Category Archives: Delta variant

Virus mutations aren’t slowing down. New omicron subvariant proves it.

Coronavirus testing sites remain in business more than two years after the pathogen emerged. A medical worker administers tests April 18 in New York. (Spencer Platt/Getty Images)
Washington Post, By Joel Achenbach, May 1, 2022

During those terrifying early days of the pandemic, scientists offered one piece of reassuring news about the novel coronavirus: It mutated slowly. The earliest mutations did not appear to be consequential. A vaccine, if and when it was invented, might not need regular updating over time.

This proved overly optimistic.

The coronavirus, SARS-CoV-2, has had billions of chances to reconfigure itself as it has spread across the planet, and it continues to evolve, generating new variants and subvariants at a clip that has kept scientists on their toes. Two-and-a-half years after it first spilled into humans, the virus has repeatedly changed its structure and chemistry in ways that confound efforts to bring it fully under control.

And it’s not showing signs of settling down into a drowsy old age. Even with all the changes so far, it still has abundant evolutionary space to explore, according to virologists who are tracking it closely. What that means in practical terms is that a virus that’s already extremely contagious could become even more so.

“This virus has probably got tricks we haven’t seen yet,” virologist Robert F. Garry of Tulane University said. “We know it’s probably not quite as infectious as measles yet, but it’s creeping up there, for sure.”

The latest member of the rogue’s gallery of variants and subvariants is the ungainly named BA.2.12.1, part of the omicron gang. Preliminary research suggests it is about 25 percent more transmissible than the BA.2 subvariant that is currently dominant nationally, according to the Centers for Disease Control and Prevention. The CDC said the subvariant has rapidly spread in the Northeast in particular, where it accounts for the majority of new infections.

“We have a very, very contagious variant out there. It is going to be hard to ensure that no one gets covid in America. That’s not even a policy goal,” President Biden’s new covid-19 coordinator, Ashish Jha, said in his inaugural news briefing Tuesday.

He was answering a question about Vice President Harris, who recently tested positive for the virus and went into isolation. Harris had recently been boosted for the second time — her fourth shot of vaccine.

Her case highlights what has become painfully obvious in recent months: No amount of vaccination or boosting can create a perfect shield against infection from SARS-CoV-2. What the vaccines do very well, however, is greatly reduce the risk of severe illness. That is hugely consequential as a matter of public health, as is the wider use of therapeutics, such as the antiviral Paxlovid.

The vaccines currently deployed were all based on the genomic sequence of the original strain of the virus that spread in late 2019 in Wuhan, China. They essentially mimic the spike protein of that version of the virus and trigger an immune response that is protective when the real virus shows up.

But the variants that have emerged can evade many of the neutralizing antibodies that are the immune system’s front line of defense.

“It’s evolving at a fairly rapid rate,” said Jesse Bloom, a computational biologist at the Fred Hutchinson Cancer Research Center in Seattle. “I do think we need to aggressively consider whether we should update vaccines, and do it soon.”

Vaccines have reduced the virus’s worst effects. Community of Hope clinical nurse manager Imani Mark injects Ezekiel Akinyeni with a shot July 31, 2021, in D.C. (Craig Hudson/For the Washington Post)

BA.2.12.1 brings the novel coronavirus up another step on the contagiousness scale. Its close relative, BA.2, was already more transmissible than the first omicron strain that hit the country in late 2021.

And omicron was more transmissible than delta, and delta was more transmissible than alpha, and alpha was more transmissible than earlier variants that did not have the glory of a Greek alphabet name.

Most mutations are not advantageous to the virus. But when a mutation offers some advantage, the process of natural selection will favor it.

There are two fundamental ways that the virus can improve its fitness through mutation. The first could be described as mechanical: It can become innately better at infecting a host. Perhaps it improves its ability to bind to a receptor cell. Or perhaps the mutation allows the virus to replicate in greater numbers once an infection has begun — increasing the viral load in the person and, commensurately, the amount of virus that is shed, potentially infecting other people.

The other strategy involves the workaround of immunity. The human immune system, when primed by vaccines or previous infection to be alert for a specific virus, will deploy antibodies that recognize and neutralize it. But mutations make the virus less familiar to the immune system’s front-line defense.

