Genome surveillance: How scientists know which COVID variants are circulating

The omicron variant quickly took over the global coronavirus landscape after it was first reported in South Africa in end of November 2021. The United States has become 24th country to report a case of omicron infection when health officials have announced On December 1, 2021, a new strain of bacteria was identified in a patient in California.

How do scientists know which versions of the coronavirus are present? How quickly can they tell which virus variants are entering the population?

Alexander Sundermann and Lee Harrison are research epidemiologists new approach because the boom search. Here, they explain how the genome surveillance system in the United States works and why it’s important to know what virus variants are circulating.

What is genomic surveillance?

Genomic surveillance provides an early warning system for SARS-CoV-2. In the same way that smoke alarms help firefighters know where fires are starting, genomic monitoring helps public health officials know which coronavirus variants are showing up where.

The lab sequenced the genome in coronavirus samples taken from patients’ COVID-19 tests. These are diagnostic PCR tests has come back positive for SARS-CoV-2. Scientists can then tell from the virus’s genome which coronavirus variant has infected the patient.

By sufficiently sequencing the coronavirus genome, scientists can build a representative picture of the variants circulating in the general population. Some variants have genetic mutations that are significant in the prevention and treatment of COVID-19. So genomic surveillance can inform decisions about appropriate countermeasures – helping to control and extinguish a fire before it spreads.

Eg, the omicron variant has descending mutations How well the existing COVID-19 vaccine works. In response, officials recommended booster shots for enhanced protection. Similarly, mutations in the omicron reduce the effectiveness of some monoclonal antibodies, which are used to prevent and treat COVID-19 in high-risk patients. Therefore, knowing which variants are circulating is important to determine which monoclonal antibodies are likely to be effective.

How does genomic surveillance work in the US?

The US Centers for Disease Control and Prevention leads an association known as the National SARS-CoV-2 Stress Monitor (NS3) system. It collects approximately 750 SARS-CoV-2 positive samples per week from state public health laboratories across the United States.

Each type of laboratory has its own strengths in genomic monitoring. Commercial laboratories can arrange a large number of tests quickly. Academic partners can provide research expertise. And public health laboratories can provide insights into local transmission dynamics and outbreaks.

Regardless of the source, sequence data are often publicly available and thus contribute to genome surveillance.

What data is tracked?

When the lab sequence the SARS-CoV-2 genome, the lab will upload the results to a public database that includes when and where the coronavirus sample was collected.

The Global Open Access Initiative on Sharing Avian Influenza Data (GISAID) is an example of one of these databases. Scientists put forward GISAID in 2008 to provide a quick and easy way to see what strains of flu are circulating globally. Since then, GISAID has evolved and pivoted to now provide access to the SARS-CoV-2 gene sequences.

The database compares a sample’s genetic information with all other samples collected and shows how that particular strain has evolved. Now, more than 6.7 million SARS-CoV-2 sequences from 241 countries and regions have been uploaded to GISAID.

Taken together, this patchwork of genome surveillance data provides a picture of the variants currently widespread in the United States. For example, on December 4, 2021, CDC predicts that omicrons account for 0.6% of COVID-19 cases in the United States. estimated rate increased to 95% by January 1, 2022. Monitoring gave a clear warning about how quickly this variation was dominating, allowing researchers to study which countermeasures would work well Best.

However, it is important to note that genomic surveillance data is often up-to-date. The time from when a patient is tested for COVID-19 to when the viral genome sequence is uploaded to GISAID can be days or even weeks. Because there are many steps in the process, average time from collection to GISAID in the US ranges from seven days (Kansas) to 27 days (Alaska). CDC uses statistical methods to estimate rates of variations in the most recent past until official data are available.

How many COVID-19 samples were sequenced?

Earlier in 2021, the CDC and other public health labs sequenced a total of about 10,000 COVID-19 samples per week. Consider that hundreds of thousands of cases diagnosed weekly in most pandemics, epidemiologists consider that number to be too small a percentage to provide a complete picture of circulating strains. More recently, CDC and public health laboratories have sequenced closer to 60,000 cases per week.

Despite this improvement, there is still a large gap in the percentage of COVID-19 cases in order from state to state, from a low of 0.19% in Oklahoma to a high of 10. .0% in North Dakota. within the last 30 days.

Furthermore, the US as a whole handles a much smaller proportion of COVID-19 cases than some other countries: 2.3% in the US compared with 7.0% in the UK, 14.8% in New Zealand and 17% in Israel.

What COVID-19 tests are in sequence?

Imagine if researchers collected COVID-19 tests from just one neighborhood in the entire state. Surveillance data will favor the variant circulating in that neighborhood, since people are likely to transmit the same strain locally. The system may not even register another variant that is gaining steam in a different city.

That’s why scientists want to collect a diverse range of samples from across an area. Sampling that is geographically and demographically representative at random gives researchers a good sense of the big picture of whether variations are dominant or declining.

Why are patients in the US not receiving variant results?

There are a number of reasons that patients are often not informed of the results if their samples are sequenced.

First, the time between specimen collection and sequencing results is often too long to render clinically useful information. Many patients will have far advanced into their disease by the time their variant is identified.

Second, the information is often unrelated to patient care. Treatment options are largely the same regardless of which variant has caused the COVID-19 infection. In some cases, doctors can select the most appropriate monoclonal antibodies to treat based on the variant a patient has, but this information can often be gathered from faster laboratory method.

As we head into 2022, it’s more important than ever to have a robust genomic surveillance program that can catch anything. next new coronavirus variant To be. A system that provides a representative picture of current variations and quick turnaround is ideal. Appropriate investment in genomic surveillance for SARS-CoV-2 and other pathogens and data infrastructure will support the United States against future waves of COVID-19 and other infectious diseases.

Alexander Sundermann, Clinical Research Coordinator & Ph.D. Candidate in Epidemiology, University of Pittsburgh Health Sciences and Lee HarrisonProfessor of Epidemiology, Medicine, Infectious Diseases and Microbiology, University of Pittsburgh Health Sciences

This article was republished from Conversation under a Creative Commons license. Genome surveillance: How scientists know which COVID variants are circulating

Caroline Bleakley

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