key: cord-0291426-8q4m1gxd
authors: Mutnal, M. B.; Johnson, S.; Mohamed, N.; Abddelgader, R.; Morales, L.; Volz, M.; Walker, K.; Arroliga, A. C.; Rao, A.
title: Surveillance genome sequencing reveal multiple SARS-CoV-2 variants circulating in the central Texas, USA with a predominance of Delta variant and review of vaccine breakthrough cases.
date: 2021-08-08
journal: nan
DOI: 10.1101/2021.08.06.21261727
sha: 76e395398185322a1a01922a6a37aece6fcb4312
doc_id: 291426
cord_uid: 8q4m1gxd

As surges in the COVID-19 pandemic have continued worldwide, SARS-CoV-2 has mutated, spawning several new variants, and impacting, to various degrees, transmission, disease severity, diagnostics, therapeutics, and natural and vaccine-induced immunity. Baylor Scott & White Health has implemented, along with laboratory diagnosis, SARS-CoV-2 sequencing to identify variants in its geographical service area. We analyzed virus sequencing results of specimens collected across Central Texas and found dramatic changes in variant distribution in the first half of 2021. The alpha variant (B 1.1.7) became predominant at week 13 and continued dominance until week 25. A growth rate of 1.20 (R2 = 0.92) for the first 15 weeks was noted and this growth gradually declined to -0.55 (R2 = 0.99) for the final 13 weeks. Currently, B.1.1.7 is being displaced with B.1.617.2 at 0.58 growth rate (R2 = 0.97). We also investigated vaccine breakthrough cases within our healthcare system and present clinical data on 28 symptomatic patients.

reports generated were not released to patients' electronic health records but were provided to 72 public health officials for necessary interventions when a variant of concern (VOC) or variant of 73 interest (VOI) was identified. Similarly, vaccine breakthrough cases were identified and reported 74 according to Centers for Disease Control and Prevention (CDC) definitions.(9) 75 In this report, we present evolution of SARS-CoV-2 lineages in the Central Texas area, and their 76 association with vaccine breakthrough cases, along with clinical history of those breakthrough 77 cases. In large, randomized-controlled trials, each vaccine was found to be safe and efficacious 78 in preventing symptomatic, laboratory-confirmed COVID-19 (10) (11). In this report, we present 79 evolution of SARS-CoV-2 lineages in the limited geography of Central Texas and their 80 . 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 August 8, 2021. ; https://doi.org/10.1101/2021.08.06.21261727 doi: medRxiv preprint association with vaccine breakthrough along with clinical history of vaccinated patients exposed 81 to variants. Specimen Selection for sequencing 88 Since the beginning of the pandemic our laboratory has archived all the positive specimens 89 confirmed by one of the nucleic acid amplification methods that were deployed for diagnosis of 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. (which was not certified by peer review)

The copyright holder for this preprint this version posted August 8, 2021. ; https://doi.org/10.1101/2021.08.06.21261727 doi: medRxiv preprint <30 on a polymerase chain reaction (PCR) method, or RLU >1000 on a transcription mediated 103 amplification (TMA) method. We randomly selected 1% of the positive specimens for 104 sequencing when positivity rates were higher than 5% and all positive specimens when positivity 105 rates were <5%, to identify the variants in circulation.

Vaccine breakthrough cases 107 An electronic query was set up in the electronic health record to identify patients with a COVID-108 19 vaccination history. If patients were tested multiple times post vaccination they were 109 distinctly counted, and the first positive was counted for statistical purposes.

Nucleic acid was purified from each specimen and subjected to reverse transcription, next-112 generation sequencing library preparation, sequencing, and data analysis according to the 113 manufacturer's recommendation using two different platforms;

Sequencing on Ion Torrent (ThermoFisher) S5 system 115 Extracted RNA was subject to reverse transcription using the SuperScript VILO cDNA Growth rate statistical analyses were performed in SAS 9.4. All graphs were created in R version 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 August 8, 2021. 145 Since the beginning of the pandemic our laboratory has archived all the positive specimens 146 confirmed by one of the nucleic acid amplification methods that were deployed for diagnosis of 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 August 8, 2021. Clinical presentation of vaccine breakthrough cases. 189 We performed a review of electronic health records of patients who were fully vaccinated and 190 experienced vaccine breakthrough (Table 1) . Among the 33 vaccine breakthrough cases that 191 were sequenced, 28 were included in the VBT study as their clinical data existed in our EHR. Of 192 the 28 VBT cases reviewed, 17 (60%) were females, and the mean age of these 28 patients was 

Approximately 45% of the patients reported being either active (10%) or former smokers (35%).

198 Table 1 shows the symptoms associated with breakthrough under each vaccine brand in our 199 sample. However, direct comparisons between brands cannot be made with our data, given both (14) . In this study, we showed SARS- 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. (which was not certified by peer review) 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. (which was not certified by peer review)

The copyright holder for this preprint this version posted August 8, 2021. ; https://doi.org/10.1101/2021.08.06.21261727 doi: medRxiv preprint Sequencing weeks

Genomic Surveillance for SARS

Variants Circulating in the United States

Executive Order GA-34. Texas Department of State Health Services

COVID-19 in Texas -Texas Tests and Hospitals (Dashboard)

Rate and risk factors for 359 breakthrough SARS-CoV-2 infection after vaccination

Elucidating causes of COVID-19 infection and related 362 deaths after vaccination

COVID-19 Vaccine Breakthrough Infections Reported to CDC -364

United States