The omicron subvariants keep coming: Scientists in South Africa have identified BA.4 and BA.5, which have mutations that were seen in earlier variants and are associated with immune evasion. Caseloads there are rising. New laboratory research, posted online Sunday but not yet peer-reviewed, indicated that the emerging subvariants are adept at eluding the neutralizing antibodies seen in people who recovered from infections with the original omicron variant. The authors of the study concluded that BA.4 and BA.5 have the “potential to result in a new infection wave.”

“The evolution is much more rapid and expansive than we initially estimated,” said Michael T. Osterholm, a University of Minnesota infectious-disease expert. “Every day I wake up, I fear there will be a new subvariant that we will have to consider. … We’re seeing subvariants of subvariants.”

Garry, the Tulane scientist, points out that mutations in the virus do not change its appearance dramatically. In fact, he said, even the heavily mutated variants don’t look much different from the original Wuhan strain, or different from other coronaviruses that cause common colds. These are subtle changes.

Garry has a software program that allows him to create a graphic image of the virus, and even rotate it, to observe the locations of mutations and draw inferences for why they matter. On Friday, asked about BA.2.12.1, and why it is spreading, he noted it has a mutation, named S704L, that probably destabilizes a portion of the spike protein on the virus’s surface. That essentially loosens up part of the spike in a way that facilitates infection.

This S704L mutation distinguishes this subvariant from BA.2.

The “704” refers to the 704th position for an amino acid on a chain of roughly 1,100 amino acids that form the protein. The S is one type of amino acid (“serine”) seen in the original strain of the virus, and the L (“leucine”) is what is there after the mutation. (The mutation is caused by a change in one nucleotide, or “letter,” in the genetic code of the virus; three nucleotides encode for an amino acid.)

The virus is spreading today in the United States on an immunological landscape much different from the one it first encountered in early 2020. Between vaccinations and infections, there aren’t many people entirely naive to the virus. The latest CDC data suggest the virus has managed to infect nearly 200 million people in the nation, which has a population of about 330 million. Among children and teenagers, about three out of four have been infected, the CDC estimates.

For the new CDC study, researchers looked at blood samples from thousands of people and searched for an antibody that is found after a natural infection, but not found after vaccination. The CDC concluded that the omicron variant managed to plow through the United States population during the winter almost as if it were an entirely new virus. The country by then was largely vaccinated. And yet 80 million people, approximately, became infected for the first time in that omicron wave.

On the family tree of this coronavirus, omicron is a distant cousin of delta, alpha and the other variants that had spread earlier — it came out of virologic left field. No one is sure of the origin of omicron, but many disease experts assume it came from an immunocompromised patient with a very lengthy illness, and the virus continued to use mutations to evade the immune system’s efforts to clear it.

Technicians inside a high-security coronavirus research lab in Durban, South Africa, on Dec. 15, 2021. (Waldo Swiegers/Bloomberg)

Omicron was mercifully less likely to kill a person than previous variants. But infectious-disease experts are clear on this point: Future variants could be more pathogenic.

As if mutation wasn’t enough of a problem, the virus has another trick up its sleeve: recombination. It happens when two distinct strains infect a single host simultaneously and their genes becoming entangled. The recombination process is the origin of what’s known as omicron XE. That recombinant probably emerged from a person co-infected with the original omicron variant and the BA.2 subvariant.

It was always possible in theory, but the identification of actual recombinants provides “proof of concept,” as Jeremy Luban, a virologist at the University of Massachusetts Medical School, puts it.

The worst-case scenario would be the emergence of a variant or recombinant that renders current vaccines largely ineffective at blocking severe disease. But so far, that hasn’t happened. And no “recombinant” has spread like omicron or other recent variants and subvariants.

This is the first catastrophic pandemic to occur in the age of modern genomic sequencing. A century ago, no one knew what a coronavirus was, and even a “virus” was a relatively new concept. But today, with millions of samples of the virus analyzed at the genetic level, scientists can track mutations virtually in real time and watch the virus evolve. Scientists across the planet have uploaded millions of sequences to the database known as GISAID.

