New research by a team at Houston Methodist Hospital in the United States has modeled the aggressive genomic sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) observed in the United Kingdom to document viral community spread in Houston, Texas.
Houston has thus become the first American city to document four SARS-CoV-2 variants of concern.
Here we report discovery of the UK (B.1.1.7), South Africa (B.1.351), and Brazil (P.1) SARS-CoV-2 variants of concern from patients in the Houston metropolitan region. We also identified geographically-widespread dissemination of the Cal.20C California (B.1.429 and B.1.427) variants of interest. These four SARS-CoV-2 variants are distributed across a large geospatial region in the metropolitan region, indicating successful patient-to-patient transmission among Houstonians.”
The results coincide on the same day government officials in Texas lifted the mask mandate and allowed all businesses to reopen.
The United States currently leads the world with the highest number of coronavirus cases at over 28.7 million cases and the highest number of coronavirus-related deaths at around 518,000. Texas is the third-highest state for COVID-19 cases, with over 2.6 million cases to date.
The study “Sequence Analysis of 20,453 SARS-CoV-2 Genomes from the Houston Metropolitan Area Identifies the Emergence and Widespread Distribution of Multiple Isolates of All Major Variants of Concern” is available as a preprint on the medRxiv* server, while the article undergoes peer review.
Extensive genomic surveillance in a Houston hospital
Starting from March 2020, the team collected 20,453 viral samples from patients hospitalized in Houston Methodist Hospital who lived in Houston and showed COVID-19 symptoms.
The dataset represents 56% of the hospitalized patients with COVID-19 and 4.1% of all cases in the Houston area.
Due to the very wide geographic catchment of our eight-hospital system that serves a very diverse patient population, the data presented here likely reflect a reasonably detailed overview of SARS-CoV-2 genomic diversity throughout our metroplex,” wrote the researchers.
Virus genome sequencing was used to identify variants of concern. Viral samples positive for a variant were traced back to the geographic location where it most likely was spreading. The researchers collected home addresses and zip codes from patients to analyze the geospatial distribution of COVID transmission per variant.
Identifying multiple variants of concern in Houston, Texas
The researchers identified 23 patients with B.1.1.7 variants. The first three patients identified with the B.1.1.7 variant — initially detected in the United Kingdom — did not travel internationally, which means it may have been obtained through local or domestic travel.
Two patients were identified with the B.1.351 variant that was first found in South Africa. They also did not travel internationally, which suggests domestic spread and acquisition of the virus.
About four patients had the P.1 variants, and 39 patients had the P.2 variant — both found initially in Brazil. Although P.2 only caused a few infections, the researchers found it was the most common COVID variant of concern in this population.
There were 143 patients positive for B.1.429 and 19 patients positive for B.1.427 — two lineages first identified in California. The variants were found in the last week of December 2020.
The California variants are noteworthy primarily for their emergence and very rapid spread in Los Angeles County and identification elsewhere in the US. However, as of February 17, 2021, they have not been designated as variants of concern by the Centers for Disease Control,” wrote the researchers.
Except for the B.1.351 variant, all other variants were widespread throughout the metropolitan area. The researchers suggest this result is consistent with previous studies finding a rapid spread of variants amongst individuals.
The E484K mutation was found 84 times or in 0.4% of the total sequenced genome. The Q677H amino acid change in the spike protein was detected 288 times or in 1.4% of Houston genomes. The 677P amino acid change was detected in 330 genomes, and the Q677K was found in only two genomes.
medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.