key: cord-0800871-8vdknrdv
authors: Olsen, R. J.; Christensen, P.; Long, S. W.; Subedi, S.; Hodjat, P.; Olson, R.; Nguyen, M.; Davis, J.; Yerramilli, P.; Ojeda-Saavedra, M.; Pruitt, L.; Reppond, K.; Shyer, M.; Cambric, J.; Gadd, R.; Finkelstein, I.; Gollihar, J.; Musser, J.
title: Identification and trajectory of growth of concerning SARS-CoV-2 variants in Houston, Texas, January through April 2021 based on 11,568 genome sequences
date: 2021-05-23
journal: nan
DOI: 10.1101/2021.05.20.21257552
sha: 58158e4fdd64d5c51cdac25913ce99e3f8dd6815
doc_id: 800871
cord_uid: 8vdknrdv

Genetic variants of the SARS-CoV-2 virus are of substantial concern because they can detrimentally alter the trajectory of the ongoing pandemic, and disease course in individual patients. Here we report genome sequences from 11,568 COVID-19 patients in the Houston Methodist healthcare system dispersed throughout the metroplex that were diagnosed from January 1, 2021 through April 30, 2021. This sample represents 94% of Houston Methodist cases and 4.6% of all reported cases in the metropolitan area during this period. The SARS-CoV-2 variant designated UK B.1.1.7 increased very rapidly, and now causes 75%-90% of all new cases in the Houston area. Five of the 2,543 B.1.1.7 genomes had an E484K change in spike protein. Compared with non-B.1.1.7 patients, individuals infected with B.1.1.7 had a significantly lower cycle threshold value (considered to be a proxy for higher virus load) and higher rate of hospitalization. Other variants (e.g., B.1.429, B.1.427, P.1, P.2, and R.1) also increased rapidly in frequency, although the magnitude was less than for B.1.1.7. We also identified 42 patients with a recently described R.1 variant that has an E484K amino acid replacement, and seven patients with the B.1.617 "India" variants. In the aggregate, our study shows the occurrence of a diverse array of concerning SARS-CoV-2 variants circulating in a major metropolitan area, documents B.1.1.7 as the major cause of new cases in Houston and heralds the arrival and spread of B.1.617 variants in the metroplex.

The global pandemic caused by SARS-CoV-2 that began in early 2020 has proved to be challenging for every academic health center and health system, hospital, and public health system in the United States and countries worldwide. [1] [2] [3] [4] [5] [6] [7] The pandemic has also provided unprecedented opportunities for basic and translational research in all biomedical fields. We have systematically analyzed the molecular population genomics of SARS-CoV-2 in the ethnically and socioeconomically diverse metropolitan Houston area (population 7 million) since the first COVID-19 cases were reported in very early March 2020. [8] [9] [10] [11] Our studies are facilitated by a central molecular diagnostic laboratory that comprehensively identifies and retains all COVID-19 diagnostic specimens from our large healthcare system that includes eight hospitals, emergency care clinics, and outpatient centers distributed throughout the metropolitan region. In addition, we have leveraged our longstanding interest in pathogen genomics and sequencing infrastructure to investigate the spread of SARS-CoV-2 in metropolitan Houston. [8] [9] [10] [11] [12] [13] [14] [15] [16] Among other discoveries, we have reported that the SARS-CoV-2 viruses causing infections in the earliest phase of the pandemic affecting Houston had substantial genomic diversity and are progeny of strains derived from several continents, including Europe and Asia. 8, 9 These findings indicated that SARS-CoV-2 was introduced into our region many times independently by individuals who had traveled from different parts of the country and the world. Subsequently, sequence analysis of 5,085 genomes causing the first disease wave and massive second disease wave in Houston showed that all strains in the second wave had a Asp614Gly amino acid replacement in the spike protein. 9 Importantly, this study was the first analysis of the molecular architecture of SARS-CoV-2 in two infection waves in any major metropolitan region. The Asp614Gly polymorphism increases human transmission and infectivity in vitro and in vivo in animal infection models. [17] [18] [19] [20] [21] [22] One key goal since the start of the pandemic has been to sequence all positive SARS-CoV-2 specimens and rapidly identifying mutations that may be associated with detrimental patient outcome, including therapeutic or vaccine failure. Similarly, with the recognition of an increasing number of SARS-CoV-2 variants of interest (VOIs) and variants of concern (VOCs) by public health agencies such as the United States Centers for Disease Control and Prevention https://www.gov.uk/government/collections/new-sars-cov-2-variant, last accessed: May 16, 2021) , there is now substantial domestic and international need to identify these virus genotypes rapidly and understand their velocity and patterns of dissemination. In particular, VOC UK B.1.1.7 is of special interest because it has the ability to transmit very effectively, spread through populations rapidly, and has been reported to have a significantly higher mortality rate than non-B.1.1.7 infections (https://virological.org/t/preliminary-genomic-characterisation-of-anemergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563, last be causing widespread disease and extensive public health concern in India. [43] [44] [45] [46] [47] [48] In the aggregate, our genome data show that VOC and VOI now account for the great majority of all new COVID-19 cases in our region.

