medRxiv preprint doi: https://doi.org/10.1101/2020.09.22.20199125; this version posted September 29, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . 1 Molecular Architecture of Early Dissemination 2 and Massive Second Wave of the SARS-CoV-2 Virus in a 3 Major Metropolitan Area 4 5 Running Title: Two waves of COVID-19 disease in Houston, Texas 6 7 S. Wesley Long,a,b,1 Randall J. Olsen,a,b,1 Paul A. Christensen,a,1 David W. 8 Bernard,a,b James J. Davis,c,d Maulik Shukla,c,d Marcus Nguyen,c,d Matthew 9 Ojeda Saavedra,a Prasanti Yerramilli,a Layne Pruitt,a Sishir Subedi,a Hung- 10 Che Kuo,e Heather Hendrickson,a Ghazaleh Eskandari,a Hoang A. T. 11 Nguyen,a J. Hunter Long,a Muthiah Kumaraswami,a Jule Goike,e Daniel 12 Boutz,f Jimmy Gollihar, a,f Jason S. McLellan,e Chia-Wei Chou,e Kamyab 13 Javanmardi,e Ilya J. Finkelstein,e,g, and James M. Mussera,b# 14 15 aCenter for Molecular and Translational Human Infectious Diseases Research, 16 Department of Pathology and Genomic Medicine, Houston Methodist Research 17 Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 18 77030 19 bDepartments of Pathology and Laboratory Medicine, and Microbiology and 20 Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New 21 York 10065 NOTE: This preprint reports new research that has not been certified1 by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2020.09.22.20199125; this version posted September 29, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . 22 cConsortium for Advanced Science and Engineering, University of Chicago, 5801 23 South Ellis Avenue, Chicago, Illinois, 60637 24 dComputing, Environment and Life Sciences, Argonne National Laboratory, 9700 25 South Cass Avenue, Lemont, Illinois 60439 26 eDepartment of Molecular Biosciences and Institute of Molecular Biosciences, 27 The University of Texas at Austin, Austin, Texas 78712 28 fCCDC Army Research Laboratory-South, University of Texas, Austin, Texas 78712 29 gCenter for Systems and Synthetic Biology, University of Texas at Austin, Austin, 30 Texas 78712 31 32 1S.W.L., R.J.O., and P.A.C. contributed equally to this article. The order of co-first 33 authors was determined by discussion and mutual agreement between the three 34 co-first authors. 35 36 #Address correspondence to: James M. Musser, M.D., Ph.D., Department of 37 Pathology and Genomic Medicine, Houston Methodist Research Institute, 6565 38 Fannin Street, Suite B490, Houston, Texas 77030. Tel: 713.441.5890, E-mail: 39 [email protected]. 40 41 This article is a direct contribution from James M. Musser, a Fellow of the 42 American Academy of Microbiology, who arranged for and secured reviews by 43 Barry N. Kreiswirth, Center for Discovery and Innovation, Hackensack Meridian 2 medRxiv preprint doi: https://doi.org/10.1101/2020.09.22.20199125; this version posted September 29, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . 44 Health, New Jersey; and David M. Morens, National Institute of Allergy and 45 Infectious Diseases, National Institutes of Health, Maryland. 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 3 medRxiv preprint doi: https://doi.org/10.1101/2020.09.22.20199125; this version posted September 29, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . 66 ABSTRACT We sequenced the genomes of 5,085 SARS-CoV-2 strains 67 causing two COVID-19 disease waves in metropolitan Houston, Texas, an 68 ethnically diverse region with seven million residents. The genomes were 69 from viruses recovered in the earliest recognized phase of the pandemic in 70 Houston, and an ongoing massive second wave of infections. The virus 71 was originally introduced into Houston many times independently. Virtually 72 all strains in the second wave have a Gly614 amino acid replacement in the 73 spike protein, a polymorphism that has been linked to increased 74 transmission and infectivity. Patients infected with the Gly614 variant 75 strains had significantly higher virus loads in the nasopharynx on initial 76 diagnosis. We found little evidence of a significant relationship between 77 virus genotypes and altered