SARS-CoV-2 variants: Impact on biological and clinical outcome

Mahilkar, Shakuntala; Agrawal, Sachee; Chaudhary, Sakshi; Parikh, Swapneil; Sonkar, Subash Chandra; Verma, Deepali; Chitalia, Vidushi; Mehta, Divya; Koner, Bidhan Chandra; Vijay, Neetu; Shastri, Jayanthi; Sunil, Sujatha

doi:10.3389/fmed.2022.995960

Cited by 21 publications

(15 citation statements)

References 130 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Molecular diagnostic assays that directly impact patient care were prioritized over SARS-CoV-2 sequencing, posing a challenge to continue RUO sequencing at high capacity. This was particularly the case during SARS-CoV-2 waves, when staffing was reduced due to illness and supplies were in high demand ( 15 ). As a result, there were substantial delays (>1 month) in sequencing SARS-CoV-2 specimens, contrasting with our original plan of using COVIDSeq to capture shifts and emergence of SARS-CoV-2 lineages.…”

Section: Clinical Relevance/discussionmentioning

confidence: 99%

NGS implementation for monitoring SARS-CoV-2 variants in Chicagoland: An institutional perspective, successes and challenges

Tartaninan

Mulroney

Poselenzny

et al. 2023

Front. Public Health

View full text Add to dashboard Cite

Identification of SARS-CoV-2 lineages has shown to provide invaluable information regarding treatment efficacy, viral transmissibility, disease severity, and immune evasion. These benefits provide institutions with an expectation of high informational upside with little insight in regards to practicality with implementation and execution of such high complexity testing in the midst of a pandemic. This article details our institution’s experience implementing and using Next Generation Sequencing (NGS) to monitor SARS-CoV-2 lineages in the northern Chicagoland area throughout the pandemic. To date, we have sequenced nearly 7,000 previously known SARS-CoV-2 positive samples from various patient populations (e.g., outpatient, inpatient, and outreach sites) to reduce bias in sampling. As a result, our hospital was guided while making crucial decisions about staffing, masking, and other infection control measures during the pandemic. While beneficial, establishing this NGS procedure was challenging, with countless considerations at every stage of assay development and validation. Reduced staffing prompted transition from a manual to automated high throughput workflow, requiring further validation, lab space, and instrumentation. Data management and IT security were additional considerations that delayed implementation and dictated our bioinformatic capabilities. Taken together, our experience highlights the obstacles and triumphs of SARS-CoV-2 sequencing.

show abstract

Section: Clinical Relevance/discussionmentioning

confidence: 99%

NGS implementation for monitoring SARS-CoV-2 variants in Chicagoland: An institutional perspective, successes and challenges

Tartaninan

Mulroney

Poselenzny

et al. 2023

Front. Public Health

View full text Add to dashboard Cite

show abstract

“…Notable subvariants, including BA.2, BA.5, and XBB were of particular interest due to their rapid spread across the globe and evasion from neutralizing and monoclonal antibodies 3,4 . Speci c genetic changes within the virus have conferred selective advantages, augmenting its ability to propagate and evade host immune responses, thereby presenting formidable challenges to containment and treatment strategies 5 .…”

Section: Introductionmentioning

confidence: 99%

Emergence of SARS-CoV-2 Omicron Variant JN.1 in Tamil Nadu, India - Clinical Characteristics and Novel Mutations

Selvavinayagam,

Sankar,

Yong

et al. 2024

Preprint

View full text Add to dashboard Cite

In December 2023, we observed a notable shift in the COVID-19 landscape, when the JN.1 emerged as a predominant SARS-CoV-2 variant with a 95% incidence. We characterized the clinical profile, and genetic changes in JN.1, an emerging SARS-CoV-2 variant of interest. Whole genome sequencing was performed on SARS-CoV-2 positive samples, followed by sequence analysis. Mutations within the spike protein sequences were analyzed and compared with the previous lineages and sublineages of SARS-CoV-2, to identify the potential impact of these unique mutations on protein structure and possible functionality. Several unique and dynamic mutations were identified herein. Our data provides key insights into the emergence of newer variants of SARS-CoV-2 in our region and highlights the need for robust and sustained genomic surveillance of SARS-CoV-2.

show abstract

“…In nature, bats are known to be primary reservoirs of many coronaviruses, from where viruses spill over to intermediate animals such as palm civet, pangolins, rodents, camels, pigs, cattle where viruses evolve and then spillover to humans, causing mild to severe disease (17,18). The rapid emergence of different variants of SARS-CoV-2 indicates that the viral genome acquire multiple mutations during replication (19,20). In this context, it is crucial to study the host factors and compounds that can enhance or reduce replication of SARS-CoV-2 (21)(22)(23).…”

Section: Introductionmentioning

confidence: 99%

Effect of exportin 1/XPO1 nuclear export pathway inhibition on coronavirus replication

Rahman

Estifanos

Glenn

et al. 2023

Preprint

View full text Add to dashboard Cite

Nucleocytoplasmic transport of proteins using XPO1 (exportin 1) plays a vital role in cell proliferation and survival. Many viruses also exploit this pathway to promote infection and replication. Thus, inhibiting XPO1-mediated nuclear export with selective inhibitors activates multiple antiviral and anti-inflammatory pathways. The XPO1 inhibitor, Selinexor, is an FDA-approved anticancer drug predicted to have antiviral function against many viruses, including SARS-CoV-2. Unexpectedly, we observed that pretreatment of cultured human cells with Selinexor actually enhanced protein expression and replication of coronaviruses, including SARS-CoV-2. Knockdown of cellular XPO1 protein expression significantly enhanced the replication of coronaviruses in human cells. We further demonstrate that Selinexor treatment reduced the formation of unique cytoplasmic antiviral granules that include RNA helicase DHX9 in the virus-infected cells. These results, for the first time, show that the anti-cancer drug Selinexor enhances the replication of coronaviruses in human cells in vitro and thus should be further explored in vivo for the potential impact on the dual use for anticancer and antiviral therapy.

show abstract

SARS-CoV-2 variants: Impact on biological and clinical outcome

Cited by 21 publications

References 130 publications

NGS implementation for monitoring SARS-CoV-2 variants in Chicagoland: An institutional perspective, successes and challenges

NGS implementation for monitoring SARS-CoV-2 variants in Chicagoland: An institutional perspective, successes and challenges

Emergence of SARS-CoV-2 Omicron Variant JN.1 in Tamil Nadu, India - Clinical Characteristics and Novel Mutations

Effect of exportin 1/XPO1 nuclear export pathway inhibition on coronavirus replication

Contact Info

Product

Resources

About