Genomic sequencing has a major limitation in that, although scientists can track changes in the genome, they don’t automatically know what each of those changes is doing to the virus. Which mutations matter most is a question that can be discerned through laboratory experiments, modeling or epidemiological surveillance, but it’s not always simple or obvious.

Erica Saphire, president of the La Jolla Institute for Immunology, speculates that omicron has mutations that have changed the virus in ways not yet understood but which make it more resistant to antibody-mediated neutralization.

“It may have acquired some new trick that we haven’t uncovered yet,” Saphire said. “It’s harder to neutralize than I would have expected, based on the number of mutations alone.”

A reality check comes from Jeremy Kamil, associate professor of microbiology and immunology at Louisiana State University Health Shreveport: “These are all SARS-CoV-2.”

What he means is that these are all variations of the same virus, despite what seems like a tremendous amount of mutation. Correspondingly, someone who gets infected with one of these new variants has the same disease as people who got infected previously.

“They got covid,” he said.

Seven new COVID deaths reported in Solano County, Benicia’s 7-day transmission rate is HIGH

NOTE: This information is archived.  Click HERE for today’s latest information

By Roger Straw, Wednesday, October 13, 2021

Wednesday, October 13: Solano County reports 7 new deaths and 207 new infections, remains in the CDC’s SUBSTANTIAL transmission rate.  Benicia sees 24 new cases, still in HIGH transmission rate.

Solano County COVID dashboard SUMMARY:
[Sources: see below.]

DEATHS: Solano reported 7 new COVID-related deaths today, 2 age 50-64 and 5 age 65+; including 1 each Black and White, and 2 each Hispanic and Multi-raceThe County has reported 42 COVID deaths just since Sept 1.  A total of 312 Solano residents have died of COVID or COVID-related causes over the course of the pandemic.

CASES: The County reported 207 new COVID cases over the holiday weekend, 41 per day.  AGES: 40 of these 207 cases (19%) were youth and children under 18.  48% were age 18-49, 21% were age 50-64, and only 11% were 65+.

COMMUNITY TRANSMISSION RATE: Over the last 7 days, Solano has seen 413 new cases, up from 375  on last Friday.  This increase isn’t enough to move Solano up into the CDC’s population-based definition of a HIGH transmission rate, but it’s not far off.  Solano remains in SUBSTANTIAL transmission rate.

(CDC FORMULA: Based on Solano County population of 449,432, the CDC would rate us in “SUBSTANTIAL” transmission with 225 cases over the last 7 days.  Double that, or 450 cases in the last 7 days would rank us in “HIGH” transmission.  Reference: CDC’s “Level of SARS-CoV-2 Community Transmission”.]

ACTIVE CASES: Solano’s 396 ACTIVE cases is down from last Friday’s 486, but still far above our summer rates.

CASES BY CITY on Wednesday, October 13:

    • Benicia added 24 new cases today, a total of 1,491 cases since the outbreak began.  Although Benicia’s population is only 6.2% of Solano’s total, today’s 24 new Benicia cases are nearly double that (11.6%) as a percentage of today’s 207 new cases.  Benicia has seen 31 new cases over the last 7 days, continuing in the CDC’s definition of HIGH community transmission (defined as 28 or more cases, based on Benicia population – SEE CHART BELOW).  [Note that Solano County is at a level of SUBSTANTIAL transmission, and Solano’s 6 other cities (below) are likely also individually experiencing high or substantial transmission.]

    • Dixon added 11 new cases today, total of 2,510 cases.
    • Fairfield added 49 new cases today, total of 12,072 cases.
    • Rio Vista added 9 new cases today, total of 591 cases.
    • Suisun City added 14 new cases today, total of 3,190 cases.
    • Vacaville added 49 new cases today, a total of 11,834 cases.
    • Vallejo added 51 new cases today, a total of 13,208 cases.
    • Unincorporated added 0 new cases today, a total of 139 cases (population figures not available).

