key: cord-0882440-jznymitp authors: Long, S. Wesley; Olsen, Randall J.; Christensen, Paul A.; Subedi, Sishir; Olson, Robert; Davis, James J.; Saavedra, Matthew Ojeda; Yerramilli, Prasanti; Pruitt, Layne; Reppond, Kristina; Shyer, Madison N.; Cambric, Jessica; Finkelstein, Ilya J.; Gollihar, Jimmy; Musser, James M. title: 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 date: 2021-03-16 journal: Am J Pathol DOI: 10.1016/j.ajpath.2021.03.004 sha: 45f653f2855e2a752f4cb6c90a5cd6dbe94b9547 doc_id: 882440 cord_uid: jznymitp Since the beginning of the SARS-CoV-2 pandemic, there has been international concern about the emergence of virus variants with mutations that increase transmissibility, enhance escape from the human immune response, or otherwise alter biologically important phenotypes. In late 2020, several “variants of concern” emerged globally, including the UK variant (B.1.1.7), South Africa variant (B.1.351), Brazil variants (P.1 and P.2), and two related California “variants of interest” (B.1.429 and B.1.427). These variants are believed to have enhanced transmissibility. For the South Africa and Brazil variants, there is evidence that mutations in spike protein permit it to escape from some vaccines and therapeutic monoclonal antibodies. Based on our extensive genome sequencing program involving 20,453 COVID-19 patient samples collected from March 2020 to February 2021, we report identification of all six of these SARS-CoV-2 variants among Houston Methodist Hospital patients residing in the greater metropolitan area. Although these variants are currently at relatively low frequency (aggregate of 1.1%) in the population, they are geographically widespread. Houston is the first city in the United States in which active circulation of all six current variants of concern has been documented by genome sequencing. As vaccine deployment accelerates, increased genomic surveillance of SARS-CoV-2 is essential to understanding the presence, frequency, and medical impact of consequential variants and their patterns and trajectory of dissemination. late 2020, several "variants of concern" emerged globally, including the UK variant (B. United States in which active circulation of all six current variants of concern has been 58 documented by genome sequencing. As vaccine deployment accelerates, increased genomic 59 Introduction B.1.1.7, Brazil P.1, and South Africa B.1.351) also have a N501Y mutation in spike protein that is 109 associated with stronger binding to the ACE2 receptor, possibly contributing to increased 110 transmissibility. 31,32 111 The Houston metropolitan area is the fifth largest and most ethnically diverse city in the 112 US, with a population of approximately 7 million (https://www.houston.org/houston-data/us-113 most-populous-metro-areas Last accessed: March 9, 2021). 33 The 2,400-bed Houston Methodist 114 health system has eight hospitals and cares for a large, multiethnic, and geographically and 115 socioeconomically diverse patient population throughout greater Houston. The eight Houston 116 Methodist hospitals have a single central molecular diagnostic laboratory, which means that all 117 RT-PCR-specimens can readily be identified, banked, and subjected to further study as needed. 118 In addition, the Department of Pathology and Genomic Medicine has a long-standing record of 119 integrating genome sequencing efforts into clinical care and research, especially related to 120 microbial pathogens infecting our patients. [34] [35] [36] [37] [38] [39] [40] [41] In the aggregate, strategic co-localization of 121 these diagnostic attributes coupled with a contiguous research institute building seamlessly 122 facilitates comprehensive population genomic studies of SARS-CoV-2 viruses causing infections 123 in the Houston metropolitan region. 38, 41 124 Before the SARS-CoV-2 virus arrived in Houston, we planned an integrated strategy to 125 confront and mitigate this microbial threat to our patients. In addition to rapidly validating an 126 RT-PCR test for the virus, we instituted a plan to sequence the genome of every positive 127 specimen from patients within the Houston Methodist system, with the goal of understanding 128 pathogen spread in our community and identifying biologically-important mutant viruses. We CoV-2 in the Houston metropolitan region. 38, 41 We have continued to sequence positive SARS-131 CoV-2 specimens with the goal of monitoring for variants of concern and genome mutations 132 that may be associated with patient outcome or therapeutic failure. 