How many Delta cases are there in Fresno, Valley? Testing paints an incomplete picture
Dr. Rais Vohra knows there have been at least 30 people with confirmed cases of the Delta variant of coronavirus in Fresno County.
But it’s the number of cases he doesn’t know about that has him worried.
Vohra, interim health officer with the Fresno County Department of Public Health, said his office only finds out about variant strains of COVID-19 from state health officials two to three weeks after test samples are collected and sent to state testing labs. By that time, the figures are very likely outdated.
“These cases are really from reports that are a couple of weeks in the making just because our genetic testing for these variants is lagging behind at the state level,” Vohra said this month.
That backlog at the California Department of Public Health and its labs means the actual current number of variant cases is unknown, but perhaps 10 times what the county knows about.
At the global, national, state and local levels, health authorities are warning that the Delta, or B.1.617.2, variant of coronavirus first identified last October in India is proving to be more contagious than previous versions of COVID-19 that have arisen since the worldwide pandemic began more than a year and a half ago.
The fast-spreading strain, which is now estimated to represent almost 60% of all new coronavirus cases nationwide, also tends to hit victims harder if they come down with symptoms of the virus, Vohra said.
“For those of us who are not yet vaccinated, you need to be aware that this is the one that’s going to get you in the hospital,” he said. “I’m sure about that because that’s exactly what it’s doing around the country and around the world.”
An incomplete picture
Further confounding the accuracy of case estimates for the Delta variant and other mutated forms of the coronavirus is that most positive COVID-19 tests are not submitted for the detailed genomic sequencing that can determine the particular viral strain.
“Anyone who gets tested will get their swab … in the nose,” Vohra said. “With that PCR testing, we can find out – sometimes within an hour, sometimes it takes about a day – whether a person has COVID or not.”
But to be sent for variant analysis, samples have to meet certain criteria, Vohra said, including containing a high number of viruses or whether the person has been hospitalized or has a “breakthrough infection” of COVID-19 after being fully vaccinated.
Otherwise, the state randomly selects tests to be sent to labs. In June, the state health department reported that 11% of the cases in California were sequenced, down from 15% in May.
Statewide, California has experienced almost 3.8 million confirmed cases of COVID-19 since February 2020. As of last week, fewer than 81,000 samples had been sequenced in the state.
“That’s why … this is most likely an undercount of the actual number of Delta cases that we have in our county, and it’s very concerning to us,” Vohra said.
Madera County health officials say they also rely on the California Department of Public Health to notify them of Delta and other variant cases in the county – and experience the same delays in reporting.
As of Tuesday afternoon, the state health agency did not respond to questions submitted by The Bee this week about its genomic sequencing program, including the two- to three-week period for counties to get variant results back, numbers of variant cases by county, or how it determines which positive COVID-19 tests to send off for genomic sequencing.
The Tulare County Department of Health & Human Services has a public health lab that is capable of doing its own variant sequencing of test samples.
Of 24 Delta variant cases identified in Tulare County as of last week, all but one was detected “through sequencing efforts at our local Public Health Lab without delays,” said Carrie Monteiro, a spokesperson for the Tulare County health department. All COVID test samples collected by the county are tested at the local lab, where the turnaround time can be as short as a week, Monteiro added. Samples collected at state-sponsored testing sites may be sent to a state health lab in Valencia, in Southern California.
It’s a capability that is on Vohra’s wish list for Fresno County’s new public health lab, which is in the process of ramping up to full operations. But while the lab can do basic yes-or-no COVID-19 testing, he added, the lab does not currently include the technology for genomic sequencing.
Why does it matter?
The relatively small proportion of samples processed by the state, combined with the lag time, “obviously introduces a lot of delays,” Vohra said. “And during that two weeks, if that person’s not careful, they’re going to be spreading it to other people, or even before they got tested they managed to shed viral particles and spread it to other people.”
“This Delta variant, part of the reason we’re all talking about it is because it’s very contagious,” he added. “It likes to spread itself even faster than the other variants of the virus.”
In late April, the U.S. Centers for Disease Control estimated that the Delta strain represented almost less than 1% of all new coronavirus cases in the country. In less than three months, by early July, Delta’s proportion of new cases had ballooned to almost 58%.
By contrast, the B.1.1.7 variant – now dubbed the Alpha variant by the World Health Organization – that emerged in the United Kingdom last September accounted for almost 70% of new cases arising in the U.S. over a two-week period in late April and early May, but as of July 3 had subsided to less than 25% of new cases.
While the true number of variant cases in Fresno County remains uncertain, Vohra pointed to evidence that suggests the more contagious strain is being felt through a recent increase in the number of coronavirus cases locally.
As of Tuesday, Fresno County had 497 new cases of COVID-19 over a seven-day period, or an average of 71 per day. That included 295 cases since Friday. More people have also been hospitalized in Fresno County for confirmed or suspected coronavirus infections – 70 on Monday. That’s the highest number in almost two months, and includes 16 people sick enough to require treatment in intensive-care units.
A threat to reopening?
The rise in cases and increase in hospitalizations illustrate the potential for backsliding into another surge of cases that could jeopardize the relatively reent reopening of the economy after months of virus-prevention limitations on businesses and social activities.
“We’re not out of this pandemic and we need to be careful,” Vohra said. “We may be in for some turbulence as this Delta (strain) takes off here in Fresno County.”
Vohra and Dr. John Zweifler, another county health official, both pointed to the importance of vaccines and face masks as layers of protection, especially for the unvaccinated portion of the population.
“Delta variant cases are rising, particularly among the unvaccinated,” Zweifler said recently. “Fortunately, the number of hospitalizations and deaths have not increased as much, but 98% to 99% have been among the unvaccinated.”
“To sustain the reopening, those who are unvaccinated are expected to follow the California Department of Public Health face covering guidance and wear a face covering in public,” Zweifler added. “Everyone, including those who are vaccinated, should be aware of high-risk situations including being indoors, in crowds, and around unvaccinated and unmasked individuals and consider wearing a face covering in these settings.”
The percentage of coronavirus test samples that are coming back positive for the virus is also on the rise, Vohra said last week. “If nothing else has changed, if we haven’t started doing more testing and we’re not doing more selective testing, then why is the positivity rate going up?” he asked. “One explanation is we have a variant that’s more contagious and is now being found in more and more people as it makes its way across the population.”
This story was originally published July 20, 2021 at 2:04 PM.
