Targeted Hybridization Capture of SARS-CoV-2 and Metagenomics Enables Genetic Variant Discovery and Nasal Microbiome Insights

Nagy‐Szakal, Dorottya; Couto-Rodriguez, Mara; Wells, Heather L.; Barrows, Joseph; Debieu, Marilyne; Butcher, Kristin; Chen, Siyuan; Berki, Agnes; Hager, Courteny N.; Boorstein, Robert J.; Taylor, Martha J.; Jonsson, Colleen B.; Mason, Christopher E.; O’Hara, Niamh B.

doi:10.1128/spectrum.00197-21

Cited by 35 publications

(25 citation statements)

References 46 publications

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“…Multiple studies found increases in antimicrobial resistance genes in COVID-19 patients, involving a wide range of resistance mechanisms [44,46,62,69]. Reflecting increased antibiotic usage in more severe patients, Li et al found greater multidrug efflux pumps (SatA and SatB) in more severe patients [46].…”

Section: Functional Characterizations Of the Covid-19 Respiratory Mic...mentioning

confidence: 99%

“…Reflecting increased antibiotic usage in more severe patients, Li et al found greater multidrug efflux pumps (SatA and SatB) in more severe patients [46]. Ma and coworkers found resistance to penam, penem, and cephalosporin antibiotics was most abundant and unique to COVID-19 compared to Flu B patients and healthy controls [44], while Nagy-Szakal et al found macrolide resistance was most differentially abundant in COVID-19-positive samples [62].…”

Section: Functional Characterizations Of the Covid-19 Respiratory Mic...mentioning

confidence: 99%

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Alterations in the respiratory tract microbiome in COVID-19: current observations and potential significance

2022

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SARS-CoV-2 infection causes COVID-19 disease, which can result in consequences ranging from undetectable to fatal, focusing attention on the modulators of outcomes. The respiratory tract microbiome is thought to modulate the outcomes of infections such as influenza as well as acute lung injury, raising the question to what degree does the airway microbiome influence COVID-19? Here, we review the results of 56 studies examining COVID-19 and the respiratory tract microbiome, summarize the main generalizations, and point to useful avenues for further research. Although the results vary among studies, a few consistent findings stand out. The diversity of bacterial communities in the oropharynx typically declined with increasing disease severity. The relative abundance of Haemophilus and Neisseria also declined with severity. Multiple microbiome measures tracked with measures of systemic immune responses and COVID outcomes. For many of the conclusions drawn in these studies, the direction of causality is unknown—did an alteration in the microbiome result in increased COVID severity, did COVID severity alter the microbiome, or was some third factor the primary driver, such as medication use. Follow-up mechanistic studies can help answer these questions.

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Section: Functional Characterizations Of the Covid-19 Respiratory Mic...mentioning

confidence: 99%

Section: Functional Characterizations Of the Covid-19 Respiratory Mic...mentioning

confidence: 99%

Alterations in the respiratory tract microbiome in COVID-19: current observations and potential significance

2022

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“…Using the sequencing strategy, hybrid capture based enrichment of SARS-CoV-2 10 , we succeeded in obtaining 42 viral genomes from the SARS-CoV-2 cases. The cases represented throughout 12 districts of Shanghai, between April and May, 2022.…”

Section: Dear Editormentioning

confidence: 99%

Clinical and virological characteristics of SARS-CoV-2 Omicron BA.2.2 variant outbreaks during April to May, 2022, Shanghai, China

Li²,

Wei³

et al. 2022

Journal of Infection

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“…A study focused on developing a novel method validated as a “hybrid capture SARS-CoV-2 NGS (Next Generation Sequencing) assay”, designed by a combination of double-stranded DNA biotin-labeled probes and complimentary software. This approach has received emergency-use authorization from the FDA and is found to be greatly useful in the surveillance and early detection of emerging variants, thus aiming at the prevention and mitigation of future outbreaks [ 32 ]. In another study, a fast diagnostic technique was designed using the portable instrument peak PCR.…”

Section: Techniques For Identification Of Hybrid Variantmentioning

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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Targeted Hybridization Capture of SARS-CoV-2 and Metagenomics Enables Genetic Variant Discovery and Nasal Microbiome Insights

Cited by 35 publications

References 46 publications

Alterations in the respiratory tract microbiome in COVID-19: current observations and potential significance

Alterations in the respiratory tract microbiome in COVID-19: current observations and potential significance

Clinical and virological characteristics of SARS-CoV-2 Omicron BA.2.2 variant outbreaks during April to May, 2022, Shanghai, China

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

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