POSITIVE TEST RATE:  Solano’s 7-day average percent positivity rate was 7.2% today, up substantially from last Friday’s 5.8%.  COMPARE: today’s California rate is 1.7% and today’s U.S. rate is 5.8%[Source: Johns Hopkins Coronavirus Tracking Center]

HOSPITALIZATIONS:

CURRENT hospitalizations were down today from 52 to 37 persons, our lowest number since July 23.  Good news!

ICU Bed Availability is up sharply today, from an alarmingly low 12% last Friday to 27% today, but still in the yellow danger zone.  We remain in the worrisome range we saw during last winter’s surge.

Ventilator Availability is down slightly today from 51% to 46%, still in the range of last winter’s surge.

TOTAL hospitalizations: Solano County’s TOTAL hospitalized over the course of the pandemic must be independently discovered in the County’s occasional update of hospitalizations by Age Group and by Race/Ethnicity.  The County updated its Hospitalizations charts today.  See below.  The differing race/ethnicity numbers indicate a number of persons whose race/ethnicity was not given or recorded.

FACE MASKS… Required for all in Benicia and Vallejo

Benicia City Council passed a citywide indoors mask mandate that went into effect on August 24 and includes everyone 4 years old and up when indoors in public places, even those of us who are vaccinated.  Benicia was joined by Vallejo on August 31.  In the Bay Area, Solano County REMAINS the only holdout against a mask mandate for public indoors spaces.

SOLANO COUNTY BOARD OF SUPERVISORS failed to consider an agendized proposal for a countywide MASK MANDATE on Tuesday, September 14.  Last week’s Bay Area news put Solano in a sad light: all other county health officers issued a joint statement offering details on when they would be able to lift mask mandates (not likely soon).  TV news anchors had to point out that Solano would not be considering such a move since our health officer had not been able to “justify” a mask mandate in the first place.  The Solano Board of Supervisors has joined with Dr. Bela Matyas in officially showing poor leadership on the COVID-19 pandemic.


HOW DOES TODAY’S REPORT COMPARE?  See recent reports and others going back to April 20, 2020 on my ARCHIVE of daily Solano COVID updates (an excel spreadsheet).


>>The data on this page is from the Solano County COVID-19 Dashboard.  The Dashboard is full of much more information and updated Monday, Wednesday and Friday around 4 or 5pm.  On the County’s dashboard, you can hover a mouse or click on an item for more information.  Note the tabs at top for “Summary, Demographics” and “Vaccines.”  Click here to go to today’s Solano County Dashboard.


Sources

Solano falls today into CDC’s “Substantial” COVID transmission range, Benicia remains in “High” range


By Roger Straw, Friday, October 8, 2021

Friday, October 8: Solano County reports 124 new infections, drops from HIGH to SUBSTANTIAL transmission rate.  Benicia remains just barely in HIGH transmission rate.

Solano County COVID dashboard SUMMARY:
[Sources: see below.]

DEATHS: Solano reported no new COVID-related deaths todayBut the County reported 39 COVID deaths over the last 39 days (from August 30).  A total of 305 Solano residents have died of COVID or COVID-related causes over the course of the pandemic.

CASES: The County reported 124 new COVID cases over the last two days, 62 per day.  AGES: 18 of these 124 cases (15%) were youth and children under 18.  52% were age 18-49, 16% were age 50-64, and 18% were 65+.

COMMUNITY TRANSMISSION RATE: Over the last 7 days, Solano has seen 375 new cases, down from 451  on Wednesday and 639 on Monday.  This good news drops Solano into the CDC’s population-based definition of a SUBSTANTIAL transmission rate for only the 2nd time since July 21.

(CDC FORMULA: Based on Solano County population of 449,432, the CDC would rate us in “SUBSTANTIAL” transmission with 225 cases over the last 7 days.  Double that, or 450 cases in the last 7 days would rank us in “HIGH” transmission.  Reference: CDC’s “Level of SARS-CoV-2 Community Transmission”.]

ACTIVE CASES: Solano’s 486 ACTIVE cases is up from Wednesday’s 467, and still far above our summer rates.

