Severe Acute Respiratory Syndrome Coronavirus-2 Lambda Variant Collected from a Child from Arkansas and Sequenced.

An eleven-year-old tested positive for SARS-CoV-2 Lambda variant. Sequencing was performed on the Oxford Nanopore and the Illumina NextSeq 500. Both platforms identified all 7 of the synonymous mutations in the sample, while all 28 nonsynonymous mutations were identified from Oxford Nanopore and 20 nonsynonymous mutations were identified from Illumina.

Genomic surveillance for SARS-CoV-2 for New Mexico and the Mountain West

OBJECTIVES/GOALS: Understanding how SARS-CoV-2 is evolving as well as spreading within and between communities is vital for the design of rational, evidence-based control measures. Continuous genomic surveillance is imperative to identify and track variants and can be paired with clinical data, to identify associations with severity or vaccine breakthroughs. METHODS/STUDY POPULATION: In June of 2021, we established UNM as a CDC-funded hub for genomic surveillance of SARS-CoV-2 for New Mexico and 3 other Rocky Mountain region states (Wyoming, Idaho, Montana). Through our Rocky Mountain COVID Consortium (RMCC), we have sequenced over 6,000 genomes of SARS-CoV-2 from RMCC partners. For New Mexico we integrate county and zip code data to provide more granular insights into how SARS-CoV-2, and particular variants, are transmitting within the state. We also pair this data with vaccine breakthrough cases identified by the NMDOH, as well as with clinical outcome data. RESULTS/ANTICIPATED RESULTS: We sequenced over 6,000 SARS-CoV-2 genomes from New Mexico (n=3091), Idaho (n=1538), Arkansas (n=1101), Wyoming (n=251), and Montana (n=33). We used this data to infer the transmission dynamics, identify variants, and map the spread of the virus. We identified a novel local variant that spread across New Mexico in early 2021, but was quickly replaced by the Alpha variant. In all RMCC states, the Delta variant overtook Alpha and has become nearly the only variant currently circulating in these states. We identified sequenced isolates from vaccine breakthrough cases in NM and demonstrate their role in onward transmission. We can identify shifts at a county or zip-code level in circulating lineages which may correspond to clinical outcomes or fluctuating case counts. DISCUSSION/SIGNIFICANCE: This integrated genomic data can be used by policy and decision makers within the New Mexico Department of Health and our RMCC partners to guide their public health response to the COVID-19 pandemic.

Genomic epidemiology of SARS-CoV-2 across New Mexico and the Mountain West

IMPACT: Genomic data can be used by policy and decision makers to guide, and assess the impact of, public health responses to the COVID-19 pandemic. OBJECTIVES/GOALS: Our objective is to investigate the transmission and population dynamics of SARS-CoV-2 in New Mexico and other Mountain West states using whole genome sequencing. Understanding how the virus is spreading within and between communities is vital for the design of rational, evidence-based control measures. METHODS/STUDY POPULATION: We obtained an aliquot of 500ul - 1 ml of inactivated viral transport media (VTM) from positive SARS-CoV-2 nasopharyngeal swabs as determined by qPCR from the New Mexico Department of Health, TriCore Reference Laboratory, Idaho Bureau of Laboratories, and Wyoming Public Health Laboratory. We extracted viral RNA from the VTM, and sequenced the genomes using the methodology as described by the widely adopted ARTIC amplicon tiling protocol for SARS-CoV-2. Viral genomes were then sequenced on either an Illumina MiSeq or an Oxford Nanopore Technologies (ONT) GridION. We placed these samples within the context of globally representative sequences made available via the GISAID database. Consensus sequences were aligned and added into this global dataset using the Nextstrain augur pipeline. RESULTS/ANTICIPATED RESULTS: We sequenced over 1,000 SARS-CoV-2 genomes thus far from New Mexico (n=861), Wyoming (n=213) and Idaho (n=44). We used this sequence data to infer the transmission dynamics and spread of the virus, both within states and in context of regional and international spread. We inferred at least 128 separate introductions of the virus into New Mexico and at least 29 introductions into Wyoming. The origins of these introductions are diverse, spread across multiple regions in the US and abroad. We also sequenced samples from an individual who had multiple positive tests over time. Our results suggest that this individual was re-infected with a different strain than that of the initial infection. DISCUSSION/SIGNIFICANCE OF FINDINGS: Our data show that New Mexico and other Mountain West states have continually experienced many introductions of the virus that then seed local outbreaks. By understanding the number of introductions over time, we can assess the impact of travel restrictions on transmission. Our data also supports that some individuals can be re-infected.

Highly Accurate Chip-Based Resequencing of SARS-CoV-2 Clinical Samples.

SARS-CoV-2 has infected over 128 million people worldwide, and until a vaccine is developed and widely disseminated, vigilant testing and contact tracing are the most effective ways to slow the spread of COVID-19. Typical clinical testing only confirms the presence or absence of the virus, but rather, a simple and rapid testing procedure that sequences the entire genome would be impactful and allow for tracing the spread of the virus and variants, as well as the appearance of new variants. However, traditional short read sequencing methods are time consuming and expensive. Herein, we describe a tiled genome array that we developed for rapid and inexpensive full viral genome resequencing, and we have applied our SARS-CoV-2-specific genome tiling array to rapidly and accurately resequence the viral genome from eight clinical samples. We have resequenced eight samples acquired from patients in Wyoming that tested positive for SARS-CoV-2. We were ultimately able to sequence over 95% of the genome of each sample with greater than 99.9% average accuracy.

Severe Acute Respiratory Syndrome Coronavirus 2: Genomic Observations and Emerging Therapies.

Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent of the disease COVID-19, first emerged in late December 2019 in China, and has subsequently become a pandemic with unprecedented clinical impact. The virus appears to more severely affect older individuals and those with co-morbid medical conditions, specifically those with chronic lung disease, obesity, heart failure and diabetes. Fortunately, children appear to be less severely affected, though mortality and severe disease have been reported. In addition, children's role in spreading the disease (potentially through asymptomatic shedding of the virus) remains an important area requiring further investigation. The emergence of SARS-CoV-2 has highlighted the importance of metagenomic next generation sequencing as a tool for pandemic investigation. Though no proven therapeutic options currently exist, ongoing genomic and clinical trial data may help inform the identification and development of both repurposed and novel therapeutic agents for use in this disease.