Genome sequencing shows COVID-19 spreading pattern

New studies indicate the role that viral genome sequencing can play in the current COVID-19 pandemic.

Viral Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic is rapidly spreading worldwide, affecting more than 2.6 million people and killing more than 183,000 people. The only interventions currently possible are non-pharmacological means, mainly contact traces, quarantine means, social distances, and forms of blockade.

Do these work well? Without the universal test, it is often asymptomatic and difficult to determine. Sequences can play an important role here.

Color scanning electron micrograph of Middle East respiratory syndrome virus particles (yellow) attached to the surface of VERO E6 cells infected with MERS virus particles (blue). Color-enhanced image captured at the NIAID Integrated Research Facility in Fort Detrick, Maryland. Credit: NIAID

Beginning of genome surveillance

In China, scientists rapidly sequenced the viral genome and identified it as a beta coronavirus, similar to the virus that caused the 2002 SARS epidemic. Through the spread of the virus, genomic sequencing has played a role in the epidemiological tracking of virus strains carried around the world. Such strains trace their origins by their unique mutations and help correlate distant infections.

This method has taken a major step forward with the development of the Targeted Sequencing Protocol, the GISAID (Global Initiative for Sharing All Influenza Data) repository that enables open real-time sharing of sequences, and Nextstrain. This analysis platform allows you to quickly track mutations in specific virus strains. All of these have been used to advantage in visualizing the routes by which the virus can spread.

Some unexpected findings were associated with those found in travelers five weeks ago, with gene sequences in Seattle area patients without a history of travel to hot spots or contact with COVID-19 cases. Includes discoveries. The spread of the community, though much quieter, was widespread.

Computer monitor shows DNA sequence. D-VISIONS / Shutterstock

New York – the new epicenter

New York City has witnessed the inferno of illness and death since its first confirmed case on March 3, 2020. world.

However, New York City alone accounts for more than half of all cases in the state, with more than 142,000 confirmed cases. The epicenter of the epidemic in New York now feeds the hospital’s New York University Langone Health System. Current research aims to document the characteristics of the early COVID-19 epidemic in large cities and trace the strain back to its oldest known origin.

How was the research done?

Researchers wanted to know how the virus spreads within the catchment of the NYU Langone Health network of hospitals in Brooklyn, Manhattan, and Nassau County. They first set up an optimally designed workflow for genome sequencing and analysis. They randomly sampled a population of confirmed cases tested between 12 March and 1 April 2020.

The RNA was sequenced and a robot library was constructed. We directly generated high quality sequences using the Shotgun sequencing method. Viral genome analysis was performed on 156 sequences that passed all quality tests. Medical records were analyzed to identify the exposure.

What did the study show?

Researchers found that the samples were from the entire region above, but mostly from Brooklyn and Manhattan. Most of these were in hospital catchments in the New York metropolitan area.

However, West Chester County, a region located north of the city and outside the area served by hospitals, was not represented, although an outbreak in the first region was seen.

No history of exposure was recorded in more than 50% of cases. Therefore, researchers performed sequencing and phylogenetic analysis of sample sequences to see how closely they were related to each other. If the case spreads from one or several index cases, the virus is almost the same.

They colored each sequence according to where the patient lived. This indicated that there were multiple strains of coronavirus circulating in the sampling area dating back to the first week of March.

Next, the GISAID EpiCov repository was used to compare the genome with more than 7,600 sequences collected globally. After tracking the lineage, each sequence was colored according to the most similar sequence from another region. Surprisingly, the researchers found that over 41% of the samples were most closely associated with Europe and 46% were from the United States or Canada.

They looked at the latest common stock collection date, stratified by region, and found that from the last week of February 2020, about 66% were similar to European samples. It was.

Few data are available on the early spread of the January and February pandemics, as few sequences were collected from the transmission route. As a result, investigators do not say that they found a specific infection event or found a timeline, even if they found only links to European samples.

Overall, they found almost 190 nucleotide variants and 97 altered amino acids. As more sample sequences run, more will continue to be found. This means that surveillance must be sustainable at the local, regional, national, and even international levels in order to properly monitor a pandemic.

How important is research?

Mutations in the influenza virus that cause seasonal influenza are essential for pathogenicity and allow the virus to escape the immune system even after vaccination. It also allows the virus to develop resistance to the antiviral drug oseltamivir. However, this does not apply to most mutations of the SARS-CoV-2 virus that are not expected to function. Researchers say these are the result of genetic drift.

Again, genome tracking helps track viral spread independent of medical history. This is a way to show that the current sampling from the New York area has resulted in a much wider range of infections than was thought to be the case in Seattle. This type of analysis may need to be performed retrospectively to see how spreads occur invisibly in communities within each region.

It also sheds light on the effects of public health policies and behavioral changes such as social distance and quarantine. It also helps shape future management of current outbreaks.

However, setting up such monitoring on the fly is not easy. Therefore, given these important capabilities, scientists said, “Given the logistics and regulatory hurdles to establish such oversight, we have already prepared this infrastructure for the future wave of COVID-19. It is important to do this. “