POSITIVE TEST RATE:  Solano’s 7-day average percent positivity rate was only 5.8% today, down from Wednesday’s 6.2%.  COMPARE: today’s California rate is 2.1% and today’s U.S. rate is 6.3%[Source: Johns Hopkins Coronavirus Tracking Center]

HOSPITALIZATIONS:

CURRENT hospitalizations were up today from 50 to 52 persons, and still in the range we saw during the winter surge.

ICU Bed Availability is down sharply today, from 29% to an alarming 12%, barely above the red warning zone.  We saw rates this low once in September and twice in August – and before that, not since January.  Again, we are in the worrisome range we saw during the winter surge.

Ventilator Availability is up slightly today from 49% to 51%, but still in the range of last winter’s surge.

TOTAL hospitalizations: Solano County’s TOTAL hospitalized over the course of the pandemic must be independently discovered in the County’s occasional update of hospitalizations by Age Group and by Race/Ethnicity.  The County updated its Hospitalizations charts today.  See below.  The differing race/ethnicity numbers indicate a number of persons whose race/ethnicity was not given or recorded.

FACE MASKS… Required for all in Benicia and Vallejo

Benicia City Council passed a citywide indoors mask mandate that went into effect on August 24 and includes everyone 4 years old and up when indoors in public places, even those of us who are vaccinated.  Benicia was joined by Vallejo on August 31.  In the Bay Area, Solano County REMAINS the only holdout against a mask mandate for public indoors spaces.

SOLANO COUNTY BOARD OF SUPERVISORS failed to consider an agendized proposal for a countywide MASK MANDATE on Tuesday, September 14.  Today’s Bay Area news put Solano in a sad light: all other counties’ health officers issued a statement offering details on when they would be able to lift mask mandates (not likely soon).  TV news anchors had to point out that Solano would not be considering such a move since our health officer had not been able to “justify” a mask mandate in the first place.  The Solano Board of Supervisors has joined with Dr. Bela Matyas in officially showing poor leadership on the COVID-19 pandemic.

Cases by City on Friday, October 8:
    • Benicia added 7 new cases today, a total of 1,467 cases since the outbreak began.  Benicia has seen 28 new cases over the last 7 days, continuing (just barely) in the CDC’s definition of HIGH community transmission (defined as 28 or more cases, based on Benicia population – SEE CHART BELOW).  [Note that Solano County is at a level of HIGH transmission, and Solano’s 6 other cities are likely also individually experiencing high or substantial transmission.]

    • Dixon added 6 new cases today, total of 2,499 cases.
    • Fairfield added 29 new cases today, total of 12,023 cases.
    • Rio Vista added 6 new cases today, total of 582 cases.
    • Suisun City added 6 new cases today, total of 3,176 cases.
    • Vacaville added 36 new cases today, a total of 11,785 cases.
    • Vallejo added 34 new cases today, a total of 13,157 cases.
    • Unincorporated added 0 new cases today, a total of 139 cases (population figures not available).

HOW DOES TODAY’S REPORT COMPARE?  See recent reports and others going back to April 20, 2020 on my ARCHIVE of daily Solano COVID updates (an excel spreadsheet).


>>The data on this page is from the Solano County COVID-19 Dashboard.  The Dashboard is full of much more information and updated Monday, Wednesday and Friday around 4 or 5pm.  On the County’s dashboard, you can hover a mouse or click on an item for more information.  Note the tabs at top for “Summary, Demographics” and “Vaccines.”  Click here to go to today’s Solano County Dashboard.


Sources

Solano County reports only 82 new COVID infections (but transmission remains HIGH)


By Roger Straw, Wednesday, October 6, 2021

Wednesday, October 6: Solano County reports 82 new infections, 13 in Benicia

Solano County COVID dashboard SUMMARY:
[Sources: see below.]

DEATHS: Solano reported no new COVID-related deaths todaySolano deaths over the course of the pandemic now total 305The County reported 32 COVID deaths over the last 32 days.

CASES: The County reported 82 new COVID cases over the last two days, 41 per day.  AGES: 13 of these 82 cases (16%) were youth and children under 18.  59% were age 18-49, 21% were age 50-64, and only 6% were 65+.