Specimens were obtained from registered patients at Houston Methodist hospitals, associated facilities (e.g. urgent care centers), or institutions in the Houston metropolitan region that use our laboratory services. Virtually all individuals had signs or symptoms consistent with COVID-19 disease. We analyzed a comprehensive sample obtained from January 1, 2021 through April 30, 2021. This time frame was chosen for convenience because it represents the period during which at the onset of the study, we identified an uptick in identification of VOI and VOC. The study included 11,568 unique patients. The work was approved by the Houston Methodist Research Institute Institutional Review Board (IRB1010-0199).

Specimens obtained from symptomatic patients with a suspicion for COVID-19 disease were tested in the Molecular Diagnostics Laboratory at Houston Methodist Hospital using assays granted Emergency Use Authorization (EUA) from the FDA (https://www.fda.gov/medicaldevices/emergency-situations-medical-devices/faqs-diagnostic-testing-sars-cov-2#offeringtests).

As a hedge against supply chain strictures, multiple molecular testing platforms were used, including the COVID-19 test or RP2.1 test with BioFire Film Array instruments, the Xpert Xpress SARS-CoV-2 test using Cepheid GeneXpert Infinity or Cepheid GeneXpert Xpress IV instruments, the cobas SARS-CoV-2 & Influenza A/B Assay using the Roche Liat system, the SARS-CoV-2 Assay using the Hologic Panther instrument, the Aptima SARS-CoV-2 Assay using the Hologic Panther Fusion system, the Cobas SARS-CoV-2 test using the Roche 6800 system, and the SARS-CoV-2 assay using Abbott Alinity m instruments. The great majority of tests were performed on material obtained from nasopharyngeal swabs immersed in universal transport media (UTM); oropharyngeal or nasal swabs, bronchoalveolar lavage fluid, or sputum treated with dithiothreitol (DTT) were sometimes used. Standardized specimen collection methods were used (https://vimeo.com/396996468/2228335d56).

Libraries for whole virus genome sequencing were prepared according to version 3 of the ARTIC nCoV-2019 sequencing protocol (https://artic.network/ncov-2019). We used a semiautomated workflow that employed BioMek i7 liquid handling workstations (Beckman Coulter Life Sciences) and MANTIS automated liquid handlers (FORMULATRIX). Short sequence . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. 

Patient metadata were acquired from the electronic medical record by standard informatics methods ( Table 1) 

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. Table 1) broadly reflects metropolitan Houston, which has a majority-minority population composition.

Median length of stay was (5.2 days), and the 28-day mortality rate was 4.6%.

The CDC has identified eight VOI (B. Figure 3) . Ct data for the P.2 and R.1 patient samples were also significantly lower (Figure 3) .

Taken together, these observations are consistent with the idea that, on average, several common SARS-CoV-2 variants have significantly lower Ct values, a feature that may make them better able to disseminate and become abundant. The sample sizes for the other VOI and VOIs are not adequate to analyze meaningfully.

We next examined the geospatial distribution all VOI and VOC to investigate their extent of 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 May 23, 2021. ;  In work conducted contemporaneously with the present study, we have routinely sequenced all genomes from earlier in the pandemic in Houston, including the uptick part of the third wave of disease occurring in November and December 2020 (Figure 1) . We identified five patients in the 

