Identification of a rare SARS-CoV-2 XL hybrid variant in wastewater and the subsequent discovery of two infected individuals in Nevada

Vo, Van; Harrington, Anthony; Afzal, Salman; Papp, Katerina; Chang, Ching-Lan; Baker, H. Kent; Aguilar, Perseveranda; Buttery, Erin; Picker, Michael A.; Lockett, Cassius; Gerrity, Daniel; Kan, Horng-Yuan; Oh, Edwin C.

doi:10.1016/j.scitotenv.2022.160024

Cited by 9 publications

(9 citation statements)

References 32 publications

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“…In the case of sub-lineage XL (hybrids with recombinations between the BA.1 and BA.2 variants of Omicron), the recombination is detected by identifying unique mutations in an ORF1a gene at the Leu204Phe, Val1887Ile, and Ser22981syn sites. Recombinant genomes are found to be associated with notable challenges in bioinformatics-based approaches for the detection of theiants in clinical samples [ 29 ].…”

Section: Hybrid Variantsmentioning

confidence: 99%

Immunological Studies to Understand Hybrid/Recombinant Variants of SARS-CoV-2

Chavda¹,

Mishra

Vuppu

2022

Vaccines

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The zoonotic SARS-CoV-2 virus was present before the onset of the pandemic. It undergoes evolution, adaptation, and selection to develop variants that gain high transmission rates and virulence, resulting in the pandemic. Structurally, the spike protein of the virus is required for binding to ACE2 receptors of the host cells. The gene coding for the spike is known to have a high propensity of mutations, as a result generating numerous variants. The variants can be generated by random point mutations or recombination during replication. However, SARS-CoV-2 can also produce hybrid variants on co-infection of the host by two distinct lineages of the virus. The genomic sequences of the two variants undergo recombination to produce the hybrid variants. Additionally, these sub-variants also contain numerous mutations from both the parent variants, as well as some novel mutations unique to the hybrids. The hybrid variants (XD, XE, and XF) can be identified through numerous techniques, such as peak PCR, NAAT, and hybrid capture SARS-CoV-2 NGS (next generation sequencing) assay, etc., but the most accurate approach is genome sequencing. There are numerous immunological diagnostic assays, such as ELISA, chemiluminescence immunoassay, flow-cytometry-based approaches, electrochemiluminescence immunoassays, neutralization assays, etc., that are also designed and developed to provide an understanding of the hybrid variants, their pathogenesis, and other reactions. The objective of our study is to comprehensively analyze the variants of SARS-CoV-2, especially the hybrid variants. We have also discussed the techniques available for the identification of hybrids, as well as the immunological assays and studies for analyzing the hybrid variants.

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Section: Hybrid Variantsmentioning

confidence: 99%

Immunological Studies to Understand Hybrid/Recombinant Variants of SARS-CoV-2

Chavda¹,

Mishra

Vuppu

2022

Vaccines

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“…SARS-CoV-2 viral RNA can be found in human feces and urine, enabling investigators to monitor wastewater and provide estimates of COVID-19 incidence or community prevalence . Since March 2020, we and others have demonstrated that wastewater surveillance can provide an early detection system for high-priority pathogens, antimicrobial resistance markers, high risk substances, and emerging SARS-CoV-2 variants. − …”

Section: Introductionmentioning

confidence: 99%

Environmental Surveillance of Flood Control Infrastructure Impacted by Unsheltered Individuals Leads to the Detection of SARS-CoV-2 and Novel Mutations in the Spike Gene

Harrington,

Vo,

Moshi

et al. 2024

Environ. Sci. Technol. Lett.

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In the United States, the growing number of people experiencing homelessness has become a socioeconomic crisis with public health ramifications, recently exacerbated by the COVID-19 pandemic. We hypothesized that the environmental surveillance of flood control infrastructure may be an effective approach to understand the prevalence of infectious disease. From December 2021 through July 2022, we tested for SARS-CoV-2 RNA from two flood control channels known to be impacted by unsheltered individuals residing in upstream tunnels. Using qPCR, we detected SARS-CoV-2 RNA in these environmental water samples when significant COVID-19 outbreaks were occurring in the surrounding community. We also performed whole genome sequencing to identify SARS-CoV-2 lineages. Variant compositions were consistent with those of geographically and temporally matched municipal wastewater samples and clinical specimens. However, we also detected 10 of 22 mutations specific to the Alpha variant in the environmental water samples collected during January 2022�one year after the Alpha infection peak. We also identified mutations in the spike gene that have never been identified in published reports. Our findings demonstrate that environmental surveillance of flood control infrastructure may be an effective tool to understand public health conditions among unsheltered individuals�a vulnerable population that is underrepresented in clinical surveillance data.

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“…[8][9][10] Currently, wastewater-based surveillance programs are employed globally to monitor COVID-19 trends in sewershed communities, and the priorities of these programs have evolved from general virus detection 6 to the identication of emerging variants by sequencing the whole genome of the virus in wastewater. 11,12 However, the detection of high SARS-CoV-2 RNA concentrations in raw inuent samples around the world prompts public health concerns due to possible fecal-oral or aerosol transmission of the virus, yet only limited studies addressing the SARS-CoV-2 removal efficiencies in conventional and advanced WWTPs were carried out. 13,14 To date, there is minimal or no evidence supporting the potential transmission risk of COVID-19 through wastewater.…”

Section: Introductionmentioning

confidence: 99%