key: cord-0700356-vt9fclio
authors: Avendano, Carolina; Lilienfeld, Aaron; Rulli, Liz; Stephens, Melissa; Barrios, Wendy Alvarez; Sarro, Joseph; Pfrender, Michael E.; Miranda, Marie Lynn
title: SARS-CoV-2 Variant Tracking and Mitigation During In-Person Learning at a Midwestern University in the 2020-2021 School Year
date: 2022-02-03
journal: JAMA Netw Open
DOI: 10.1001/jamanetworkopen.2021.46805
sha: d65d9aff0fd787ab645f9aa7b2f2c282fd709ecb
doc_id: 700356
cord_uid: vt9fclio

IMPORTANCE: The COVID-19 pandemic led many higher education institutions to close campuses during the 2020-2021 academic year. As campuses prepared for a return to in-person education, many institutions were mandating vaccines for students and considering the same for faculty and staff. OBJECTIVE: To determine the association between vaccination coverage and the levels and spread of SARS-CoV-2, even in the presence of highly-transmissible variants and congregate living, at a midsized university in the US. DESIGN, SETTING, AND PARTICIPANTS: This case series was conducted at a midsized Midwestern university during the spring 2021 semester. The university developed a saliva-based surveillance program capable of high-throughput SARS-CoV-2 polymerase chain reaction testing and genomic sequencing with the capacity to deliver results in less than 24 hours. On April 7, 2021, the university announced a vaccine requirement for all students for the fall 2021 semester and announced the same requirement for faculty and staff on May 20, 2021. The university hosted an onsite mass vaccination clinic using the 2-dose Pfizer-BioNTech vaccine during April 8 to 15 and April 29 to May 6, 2021. Data were analyzed for 14 894 individuals from the university population who were tested for COVID-19 on campus from January 6 to May 20, 2021. MAIN OUTCOMES AND MEASURES: Positive SARS-CoV-2 diagnosis was confirmed by quantitative reverse transcription–polymerase chain reaction of saliva specimens, and variant identity was assessed by quantitative reverse transcription–polymerase chain reaction and next-generation sequencing of viral genomes. RESULTS: Between January 6 and May 20, 2021, the university conducted 196 185 COVID-19 tests for 14 894 individuals and identified 1603 positive cases. Within those positive cases, 950 individuals (59.3%) were male, 644 (40.2%) were female, 1426 (89.0%) were students, and 1265 (78.9%) were aged 17 to 22 years. Among the 1603 positive cases, 687 were identified via polymerase chain reaction of saliva specimens. The Alpha (B.1.1.7) variant constituted 218 of the 446 total positives sequenced (48.9%). By May 20, 2021, 10 068 of 11 091 students (90.8%), 814 of 883 faculty (92.2%), and 2081 of 2890 staff (72.0%) were vaccinated. The 7-day rolling average of positive cases peaked at 37 cases on February 17 but declined to zero by May 14, 2021. The 7-day moving average of positive cases was inversely associated with cumulative vaccination coverage, with a statistically significant Pearson correlation coefficient of −0.57 (95% CI, −0.68 to −0.44). CONCLUSIONS AND RELEVANCE: This case series study elucidated the association of a robust vaccination program with a statistically significant decrease in positive COVID-19 cases among the study population even in the presence of highly transmissible variants and congregate living.

Fresh saliva samples collected from study participants were heat inactivated at 95°C for 30 min. Following the steps outlined by Ranoa et al. 1 , 2020, samples were diluted 1:1 (vol/vol) with 2XTris-Borate-EDTA buffer (0.089M Tris, 0.089M Borate, 0.002M EDTA in final 1x buffer solution), and tested for the presence of SARS-CoV-2 via RT-qPCR using the TaqPath COVID-19 Combo kit with TaqPath 1-Step Master Mix (Thermo Fisher Scientific, Cat# A47814, A28523). Following analysis, all heat inactivated positive samples were vortexed lightly, aliquoted into nuclease-free 1.5 mL tubes, and frozen at -80°C for further processing.

Saliva samples selected for extraction were identified as SARS-CoV-2 positive from the RT-qPCR assay with Ct values ≤32. These Ct values resulted from the combined average of the SARS-CoV-2 gene targets (N-gene, S-gene, ORF1ab) that were collected from two independent tests. Frozen saliva samples were thawed on ice, lightly vortexed, and pulse centrifuged for 12 seconds to a maximum speed of 1000 rpm to pellet suspended debris and solid particles. Viral RNA was then extracted from 140ul of saliva using the QIAamp Viral RNA Mini Kit according to the manufacturer's instructions for spin columns (Qiagen, Inc). RNA was eluted in 20-40 μl of nuclease free molecular grade water and placed at -80°C for storage until ready for library preparation.

RNA isolated from saliva samples was used as the starting material for library preparation using the Illumina COVIDSeq Test (Illumina Inc.), according to the manufacturer's instructions. Library preparation and sequencing was performed at the Genomics & Bioinformatics Core Facility at Notre Dame. Briefly, cDNA was synthesized from 8.5ul extracted RNA and amplified using two separate primer pools tiling the SARS-Cov-2 genome. Following PCR, the two amplicon pools were combined and a bead-linked transposome fragmented and tagged the amplicons with adapter sequence. Libraries were then indexed and pooled by volume. The pooled libraries were quality assessed using a combination of Qubit dsDNA HS Assay (Thermo Fisher Scientific), Bioanalyzer DNA 1000 Assay (Agilent Technologies), and KAPA Library Quantification Kit for Illumina (Kapa Biosystems), and normalized to 4 nM to prepare for sequencing. Library pools were sequenced on Illumina NextSeq 500 High Output v2.5 (300 cycle) flowcells using paired-end 2x150bp reads to a minimum read depth of 1 Million reads per sample.

Raw sequences were assessed for quality with FastQC version v0.11.8. 2 Information, including read depth, was extracted from the FastQC output using custom scripts. 3 FASTQ files were processed using the DRAGEN COVID Lineage app (Illumina Inc.) This app built FASTA files, established clade identity through Nextclade 4 , and lineages identity through Pangolin. 5 Clade and lineage assessments were verified through independent processing using Nextclade and Pangolin respectively. Results were deposited to GISAID 6 and Genbank. 7 Submission files were generated with custom scripts. 3 eReferences

Saliva-Based Molecular Testing for SARS-CoV-2 that Bypasses RNA Extraction

Nextstrain: real-time tracking of pathogen evolution

Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool

disease and diplomacy: GISAID's innovative contribution to global health. Glob Chall