We analyzed the molecular population genomics of SARS-CoV-2 occurring in metropolitan Houston, Texas, with a focus on infections occurring early in 2021, from January 1 through April 30. Our study was based on genome sequences from 11,568 ethnically, socioeconomically, and . CC-BY-NC-ND 4.0 International license It is made available under a 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 May 23, 2021. [43] [44] [45] A key finding from our study was the very rapid trajectory of VOC B.1.1.7 in metropolitan Houston, an area with a population size of approximately 7 million. Several investigators have reported previously that patients infected with the B.1.1.7 VOC have significantly lower Ct values on initial diagnosis, but this has not been a universal finding. 11, [58] [59] [60] [61] [62] [63] In the absence of quantitative virus cultures, the Ct value is viewed by many as a convenient proxy for virus load. We found (Table 1, Figure 3 . CC-BY-NC-ND 4.0 International license It is made available under a 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 May 23, 2021. Our data show that this variant increased rapidly in metropolitan Houston and by the end of April caused 75%-90% of new COVID-19 cases. However, the increase in B.1.1.7 as percent of new cases has occurred in the context of a substantial decrease in total COVID-19 cases in our metropolitan region (Figure 1) . Although the precise cause of these seemingly disparate trends is unknown, we hypothesize that a relatively successful early vaccination campaign in the region coupled with heightened public awareness and concern about variants contributed to the decreasing case rate, whereas the increase in percent of cases caused by B.1.1.7 is attributed to the capacity of this variant to transmit more rapidly than other variants. We cannot rule out a contribution of a small but significant ability of B.1.1.7 to evade immunity induced by either natural infection or vaccination, and our data are consistent with this idea ( Table 1 ). In this . CC-BY-NC-ND 4.0 International license It is made available under a 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 May 23, 2021. ; https://doi.org/10.1101/2021.05.20.21257552 doi: medRxiv preprint regard, data have been published showing that B.1.1.7 differs in some immunologic characteristics compared to "wild-type" SARS-CoV-2. [67] [68] [69] [70] [71] [72] [73] [74] SARS-CoV-2 variants with the E484K amino acid replacement are of particular concern in many areas including Brazil, South Africa, India and elsewhere (https://www.cidrap.umn.edu/news-perspective/2021/02/pfizer-moderna-vaccines-may-be-lesseffective-against-b1351-variant, last accessed: May 17, 2021) . Consistent with other studies, we identified the E484K change in several genetically distinct lineages of the virus, a finding likely due to convergent evolution, as noted previously by others. 39, 40, [54] [55] [56] 75 In the U.K., genome The first Houston Methodist patient with variant R.1 was identified in mid-December 2020 and its prevalence increased during the study period (Figure 2) .

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. 

. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. Schematic showing structural changes present in spike protein of the major SARS-CoV-2 variants identified in the study, including VOI, VOC, and variant R.1. S1-NTD, S1 domain-aminoterminal domain; S1-RBD, S1 domain-receptor binding domain; S1, S1 domain; S2, S2 domain. The figure is a modified version of one presented in Long et al. 10 CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. 

Clinical features of patients infected with 2019 novel coronavirus in

China Novel Coronavirus I, Research T: A Novel Coronavirus from Patients with Pneumonia in China

A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster

A new coronavirus associated with human respiratory disease in China

Coronaviridae Study Group of the International Committee on Taxonomy of V: The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2

A novel coronavirus outbreak of global health concern

Country-level factors associated with the early spread of COVID-19 cases at 5, 10 and 15 days since the onset

Molecular Architecture of Early Dissemination and Evolution of the SARS-CoV-2 Virus in Metropolitan Houston

Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area

Sequence Analysis of 20,453 Severe Acute Respiratory Syndrome Coronavirus 2 Genomes from the Houston Metropolitan Area Identifies the Emergence and Widespread Distribution of Multiple Isolates of All Major Variants of Concern

Rapid, widespread, and preferential increase of SARS-CoV-2 B.1.1.7 variant in Houston, TX, revealed by 8,857 genome sequences

Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolates

Absence of patient-to-patient intrahospital transmission of Staphylococcus aureus as determined by whole-genome sequencing

Rapidly progressive, fatal, inhalation anthrax-like infection in a human: case report, pathogen genome sequencing, pathology, and coordinated response

Evolutionary pathway to increased virulence and epidemic group A Streptococcus disease derived from 3,615 genome sequences

Integrated analysis of population genomics, transcriptomics and virulence provides novel insights into Streptococcus pyogenes pathogenesis

Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus

Spike mutation D614G alters SARS-CoV-2 fitness

The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types

SARS-CoV-2 spikeprotein D614G mutation increases virion spike density and infectivity

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

The effect of the D614G substitution on the structure of the spike glycoprotein of SARS-CoV-2