COMMUNITY TRANSMISSION RATE: Over the last 7 days, Solano has seen 451 new cases, down from 639 on Monday but still just barely in the CDC’s population-based definition of a HIGH transmission rate.

(CDC FORMULA: Based on Solano County population of 449,432, the CDC would rate us in “SUBSTANTIAL” transmission with 225 cases over the last 7 days.  Double that, or 450 cases in the last 7 days would rank us in “HIGH” transmission.  Reference: CDC’s “Level of SARS-CoV-2 Community Transmission”.]

ACTIVE CASES: Solano’s 467 ACTIVE cases is down from Monday’s 514, but still far above our summer rates.

POSITIVE TEST RATE:  Solano’s 7-day average percent positivity rate was only 6.2% today, down from Monday’s 6.7%.  COMPARE: today’s California rate is 1.9% and today’s U.S. rate is 6.3%[Source: Johns Hopkins Coronavirus Tracking Center]

HOSPITALIZATIONS:

CURRENT hospitalizations were down today from 53 to 50 persons, and still in the range we saw during the winter surge.

ICU Bed Availability is up today, from 23% to 29%, but still in the yellow danger zone.  Again, we are in the worrisome range we saw during the winter surge.

Ventilator Availability is down today from 53% to 49%, still in the range of last February’s winter surge.

TOTAL hospitalizations: Solano County’s TOTAL hospitalized over the course of the pandemic must be independently discovered in the County’s occasional update of hospitalizations by Age Group and by Race/Ethnicity.  The County did not update its Hospitalizations charts today.  See below.  The differing race/ethnicity numbers indicate a number of persons whose race/ethnicity was not given or recorded.

FACE MASKS… Required for all in Benicia and Vallejo

Benicia City Council passed a citywide indoors mask mandate that went into effect on August 24 and includes everyone 4 years old and up when indoors in public places, even those of us who are vaccinated.  Benicia was joined by Vallejo on August 31.  In the Bay Area, Solano County REMAINS the only holdout against a mask mandate for public indoors spaces.

OLD NEWS BUT SIGNIFICANT – SOLANO COUNTY BOARD OF SUPERVISORS failed to consider an agendized proposal for a countywide MASK MANDATE on Tuesday, September 14.  The Board’s agenda called for discussion of an indoors mask mandate for all and a vaccination mandate for county workers.  The Board voted 4-1 to require county-run facilities in Vallejo and Benicia to abide by local mandates.  But the Board voted down the vaccination mandate 3-2, and failed to even consider the agendized question of a county-wide mask mandate.  The Solano Board of Supervisors joined with Dr. Bela Matyas in officially showing poor leadership on the COVID-19 pandemic.

Cases by City on Wednesday, October 6:
  • Benicia added 13 new cases today, a total of 1,460 cases since the outbreak began.  Benicia has seen 38 new cases over the last 7 days, continuing in the CDC’s definition of HIGH community transmission (defined as 28 or more cases, based on Benicia population).  [Note that Solano County is at a level of HIGH transmission, and Solano’s 6 other cities are likely also individually experiencing high or substantial transmission.]
  • Dixon added 6 new cases today, total of 2,493 cases.
  • Fairfield added 14 new cases today, total of 11,994 cases.
  • Rio Vista added 5 new case today, total of 576 cases.
  • Suisun City added 4 new cases today, total of 3,170 cases.
  • Vacaville added 13 new cases today, a total of 11,749 cases.
  • Vallejo added 27 new cases today, a total of 13,123 cases.
  • Unincorporated added 0 new cases today, a total of 139 cases (population figures not available).

HOW DOES TODAY’S REPORT COMPARE?  See recent reports and others going back to April 20, 2020 on my ARCHIVE of daily Solano COVID updates (an excel spreadsheet).


>>The data on this page is from the Solano County COVID-19 Dashboard.  The Dashboard is full of much more information and updated Monday, Wednesday and Friday around 4 or 5pm.  On the County’s dashboard, you can hover a mouse or click on an item for more information.  Note the tabs at top for “Summary, Demographics” and “Vaccines.”  Click here to go to today’s Solano County Dashboard.


Sources

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