Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore–Washington metropolitan area

Abstract

evolution of the virus but also the fundamental mechanisms by which control measures affected its epidemic spread. These efforts complement the information provided by the rapidly growing public databases of SARS-CoV-2 sequences by focusing the collection of genomic data in settings where we can access extensive current and past clinical data to investigate fundamental questions about this evolving virus's changing relationship with human health. MethodsData availability. Raw nanopore and Illumina data are deposited at SRA (BioProject PRJNA629390). Consensus sequences are deposited at GISAID and Genbank (MT509452-MT509493, and MT646048-MT646120) under BioProject PRJNA650037 (accession numbers available in Supplemental Table 3).Specimens and patient data. Clinical specimens used for genetic characterization were remnant nasopharyngeal swabs available at the completion of standard of care testing at the Johns Hopkins Hospital clinical virology laboratory. In total, 143 samples were selected for analysis based on their distribution throughout March 2020 and representation of the range of disease severity observed during this period. During this period, automated patient metadata extraction was limited to the date a sample was confirmed positive; all other data required patient chart reviews. Samples were sequenced in 2 phases, with the first phase enriched for patients admitted to the ICU (14 of 55 samples collected March 11-21), and the second a convenience sample that captured as many samples as possible for sequencing, irrespective of disease severity or ICU admission (10 of 88 samples collected March 13 -31).Clinical data analysis. Data including patient demographics, symptoms, comorbidities, COVID-19 exposure, recent travel history, and results of chest imaging at presentation were abstracted from the electronic medical record (EMR). COVID-19 treatment (medication, supplemental oxygen, and invasive mechanical ventilation) and outcomes (home observation without inpatient admission, discharge after admission, ongoing admission, and death) were also abstracted from the EMR. Race as self-reported by the patient and documented in the EMR was collected in prespecified categories. Patients who reported (a) contact with an individual known to be COVID-19-infected or (b) high-risk exposure (e.g., healthcare worker) were classified as COVID-19-exposed. Comorbidities were assessed based on diagnoses in the EMR (i.e., diabetes, obesity, or alcohol use disorder) and further categorized for lung disease (e.g., asthma, COPD), cardiac disease (e.g., valvular heart disease, arrhythmias, hypertension), and immunocompromised (e.g., HIV positive, hematologic malignancy, solid organ transplant).Nucleic acid extraction. Automated nucleic acid extraction was performed using either the NucliSENS easy-Mag or eMAG instruments (bioMérieux) using software version 2.1.0.1. easyMag or eMAG lysis buffer (2 mL) was added to 500 μL of aliquoted viral transport media in a biosafety cabinet in either a BSL-3 or BSL-2 facility using BSL-3 biosafe...

Infection with the SARS-CoV-2 Delta Variant is Associated with Higher Infectious Virus Loads Compared to the Alpha Variant in both Unvaccinated and Vaccinated Individuals

“…Molecular assays used for diagnosis include RealStar® SARS-CoV-2 RT-PCR (Altona Diagnostics), Xpert Xpress SARS-CoV-2/Flu/RSV (Cepheid), NeuMoDx SARS-CoV-2 (Qiagen), Cobas SARS-CoV-2 (Roche), ePlex Respiratory Pathogen Panel 2 (Roche), Aptima SARS-CoV-2 (Hologic), and Accula SARS-CoV-2 assays (ThermoFisher Scientific) (18)(19)(20)(21). Molecular diagnosis of SARS-CoV-2 at Johns Hopkins Hospital laboratory began on March 11 2020 (22), and whole genome sequencing for identifying circulating SARS-CoV-2 variants started as early as March 2020 as well (22). Surveillance efforts for VOCs were increased at the end of October 2020 to monitor the evolution of SARS-CoV-2.…”

An Update on Severe Acute Respiratory Syndrome Coronavirus 2 Diversity in the US National Capital Region: Evolution of Novel and Variants of Concern

“…Genomes from March 2021 were compared with those from March 2020 [ 3 ]. Of the 20 lineages circulating in this area in March 2020, only 3 (B.1, B.1.1, and B.1.1.207) were seen but rarely during March 2021 ( Figure 5A ).…”

“…Whole-genome sequencing for surveillance has been critical for monitoring the evolution of SARS-CoV-2 [ 3 ]. Our data showed an increase in the diversity of the spike protein and other genomic regions that include the NSP3 and NS3 over time.…”

“…Automated nucleic acid extraction was performed using the chemagic 360 instrument (PerkinElmer), following the manufacturer’s protocol. Libraries were prepared using the ARTIC protocol, as described elsewhere [ 3 ] Nanopore reads were base-called with MinKNOW and demultiplexed with Guppy v3.5.2 barcoder software, requiring barcodes at both ends. Reads were size restricted, and alignment and variant calling were performed with the artic-ncov2019 medaka protocol.…”

“…We previously reported the genomic diversity of SARS-CoV-2 at its early introduction in March 2020 to the National Capital Region [ 3 ]. In this report, we provide an update on the diversification of SARS-CoV-2 after 1 year of the pandemic.…”