Public health actions to control new SARS-CoV-2 variants

SARS-CoV-2 Variants of Concern in the United States-Challenges and Opportunities

SARS-CoV-2 Viral Variants-Tackling a Moving Target

Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England

Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England

Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data

Changes in symptomatology, re-infection and transmissibility associated with SARS-CoV-2 variant B.1.1.7: an ecological study

Risk of mortality in patients infected with SARS-CoV-2 variant of concern 202012/1: matched cohort study

An observational cohort study on the incidence of SARS-CoV-2 infection and B.1.1.7 variant infection in healthcare workers by antibody and vaccination status

Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States

Densely sampled viral trajectories suggest longer duration of acute infection with B.1.1.7 variant relative to non-B

Grubaugh ND: Early introductions and community transmission of SARS-CoV-2 variant B.1.1.7 in the United States

Analysis of severe outcomes associated with the SARS-CoV-2 Variant of Concern 202012/01 in England using ICNARC Case Mix Programme and QResearch databases

Estimating the increased transmissibility of the B.1.1.7 strain over previously circulating strains in England using frequencies of GISAID sequences and the distribution of serial intervals

Phylogenetic relationship of SARS-CoV-2 sequences from Amazonas with emerging Brazilian variants harboring mutations E484K and N501Y

Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro

Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa

Week 49). samrc.ac

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

Convergent evolution of SARS-CoV-2 spike mutations, L452R, E484Q and P681R, in the second wave of COVID-19 in Maharashtra

Neutralization of variant under investigation B.1.617 with sera of BBV152 vaccinees

SARS CoV-2 variant B.1.617.1 is highly pathogenic in hamsters than B.1 variant

SARS-CoV-2 variant B.1.617 is resistant to Bamlanivimab and evades antibodies induced by infection and vaccination

SARS-CoV-2 B.1.617 emergence and sensitivity to vaccine-elicited antibodies

Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant

Harinivas Harshan K: N440K variant of SARS-CoV-2 has Higher Infectious Fitness

Symptomatic reinfection of SARS-CoV-2 with spike protein variant N440K associated with immune escape

Lineage Variant in a Skilled Nursing Facility After Vaccination Program -Kentucky

Household transmission of SARS-CoV-2 R.1 lineage with spike E484K mutation in Japan

Introductions and evolutions of SARS-CoV-2 strains in Japan

Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization

501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to Bamlanivimab in vitro

Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera

Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies

Traces of human migrations in Helicobacter pylori populations

Early analysis of a potential link between viral load and the N501Y mutation in the SARS-COV-2 spike protein

Increased infections, but not viral burden, with a new SARS-CoV-2 variant

Epidemiological and clinical insights from SARS-CoV-2 RT-PCR cycle amplification values

Estimating epidemiologic dynamics from cross-sectional viral load distributions

Virological and serological characterization of critically ill patients with COVID-19 in the UK: a special focus on variant detection

Genomic characteristics and clinical effect of the emergent SARS-CoV-2 B.1.1.7 lineage in London, UK: a whole-genome sequencing and hospital-based cohort study

Increased Transmissibility of SARS-CoV-2 Lineage B.1.1.7 by Age and Viral Load: Evidence from Danish Households

S-variant SARS-CoV-2 lineage B1.1.7 is associated with significantly higher viral loads in samples tested by ThermoFisher TaqPath RT-qPCR

Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera

7): an exploratory analysis of a randomised controlled trial

Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccineelicited antibodies

Neutralization of SARS-CoV-2 lineage B.1.1.7 pseudovirus by BNT162b2 vaccine-elicited human sera

Covid-19: Where are we on vaccines and variants

Increased Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7 to Antibody Neutralization

Neutralizing Antibodies Against SARS-CoV-2 Variants After Infection and Vaccination

Edwards DK: mRNA-1273 vaccine induces neutralizing antibodies against spike mutants from global SARS-CoV-2 variants

Immunity to SARS-CoV-2 variants of concern

Covid-19: The E484K mutation and the risks it poses

Chi-square Hispanic or Latino 741 (29.4%) 2656 (29.6%) 3397 (29.5%) Black 581

8%) 2455 (27.2%) 3110 (26.9%)

Fisher's exact test Odds Ratio

We thank the many talented and dedicated molecular technologists, and volunteers in the Molecular Diagnostics Laboratory and Methodist Research Institute for their dedicated efforts.