A researcher at Arizona State University’s Biodesign Institute in Phoenix examines a slide. Screenshot via ASU Biodesign Institute | Vimeo
Although COVID-19 hospitalizations are down, genetic sequencing and a recent outbreak in Maricopa County has shown the highly transmissible Delta variant of the virus is beginning to take hold in the Grand Canyon state, making up more than one in every five infections in June and accelerating rapidly.
Arizona was among the early leaders in vaccination rates, but efforts to inoculate the state’s residents has plateaued since May. Now, with Arizona lagging the nation in vaccinations, the state is currently averaging approximately 500 new cases of COVID-19 a day, several times greater than more populated states like New York and Massachusetts, which are averaging between 80 to 130 cases per day.
Among the cases of COVID that are appearing in the state is a new variant of the virus known as B.1.617.2, also known as the Delta variant, which is believed to have originated in India.
Genetic sequencing data done by Arizona-based TGen shows that the Delta variant made up about 3% of the Arizona samples that were genetically sequenced in May. By the end of June, that number had shot up to 21%.
One study by a group of UK scientists found that the Delta variant is 225% more transmissible than the original strain of the SARS-COV-2 strain that kicked off the global pandemic in early 2020. Another recent study by researchers at the Guangdong Provincial Center for Disease Control and Prevention found that people infected with the Delta variant had 1,000 times more copies of the infection in their lungs than those with the original virus.
The variant first made its appearance in Arizona back in April, but was likely from a traveler and did not create any further transmission. It wasn’t until May 5 that TGen sequenced it for the first time, said Dr. David Engelthaler, director of TGen’s infectious disease research.
TGen has been genetically sequencing COVID samples from across the state to gain a better understanding of the ecosystem of COVID that is infecting Arizonans to help public health officials get a better understanding of how the virus is spreading and in what forms.
“Without sequencing, we just count up cases — it doesn’t really give you any good actionable intelligence on the virus,” Engelthaler said, adding that the sequencing allows for them to test new versions found to see what immunities the virus may have.
Genetic sequencing is a chemical process that turns a viruses’ genetic material into code that can be read by a computer so programs can then look for changes and variations in the makeup of the virus.
“All a variant really is, is the virus that was circulating before but with a few more mutations,” Richard J. Webby, PhD, a member of the Infectious Diseases Department at St. Jude Children’s Research Hospital and the World Health Organization’s Vaccine Composition Team said. “It’s not hundreds of mutations, just a handful.”
But even with just a handful of mutations there can still be a wide ecosystem of variants.
For example, during Arizona’s surge in cases in November last year, TGen sequenced over 160 variants of COVID, Engelthaler said. Currently, that number has shrunk to less than 50 with three variants — Alpha, from the United Kingdom; Gamma from Brazil; and Delta — beginning to make up the majority of all sequenced samples.
That’s why Engelthaler said he is stressing the importance of continued sequencing and surveillance of COVID in the state as new variants appear.
“The more information we gather and have been gathering through sequencing, the more we are understanding what we didn’t know before,” Engelthaler said, citing an example of how TGen used sequencing to help identify if an outbreak was localized to a long-term care facility by seeing if the variants were all similar.
More vaccines will hamper new variants
More variants could be on the horizon, but there are some solutions to stemming the tide of cases.
“You can stop the spread of this variant just by getting the vaccine,” said Dr. Joshua LaBaer, executive director of ASU’s Biodesign Institute. “The more people we get vaccinated, the less we have to worry about these variants.”
Recent studies have shown that breakthrough cases happen for those who have been vaccinated, but those who were vaccinated were far less likely to be hospitalized than their unvaccinated counterparts. Meanwhile, one in five unvaccinated people who caught COVID-19 wound up in the intensive care unit.
“If you’re unvaccinated, it’s like a gun with five chambers and one of them is loaded to take you to the ICU,” LaBaer said.
Arizonans who are unvaccinated currently make up a majority of the cases of COVID in the state, and approximately 95% of all cases in May were from unvaccinated Arizonans.
In the end, it all comes down to a “numbers game,” as Webby put it.
Variants rely on people getting infected. The more people who get infected, the more likely a variant will appear, as the viruses mutate to continue their survival.
So if a virus has less people to infect, it will have less chance to replicate inside a host to create mutations. That’s why public health officials are pushing for everyone who can get vaccinated to get vaccinated.
“The vaccine is highly effective against the Delta variant, but you have to get the full vaccine series to get the maximum protection,” said Dr. Rebecca Sunenshine, medical director for disease control at the Maricopa County Department of Public Health in a press statement about an outbreak of COVID at a nursing home. “The majority of people who get the Delta variant are not fully vaccinated.”
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