virulence, stressing the linkage between 78 disease severity, underlying medical conditions, and host genetics. Some 79 regions of the spike protein - the primary target of global vaccine efforts - 80 are replete with amino acid replacements, perhaps indicating the action of 81 selection. We exploited the genomic data to generate defined single amino 82 acid replacements in the receptor binding domain of spike protein that, 83 importantly, produced decreased recognition by the neutralizing 84 monoclonal antibody CR30022. Our study is the first analysis of the 85 molecular architecture of SARS-CoV-2 in two infection waves in a major 86 metropolitan region. The findings will help us to understand the origin, 87 composition, and trajectory of future infection waves, and the potential 4 medRxiv preprint doi: https://doi.org/10.1101/2020.09.22.20199125; this version posted September 29, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . 88 effect of the host immune response and therapeutic maneuvers on SARS- 89 CoV-2 evolution. 90 91 IMPORTANCE There is concern about second and subsequent waves of 92 COVID-19 caused by the SARS-CoV-2 coronavirus occurring in 93 communities globally that had an initial disease wave. Metropolitan 94 Houston, Texas, with a population of 7 million, is experiencing a massive 95 second disease wave that began in late May 2020. To understand SARS- 96 CoV-2 molecular population genomic architecture, evolution, and 97 relationship between virus genotypes and patient features, we sequenced 98 the genomes of 5,085 SARS-CoV-2 strains from these two waves. Our study 99 provides the first molecular characterization of SARS-CoV-2 strains 100 causing two distinct COVID-19 disease waves. 101 102 KEYWORDS: SARS-CoV-2, COVID-19 disease, genome sequencing, molecular 103 population genomics, evolution 104 5 medRxiv preprint doi: https://doi.org/10.1101/2020.09.22.20199125; this version posted September 29, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . 105 [Introduction] 106 Pandemic disease caused by the severe acute respiratory syndrome 107 coronavirus 2 (SARS-CoV-2) virus is now responsible for massive human 108 morbidity and mortality worldwide (1-5). The virus was first documented to cause 109 severe respiratory infections in Wuhan, China, beginning in late December 2019 110 (6-9). Global dissemination occurred extremely rapidly and has affected major 111 population centers on most continents (10, 11). In the United States, the Seattle 112 and the New York City (NYC) regions have been especially important centers of 113 COVID-19 disease caused by SARS-CoV-2. For example, as of August 19, 114 2020, there were 227,419 confirmed SARS-CoV-2 cases in NYC, causing 56,831 115 hospitalizations and 19,005 confirmed fatalities and 4,638 probable fatalities (12). 116 Similarly, in Seattle and King County, 17,989 positive patients and 696 deaths 117 have been reported as of August 18, 2020 (13). 118 The Houston metropolitan area is the fourth largest and most ethnically 119 diverse city in the United States, with a population of approximately 7 million 120 (14, 15). The 2,400-bed Houston Methodist health system has seven hospitals 121 and serves a large, multiethnic, and socioeconomically diverse patient population 122 throughout greater Houston (13, 14). The first COVID-19 case in metropolitan 123 Houston was reported on March 5, 2020 with community spread occurring one 124 week later (16). Many of the first cases in our region were associated with 125 national or international travel in areas known to have SARS-CoV-2 virus 126 outbreaks (16). A central molecular diagnostic laboratory serving all Houston 127 Methodist hospitals and our very early adoption of a molecular test for the SARS- 6 medRxiv preprint doi: https://doi.org/10.1101/2020.09.22.20199125; this version posted September 29, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . 128 CoV-2 virus permitted us to rapidly identify positive patients and interrogate 129 genomic variation among strains causing early infections in the greater Houston 130 area.