New research led 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 the spread of the viral community in Houston, Texas, which has thus become the first American city to document four variants of the SARS-CoV-2 concern. All three of the most well-known variants, English, South African and Brazilian, are present; in addition, the researchers identified the geographically widespread diffusion of Cal.20C California variants of interest (B.1.429 and B.1.427). These four variants of SARS-CoV-2 are spread across a large geospatial region in the metropolitan region, indicating successful patient-to-patient transmission among Houstonians. The findings coincide on the same day Texas government officials revoked the mask’s mandate and allowed all businesses to reopen.
The United States currently leads the world with the largest number of coronavirus cases with over 28.7 million cases and the largest number of coronavirus-related deaths with approximately 518,000. Texas is the third highest state for COVID-19 cases, with over 2.6 million cases to date. As of March 2020, the team collected 20,453 viral samples from patients admitted to Houston Methodist Hospital who lived in Houston and exhibited COVID-19 symptoms. The dataset represents 56% of hospitalized patients with COVID-19 and 4.1% of all cases in the Houston area. Due to the very large geographic basin of our system of eight hospitals serving a very diverse patient population, the data presented here likely reflects a reasonably detailed overview of SARS-CoV-2 genomic diversity across the Houston metropolitan area.
Genome sequencing of the virus was used to identify variants of concern. Viral samples positive for a variant were traced to the geographic location where it was most likely spreading. Researchers collected home addresses and patient postcodes to analyze the geospatial distribution of COVID transmission by variant. Researchers identified 23 patients with B.1.1.7 variants. The first three patients identified with variant B.1.1.7 (or English) did not travel internationally, meaning they may have been obtained through local or national travel. Two patients were identified with variant B.1.351 which was first found in South Africa. They also did not travel overseas, which suggests the spread and acquisition of the virus nationwide: about four patients had the P.1 variants and 39 patients had the P.2 variant, both of which were initially found in Brazil.
There were 143 B.1.429 positive patients and 19 B.1.427 positive patients – two lineages first identified in California. The variants were found in the last week of December 2020. With the exception of variant B.1.351, all other variants were widespread throughout the metropolitan area. The researchers suggest that this finding is consistent with previous studies that have found a rapid spread of variants among 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 the Houston genomes. The 677P amino acid change was detected in 330 genomes, and Q677K was found in only two genomes. California variants are notable primarily for their very rapid emergence and spread in Los Angeles County and for identification elsewhere in the United States.
Although the American CDCs still do not consider the Californian variants worthy of concern, as declared on February 17, the diffusion seems to be spreading. The strain, which the investigators designated as CAL.20C, is believed to be in part responsible for the dramatic increase in cases over the last four months. CAL.20C includes a virus variant that the California Department of Public Health reported January 17, based on data submitted by Cedars-Sinai and other investigators. This variant, dubbed L452R, is one of five recurring mutations that constitute the CAL.20C strain, which is propagating across the country, starting in Los Angeles. The emergence of the newly detected strain tracks to a time at or before the onset of the current spike in Southern California. Of further concern, using publicly available databases, scientists have detected the CAL.20C strain in multiple recent patient samples in Northern California, New York, Washington DC and even Oceania.
- edited by Dr. Gianfrancesco Cormaci, PhD; specialist in Clinical Biochemistry.