key: cord-0816168-b04exhnk
authors: Musser, J. M.; Olsen, R. J.; Christensen, P. A.; Long, S. W.; Subedi, S.; Davis, J. J.; Gollihar, J.
title: Rapid, widespread, and preferential increase of SARS-CoV-2 B.1.1.7 variant in Houston, TX, revealed by 8,857 genome sequences
date: 2021-03-24
journal: nan
DOI: 10.1101/2021.03.16.21253753
sha: 0c8f69182e153d22deb08bd6132664da889089c7
doc_id: 816168
cord_uid: b04exhnk

Genetic variants of the SARS-CoV-2 virus have become of great interest worldwide because they have the potential to detrimentally alter the course of the SARS-CoV-2 pandemic, and disease in individual patients. We recently sequenced 20,453 SARS-CoV-2 genomes from patients with COVID-19 disease in metropolitan Houston (population 7 million), dating from March 2020 to early February 2021. We discovered that all major variants of concern or interest are circulating in the region. To follow up on this discovery, we analyzed 8,857 genome sequences from patients in eight Houston Methodist hospitals dispersed throughout the metroplex diagnosed from January 1, 2021 to March 7, 2021. This sample represents 94% of Houston Methodist cases and 4.8% of all reported cases in metropolitan Houston during this period. We discovered rapid, widespread, and preferential increase of the SARS-CoV-2 UK B.1.1.7 throughout the region. The estimated case doubling time in the Houston area is 6.9 days. None of the 648 UK B.1.1.7 samples identified had the E484K change in spike protein that can cause decreased recognition by antibodies.

Genetic variants of the SARS-CoV-2 virus are now of considerable concern internationally because some have been reported to spread rapidly, cause unusually severe infections, and be less controlled by naturally acquired or vaccine-induced immunity. [1] [2] [3] [4] [5] [6] By sequencing 20,453 SARS-CoV-2 genomes dating from March 2020 to early February 2021, we recently demonstrated all major variants of concern (VOCs) or interest (VOIs) are circulating in metropolitan Houston (population 7 million). 4 These variants emerged in Houston in late December or early January. In the aggregate, the variants constituted only 1.1% of strains causing COVID-19 disease among patients in the eight Houston Methodist hospitals geographically dispersed throughout the metropolitan region. We identified 230 patients infected with a VOC or VOI, including 23 cases caused by B.1.1.7, a VOC reportedly increasing in frequency in several regions of the United States. 5 Given their potential to detrimentally alter the course of the SARS-CoV-2 pandemic, and disease in individual patients, we tested the hypothesis that VOC and VOI are increasing in disease frequency in metropolitan Houston. We also sought to determine if any of the VOC/VOI caused an unusually severe clinical course.

We sequenced the genomes of 8,857 SARS-CoV-2 from patient samples acquired January 1, 2021 through March 7, 2021 ( Figure 1A) using Illumina instruments. 4 This sample represents 94% of the 9,445 cases of COVID-19 diagnosed in the Houston Methodist system during this period. VOCs were identified based on genome sequence data and designated by Pangolin (https://cov-All rights reserved. No reuse allowed without permission.

(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. 

We identified 648 cases caused by VOC B.1.1.7 and discovered that the variant increased in frequency during the study period ( Figure 1A) ; in contrast, the other VOCs/VOIs did not (data not shown). Patients infected with B.1.1.7 were distributed throughout the entire metropolitan region ( Figure 1B) . Together, these data indicate rapid, widespread, and preferential dissemination of B.1.1.7 in the Houston area, with an estimated case doubling time of 6.9 days ( Figure 1C) (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. 

Paper from the New and Emerging Respiratory Virus Threats Advisory Group (NERVTAG) on new coronavirus (COVID-19) variant B.1.1.7. Posted

Genetic Variants of SARS-CoV-2-What Do They Mean?

The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity

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. medRxiv

Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States. medRxiv

Emergence of a Novel SARS-CoV-2 Variant in Southern California

Additional Information: Genome data used in this study have been deposited to GISAID. All rights reserved. No reuse allowed without permission.(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint this version posted March 24, 2021. ; https://doi.org/10.1101/2021.03.16.21253753 doi: medRxiv preprint All rights reserved. No reuse allowed without permission.(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.(which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint this version posted March 24, 2021. ; https://doi.org/10.1101/2021.03.16.21253753 doi: medRxiv preprint