133 This report describes the identification of multiple isolates of important SARS-CoV-2 134 variants, including the UK B. The UK variant known as B.1.1.7 was first identified in September 2020 in the UK and was 205 designated as a variant of concern in South London on December 14, 2020. It was strongly 206 associated with a resurgence of SARS-CoV-2 infections in that region and rapidly became the 207 dominant lineage. 20 Importantly, the UK has the most extensive SARS-CoV-2 genome 208 sequencing program in the world, making them particularly well situated to rapidly identify new 209 variants. Of the ~500,000 SARS-CoV-2 genome sequences submitted to GISAID from global 210 sources, approximately one-half originated from collaborating laboratories in the UK as part of 211 the COVID-19 Genomics UK Consortium. 46 212 The UK B.1.1.7 variant is of particular concern because it has an unusually large number 213 of genome mutations, including multiple changes in spike protein ( Figure 1 ). Some of the 214 amino acid deletion (del69-70) that has arisen in multiple SARS-CoV-2 genetic backgrounds and 216 is associated with increased transmissibility 20 . In addition, evidence has been presented from 217 the UK that B.1.1.7 strains may cause increased hospitalization and mortality. 15, 17, 47 The first 218 patient we identified in Houston with a B.1.1.7 variant was diagnosed in January 2021; thus far 219 we have identified 23 patients with this variant of concern (Table 1). Of note, none of our first 220 three patients had an international travel history, suggesting that they acquired the B. variants of concern or interest, testament to our extensive sequencing of COVID-19 patient 289 samples. 290 The P.2 variant gained recent attention in the scientific and lay press because it has 291 been reported to cause SARS-CoV-2 reinfections (https://virological.org/t/spike-e484k-292 mutation-in-the-first-sars-cov-2-reinfection-case-confirmed-in-brazil-2020/584 Last accessed: 293 Feburary 19, 2021). 54 We identified 39 P.2 infections among Houston patients. Although it is 294 currently a numerically minor cause of all Houston-area infections, P.2 is now the most 295 common SARS-CoV-2 variant of concern in our population. 296 The E484K amino acid replacement in spike protein is characteristic of P.1, P.2, and 297 B.1.351 strains (Figure 1 ). It has independently arisen in many different SARS-CoV-2 genomic 298 backgrounds, including some B.1.1.7 strains. 55 This amino acid replacement has caused 299 substantial public health concern due to its potentially detrimental effects on neutralizing Among our Houston SARS-CoV-2 genomes, E484K was detected 84 times (0.4% of the total 303 genomes sequenced). It was first detected in a respiratory specimen collected in July 2020, near 304 the peak of our second massive wave of infections, 38 and has been identified in many diverse 305 genomic backgrounds thereafter. Due to this strong signal of convergent evolution, we will 306 continue to closely monitor all Houston SARS-CoV-2 genomes for the E484K amino acid change. 307 Recently, the Q677H amino acid change in spike protein has been identified in SARS-308 CoV-2 patient samples collected in multiple US states and other global locations. 58, 59 Q677H has 309 arisen in at least six distinct genomic backgrounds. 59 A Q667P amino acid change has also been 310 identified. 59 Among the Houston genomes, Q677H occurred 288 times (1.4%) and is encoded 311 by two different nucleotide changes. We also identifed two other amino acid changes, 677P (in 312 330 genomes, 1.6%) and Q677K (2 genomes, <0.1%) in Houston. Taken together, these data 313 suggest selection for a yet to be determined biologic phenotype associated with amino acid 314 replacements at position 677. 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A: Schematic showing structural changes present in the spike protein of the major S1 domain-receptor binding domain; S1, S1 domain; S2, S2 domain. B: Mapping of important 656 changes onto the cryoEM structure of spike protein. The color scheme matches that used in 657 panel A. Blue (NTD), purple (RBD), orange (S1), and yellow (S2). Aggregate mutations present in 658 variants of concern are colored in red when amino acid residues are present in the resolved 659 structure. Left, side view of SARS-CoV-2 prefusion-stabilized spike