Development of an amplicon-based sequencing approach in response to the global emergence of mpox

The 2022 multicountry mpox outbreak concurrent with the ongoing Coronavirus Disease 2019 (COVID-19) pandemic further highlighted the need for genomic surveillance and rapid pathogen whole-genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox infections, these methods are resource intensive and require samples with high viral DNA concentrations. Given the atypical clinical presentation of cases associated with the outbreak and uncertainty regarding viral load across both the course of infection and anatomical body sites, there was an urgent need for a more sensitive and broadly applicable sequencing approach. Highly multiplexed amplicon-based sequencing (PrimalSeq) was initially developed for sequencing of Zika virus, and later adapted as the main sequencing approach for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Here, we used PrimalScheme to develop a primer scheme for human monkeypox virus that can be used with many sequencing and bioinformatics pipelines implemented in public health laboratories during the COVID-19 pandemic. We sequenced clinical specimens that tested presumptively positive for human monkeypox virus with amplicon-based and metagenomic sequencing approaches. We found notably higher genome coverage across the virus genome, with minimal amplicon drop-outs, in using the amplicon-based sequencing approach, particularly in higher PCR cycle threshold (Ct) (lower DNA titer) samples. Further testing demonstrated that Ct value correlated with the number of sequencing reads and influenced the percent genome coverage. To maximize genome coverage when resources are limited, we recommend selecting samples with a PCR Ct below 31 Ct and generating 1 million sequencing reads per sample. To support national and international public health genomic surveillance efforts, we sent out primer pool aliquots to 10 laboratories across the United States, United Kingdom, Brazil, and Portugal. These public health laboratories successfully implemented the human monkeypox virus primer scheme in various amplicon sequencing workflows and with different sample types across a range of Ct values. Thus, we show that amplicon-based sequencing can provide a rapidly deployable, cost-effective, and flexible approach to pathogen whole-genome sequencing in response to newly emerging pathogens. Importantly, through the implementation of our primer scheme into existing SARS-CoV-2 workflows and across a range of sample types and sequencing platforms, we further demonstrate the potential of this approach for rapid outbreak response.

Development of an amplicon-based sequencing approach in response to the global emergence of human monkeypox virus

The 2022 multi-country monkeypox (mpox) outbreak concurrent with the ongoing COVID-19 pandemic has further highlighted the need for genomic surveillance and rapid pathogen whole genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox infections, these methods are resource intensive and require samples with high viral DNA concentrations. Given the atypical clinical presentation of cases associated with the outbreak and uncertainty regarding viral load across both the course of infection and anatomical body sites, there was an urgent need for a more sensitive and broadly applicable sequencing approach. Highly multiplexed amplicon-based sequencing (PrimalSeq) was initially developed for sequencing of Zika virus, and later adapted as the main sequencing approach for SARS-CoV-2. Here, we used PrimalScheme to develop a primer scheme for human monkeypox virus that can be used with many sequencing and bioinformatics pipelines implemented in public health laboratories during the COVID-19 pandemic. We sequenced clinical samples that tested presumptive positive for human monkeypox virus with amplicon-based and metagenomic sequencing approaches. We found notably higher genome coverage across the virus genome, with minimal amplicon drop-outs, in using the amplicon-based sequencing approach, particularly in higher PCR cycle threshold (lower DNA titer) samples. Further testing demonstrated that Ct value correlated with the number of sequencing reads and influenced the percent genome coverage. To maximize genome coverage when resources are limited, we recommend selecting samples with a PCR cycle threshold below 31 Ct and generating 1 million sequencing reads per sample. To support national and international public health genomic surveillance efforts, we sent out primer pool aliquots to 10 laboratories across the United States, United Kingdom, Brazil, and Portugal. These public health laboratories successfully implemented the human monkeypox virus primer scheme in various amplicon sequencing workflows and with different sample types across a range of Ct values. Thus, we show that amplicon based sequencing can provide a rapidly deployable, cost-effective, and flexible approach to pathogen whole genome sequencing in response to newly emerging pathogens. Importantly, through the implementation of our primer scheme into existing SARS-CoV-2 workflows and across a range of sample types and sequencing platforms, we further demonstrate the potential of this approach for rapid outbreak response.

