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Omicron sub-variants BA.4 and BA.5 found in Santa Clara County’s wastewater as cases continue to climb

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Two highly contagious omicron subvariants that recently swept through South Africa and sparked a rapid rise in coronavirus cases in that country have been detected in Santa Clara County’s wastewater systems, according to public health officials.

Health experts say the newly discovered subvariants — BA. 4 and BA.5 — are more transmissible than the nation’s current dominant variants — BA.2 and BA.2.12.1 — and have so far evaded immunity protection. This month, the European Centers for Disease Control recently classified the two strains as “variants of concern.”

Though the new subvariants account for about one percent of the total amount of COVID-19 measured in the county’s four wastewater sites, it remains to be seen whether it will become the dominant strain in Santa Clara County, said UC Berkeley epidemiologist Dr. John Swartzberg..

BA.4 and BA.5 has been present in the United States over the last couple of months and last week San Diego health officials announced that BA.4 was the source of a handful of infections.

“In South Africa, BA.4 and BA.5 have played a considerable role in the surge that they’re coming out of,” said Swartzberg. “While we know about the virus and its increased transmissibility, we don’t understand why it took off in South Africa and why it has not taken off elsewhere. It doesn’t mean it won’t.”

Santa Clara County’s Deputy Health Officer Dr. George Han concurred with Swartzberg’s analysis.

“At this point, we don’t know which one will come out on top,” said Han. “What we do know is that we will continue to have more and more subvariants. It is to be expected. Sooner or later, they’re going to find they’re way here. The real question is, how are they going to compete with all the other subvariants. If they compete and gain dominance, that’s when you’ll start seeing population impact.”

According to the Centers for Disease Control’s latest data, the BA.2.12.1 subvariant accounts for up to 62 percent of cases across the country, while BA.2 represents up to 44 percent of cases.

The discovery of the two new subvariants comes amid a recent upswing in COVID-19 cases and hospitalizations within Santa Clara County.

The county is currently experiencing a seven-day moving average of 971 cases — almost twice the number of cases during the height of the Delta wave last summer and about a fourth of the number of cases during the winter omicron surge. Hospitalizations are also slowly rising, with the number of COVID-19 patients currently at 132, compared to 68 in mid-April. Deaths still remain low, though they tend spike weeks after hospitalizations level off.

The county’s wastewater data, which has been seen as an early-warning system for public health officials to determine the trends of the virus, are showing ever increasing amounts of COVID-19, according to Marlene Wolfe, who is part of a Stanford University team that samples wastewater within the county and other parts of the state.



Two highly contagious omicron subvariants that recently swept through South Africa and sparked a rapid rise in coronavirus cases in that country have been detected in Santa Clara County’s wastewater systems, according to public health officials.

Health experts say the newly discovered subvariants — BA. 4 and BA.5 — are more transmissible than the nation’s current dominant variants — BA.2 and BA.2.12.1 — and have so far evaded immunity protection. This month, the European Centers for Disease Control recently classified the two strains as “variants of concern.”

Though the new subvariants account for about one percent of the total amount of COVID-19 measured in the county’s four wastewater sites, it remains to be seen whether it will become the dominant strain in Santa Clara County, said UC Berkeley epidemiologist Dr. John Swartzberg..

BA.4 and BA.5 has been present in the United States over the last couple of months and last week San Diego health officials announced that BA.4 was the source of a handful of infections.

“In South Africa, BA.4 and BA.5 have played a considerable role in the surge that they’re coming out of,” said Swartzberg. “While we know about the virus and its increased transmissibility, we don’t understand why it took off in South Africa and why it has not taken off elsewhere. It doesn’t mean it won’t.”

Santa Clara County’s Deputy Health Officer Dr. George Han concurred with Swartzberg’s analysis.

“At this point, we don’t know which one will come out on top,” said Han. “What we do know is that we will continue to have more and more subvariants. It is to be expected. Sooner or later, they’re going to find they’re way here. The real question is, how are they going to compete with all the other subvariants. If they compete and gain dominance, that’s when you’ll start seeing population impact.”

According to the Centers for Disease Control’s latest data, the BA.2.12.1 subvariant accounts for up to 62 percent of cases across the country, while BA.2 represents up to 44 percent of cases.

The discovery of the two new subvariants comes amid a recent upswing in COVID-19 cases and hospitalizations within Santa Clara County.

The county is currently experiencing a seven-day moving average of 971 cases — almost twice the number of cases during the height of the Delta wave last summer and about a fourth of the number of cases during the winter omicron surge. Hospitalizations are also slowly rising, with the number of COVID-19 patients currently at 132, compared to 68 in mid-April. Deaths still remain low, though they tend spike weeks after hospitalizations level off.

The county’s wastewater data, which has been seen as an early-warning system for public health officials to determine the trends of the virus, are showing ever increasing amounts of COVID-19, according to Marlene Wolfe, who is part of a Stanford University team that samples wastewater within the county and other parts of the state.

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