains. This will help us get a handle on how the virus is spreading within communities at the local level as well as across our nation and globally.
TFS: What did you expect to find when you started sequencing samples?
Dr. Kenny: Our research team started retrospectively sequencing known positive samples from 21 counties across three states. My background has been in cancer genomics, so this was the first time my team has sequenced a viral samples. The Ion AmpliSeq-CoV-2 Research Panel we used from Thermo Fisher was straightforward and worked well right out of the box, so this helped to make the transition to viral sequencing easier. Our initial research goals were to learn how the virus arrived in the region and understand the viral spread.
TFS: What does a typical transmission chain look like and how did the strain you identified originating in the Postville, Iowa, meatpacking plant behave differently?
Dr. Kenny: Our team started sequencing the virus in late March. In the early weeks we sequenced 30 to 40 cases from across the region, finding six to seven independent viral substrain introductions. Most of these substrains were limited to individuals who had traveled and brought the virus back with them. Most transmission chains we were able to study were short, between one to two subsequent infections, before being mitigated and snuffed out by public health interventions.
In the first week in April we received the first sample associated with the meatpacking plant. Over the next few weeks, we had identified 15 samples from this county with the same substrain of the virus. This was a striking difference from what we had seen with all the other viral introductions we had mapped.
By the time we had reached the cut off point for the data on the paper, we had mapped 14 viral substrains in our region. This meatpacking plant strain was the outlier in terms of how far it spread within the meatpacking plant and across our region. We analyzed 27 samples of this substrain in 13 different cities in seven counties spanning three states.
TFS: Why is it important to identify the origin of the spread of the virus?
Dr. Kenny: Trying to manage a global crisis is challenging. Viral sequencing can help to understand if something better can be done and potentially assist decision-makers adapt moving forward.
At the national level, we can see instances where the government shut off air travel from China, but at the same time left it open for Europe which helped to set off multiple chains of infections that quickly spread across the U.S. By using sequencing at the national level, we can help provide scientific insight into whether that was the correct measure, which may help inform the next crisis response in the future.
At the local level, the data we found highlights strong risks associated with unmitigated spread in certain situations. A meatpacking plant is an example of a large group of people together in a high-risk setting that encouraged the viral spread. However, there were many things that could be done to mitigate the spread of the virus. Whether it’s not punishing sick people for staying home or establishing solid public health guidelines for industries like this, knowing that so many cases originated from one meatpacking plant can help us identify ways to mitigate SARS-CoV-2 spread as the crisis continues.
TFS: What are your thoughts on sequencing wastewater as a form of surveillance?
Dr. Kenny: Our team has also been sequencing wastewater. We have witnessed strong local spread of a substrain that seems to be linked with young people socializing in bars. Review of our data revealed that the mutation defining this particular substrain was detectable in wastewater prior to the strong surge in cases, suggesting that this approach may have some utility in forecasting.
Wastewater is a challenging material to work with compared to the nasal swab but can be sequenced using the same assay we used for research samples. The sequencer does not care where the RNA comes from, but the challenge resides in extracting sufficient RNA from wastewater to obtain robust sequence data.
TFS: How can analyzing viral strains and potential mutations inform vaccine development?
Dr. Kenny: It is clear from data from labs across the world that some regions of the virus are more prone to mutation compared to others. For vaccine development, researchers will likely focus on the more conserved, stable regions. Currently, we do not have any solid data on whether any of these mutations are clinically meaningful, as it is challenging to deduce that from the sequencing information. Sequencing is a great hypothesis generating tool, but drawing firm conclusions about pathogenic differences requires functional studies in the lab. Our current assumption is that most, if not all, mutations simply reflect scars that function as markers that allow us to figure out where the virus has been.
After an effective treatment or vaccine is developed, sampling strains that came after those interventions will help identify substrains resistant to clinical interventions and that may inform crucial next steps if further strategies are needed.
For more information on the Ion AmpliSeq-CoV-2 Research Panel, visit our website.