1896. Statewide Genomic Surveillance of SARS-CoV-2 Variants in Rhode Island

Background

Global genomic surveillance has allowed identification of SARS-CoV-2 circulating variants responsible for the COVID-19 pandemic. Statewide variant characterization can guide local public health mitigations and provide educational opportunities. We characterized statewide evolution of SARS-CoV-2 variants in Rhode Island (RI).

Methods

Deidentified RI SARS-CoV-2 sequences since 2/2020, generated at authors, CDC and commercial laboratories, were extracted from https://www.gisaid.org. Genomic and phylogenetic analyses were conducted with available tools and custom python scripts and, after quality control, sequences were classified as variants of Concern (VOC), variants being monitored (VBM), or non-VOC/non-VBM, per CDC definitions. Specific mutations that are characteristic of the most recent VOCs (Delta or Omicron) were explored outside of their designated lineages.

Results

Of the 1.1 million RI population, 14,933 SARS-CoV-2 sequences were available between 2/2020 and 3/2022. These included 1,542 (11%) sequences from 37 non-VOC/non-VBM lineages until 2/2021, most commonly B.1.2 (21%), B.1.375 (13%), and B.1.517 (6%); 2,910 (19%) sequences from 7 VBM lineages between 3-6/2021, most commonly Alpha (48%), Iota (34%), and Gamma (10%); and 10,481 (70%) sequences from 2 VOC lineages, including 7,574 (72%) Delta mostly between 6/2021 and 12/2021, and 2,907 (28%) Omicron mostly between 1/2022 and 3/2022. Phylogeny showed expected clustering of local variants within regional and global sequences, and continued viral evolution over time. Further VOC evolution was observed, including 87 Delta sub-lineages, most commonly AY.103 (17%), AY.3 (15%), and AY.44 (12%); and 4 Omicron sub-lineages BA.1 (61%), BA.1.1 (32%), BA.2 (7%), and BA.3 (< 1%). Omicron-associated mutations S:del69/70, S:H655Y, or N:P13L were observed in 219 Delta sequences, and Delta-associated mutations ORF1b:G662S, N:D377Y, or M:I82T were observed in 16 Omicron sequences.

Conclusion

Statewide SARS-CoV-2 genomic surveillance allows for continued characterization of locally circulating variants and monitoring of viral evolution. Such data guide public health policies, inform the local health force, and mitigate the impact of SARS-CoV-2 on public health.

Disclosures

Rami Kantor, MD, Gilead Sciences: Grant/Research Support.

SARS-CoV-2 Variants in Rhode Island; May 2022 Update

BACKGROUND

Genomic surveillance allows identification of circulating SARS-CoV-2 variants. We provide an update on the evolution of SARS-CoV-2 in Rhode Island (RI).

METHODS

All publicly available SARS-CoV-2 RI sequences were retrieved from https://www.gisaid.org. Genomic analyses were conducted to identify variants of concern (VOC), variants being monitored (VBM), or non-VOC/non-VBM, and investigate their evolution.

RESULTS

Overall, 17,340 SARS-CoV-2 RI sequences were available between 2/2020-5/2022 across five (globally recognized) major waves, including 1,462 (8%) sequences from 36 non-VOC/non-VBM until 5/2021; 10,565 (61%) sequences from 8 VBM between 5/2021-12/2021, most commonly Delta; and 5,313 (31%) sequences from the VOC Omicron from 12/2021 onwards. Genomic analyses demonstrated 71 Delta and 44 Omicron sub-lineages, with occurrence of variant-defining mutations in other variants.

CONCLUSION

Statewide SARS-CoV-2 genomic surveillance allows for continued characterization of circulating variants and monitoring of viral evolution, which inform the local health force and guide public health on mitigation efforts against COVID-19.

Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA

The SARS-CoV-2 Delta variant rose to dominance in mid-2021, likely propelled by an estimated 40%-80% increased transmissibility over Alpha. To investigate if this ostensible difference in transmissibility is uniform across populations, we partner with public health programs from all six states in New England in the United States. We compare logistic growth rates during each variant's respective emergence period, finding that Delta emerged 1.37-2.63 times faster than Alpha (range across states). We compute variant-specific effective reproductive numbers, estimating that Delta is 63%-167% more transmissible than Alpha (range across states). Finally, we estimate that Delta infections generate on average 6.2 (95% CI 3.1-10.9) times more viral RNA copies per milliliter than Alpha infections during their respective emergence. Overall, our evidence suggests that Delta's enhanced transmissibility can be attributed to its innate ability to increase infectiousness, but its epidemiological dynamics may vary depending on underlying population attributes and sequencing data availability.

A pyrosequencing protocol for rapid identification of SARS-CoV-2 variants

Next‐generation sequencing (NGS) is the primary method used to monitor the distribution and emergence of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) variants around the world; however, it is costly and time‐consuming to perform and is not widely available in low‐resourced geographical regions. Pyrosequencing has the potential to augment surveillance efforts by providing information on specific targeted mutations for rapid identification of circulating and emerging variants. The current study describes the development of a reverse transcription (RT)‐PCR‐pyrosequencing assay targeting >65 spike protein gene (S) mutations of SARS‐CoV‐2, which permits differentiation of commonly reported variants currently circulating in the United States with a high degree of confidence. Variants typed using the assay included B.1.1.7 (Alpha), B.1.1.529 (Omicron), B.1.351 (Beta), B.1.375, B.1.427/429 (Epsilon), B.1.525 (Eta), B.1.526.1 (Iota), B.1.617.1 (Kappa), B.1.617.2 (Delta), B.1.621 (Mu), P1 (Gamma), and B.1.1 variants, all of which were confirmed by the NGS data. An electronic typing tool was developed to aid in the identification of variants based on mutations detected by pyrosequencing. The assay could provide an important typing tool for rapid identification of candidate patients for monoclonal antibody therapies and a method to supplement SARS‐CoV‐2 surveillance efforts by identification of circulating variants and novel emerging lineages.

Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant quickly rose to dominance in mid-2021, displacing other variants, including Alpha. Studies using data from the United Kingdom and India estimated that Delta was 40-80% more transmissible than Alpha, allowing Delta to become the globally dominant variant. However, it was unclear if the ostensible difference in relative transmissibility was due mostly to innate properties of Delta's infectiousness or differences in the study populations. To investigate, we formed a partnership with SARS-CoV-2 genomic surveillance programs from all six New England US states. By comparing logistic growth rates, we found that Delta emerged 37-163% faster than Alpha in early 2021 (37% Massachusetts, 75% New Hampshire, 95% Maine, 98% Rhode Island, 151% Connecticut, and 163% Vermont). We next computed variant-specific effective reproductive numbers and estimated that Delta was 58-120% more transmissible than Alpha across New England (58% New Hampshire, 68% Massachusetts, 76% Connecticut, 85% Rhode Island, 98% Maine, and 120% Vermont). Finally, using RT-PCR data, we estimated that Delta infections generate on average ∼6 times more viral RNA copies per mL than Alpha infections. Overall, our evidence indicates that Delta's enhanced transmissibility could be attributed to its innate ability to increase infectiousness, but its epidemiological dynamics may vary depending on the underlying immunity and behavior of distinct populations.

SARS-CoV-2 Variants in Rhode Island

COVID-19 is a worldwide public health emergency caused by SARS-CoV-2. Genomic surveillance of SARS-CoV-2 emerging variants is important for pandemic monitoring and informing public health responses. Through an interstate academic-public health partnership, we established Rhode Island's capacity to sequence SARS-CoV-2 genomes and created a systematic surveillance program to monitor the prevalence of SARS-CoV-2 variants in the state. We describe circulating SARS-CoV-2 lineages in Rhode Island; provide a timeline for the emerging and expanding contribution of variants of concern (VOC) and variants of interest (VOI), from their first introduction to their eventual predominance over other lineages; and outline the frequent identification of known adaptively beneficial spike protein mutations that appear to have independently arisen in non-VOC/non-VOI lineages. Overall, the described Rhode Island- centric genomic surveillance initiative provides a valuable perspective on SARS-CoV-2 in the state and contributes data of interest for future epidemiological studies and state-to-state comparisons.