Detection of SARS-CoV-2 Variants by Multiple Diagnostic Assays Second RESUBMISSION JCV-D-21-00675R2.

Introduction: The emergence of SARS-CoV-2 Variants of Concern (VOC) and Variants Being Monitored (VBM) have presented additional clinical and public health concerns regarding potential virus transmissibility, disease severity, and immune evasion. It is imperative that diagnostic assays can detect all such variants, and since commercial oligo sequences are commonly not available, empirical testing may be necessary to confirm this. To confirm the sensitivity of the SARS-CoV-2 assays used at the Wadsworth Center for the detection of VOC and VBM, relevant specimens were selected from the specimen archive and tested in the various platforms.

Cluster of Oseltamivir-Resistant and Hemagglutinin Antigenically Drifted Influenza A(H1N1)pdm09 Viruses, Texas, USA, January 2020.

Four cases of oseltamivir-resistant influenza A(H1N1)pdm09 virus infection were detected among inhabitants of a border detention center in Texas, USA. Hemagglutinin of these viruses belongs to 6B.1A5A-156K subclade, which may enable viral escape from preexisting immunity.

CACO-2 cells: A continuous cell line with sensitive and broad-spectrum utility for respiratory virus culture.

Background: Primary rhesus monkey kidney cells (RhMK) can be used for the detection of respiratory viruses, including influenza and parainfluenza. The human colon adeno-carcinoma cell line, CACO-2, has been previously used for the growth of multiple influenza viruses, including seasonal, novel and avian lineages.

Objective: We compared CACO-2, Madin-Darby Canine Kidney (MDCK), and RhMK cells for the isolation of viruses from patients presenting with influenza like-illness (ILI).

Baloxavir treatment of oseltamivir-resistant influenza A/H1pdm09 in two immunocompromised patients.

Few treatment options are available for oseltamivir-resistant influenza. It has been proposed that baloxavir can be effective in this setting due to its distinct mechanism of action but clinical experience is lacking for immunocompromised patients. We report two such cases treated with baloxavir after failure of oseltamivir and detection of oseltamivir resistance mutations.

Baloxavir for the treatment of Influenza in allogeneic hematopoietic stem cell transplant recipients previously treated with oseltamivir.

Background: Seasonal influenza causes significant morbidity and mortality in allogeneic stem cell transplant (SCT) recipients. In this population, influenza virus can replicate for prolonged periods, despite neuraminidase inhibitor treatment, leading to resistance and treatment failure. Baloxavir targets the influenza polymerase and may be an effective treatment option in these patients.

Detection and Characterization of Influenza B Virus With Reduced Neuraminidase Susceptibility in a Stem Cell Transplant Recipient.

Antiviral-resistant influenza viruses in the clinical environment, especially type B, are reported rarely. A stem cell transplant recipient remained influenza B positive for 2 months, despite repeated antiviral treatments. Laboratory tests demonstrated the evolution and persistence of neuraminidase inhibitor-resistant influenza B virus with a substitution at codon 119.

A Pyrosequencing-Based Approach to High-Throughput Identification of Influenza A(H3N2) Virus Clades Harboring Antigenic Drift Variants.

The rapid evolution of influenza A(H3N2) viruses necessitates close monitoring of their antigenic properties so the emergence and spread of antigenic drift variants can be rapidly identified. Changes in hemagglutinin (HA) acquired by contemporary A(H3N2) viruses hinder antigenic characterization by traditional methods, thus complicating vaccine strain selection. Sequence-based approaches have been used to infer virus antigenicity; however, they are time consuming and mid-throughput.

Next generation sequencing for whole genome analysis and surveillance of influenza A viruses.

Background: The Wadsworth Center, New York State Department of Health (NYSDOH), conducts routine diagnosis and surveillance of influenza viruses. Whole genome sequencing (WGS) with next generation sequencing (NGS) was initiated to provide more rapid, detailed, thorough, and accurate analysis.

Objectives: To optimize and implement a method for routine WGS of influenza A viruses.

Detection of a transient R292K mutation in influenza A/H3N2 viruses shed for several weeks by an immunocompromised patient.

We describe the case of an immunocompromised patient, positive for influenza A virus (H3N2), in whom the neuraminidase R292K mutation was transiently detected during oseltamivir treatment. The R292K mutation was identified by direct testing in 3 of 11 respiratory specimens collected throughout the patient's illness but in none of the cultures from those specimens.

Antiviral resistance in influenza viruses: laboratory testing.

Influenza continues to be a significant health care issue. Although vaccination is the major line of defense, antiviral drugs play an important role in prophylaxis and disease management. Approved drugs for influenza are currently limited to those that target the viral matrix protein or neuraminidase enzyme.

Characteristics of patients with oseltamivir-resistant pandemic (H1N1) 2009, United States.

During April 2009-June 2010, thirty-seven (0.5%) of 6,740 pandemic (H1N1) 2009 viruses submitted to a US surveillance system were oseltamivir resistant. Most patients with oseltamivir-resistant infections were severely immunocompromised (76%) and had received oseltamivir before specimen collection (89%).

Deep sequencing reveals mixed infection with 2009 pandemic influenza A (H1N1) virus strains and the emergence of oseltamivir resistance.

Mixed infections with seasonal influenza A virus strains are a common occurrence and an important source of genetic diversity. Prolonged viral shedding, as observed in immunocompromised individuals, can lead to mutational accumulation over extended periods. Recently, drug resistance was reported in immunosuppressed patients infected with the 2009 pandemic influenza A (H1N1) virus within a few days after oseltamivir treatment was initiated.

Influenza antiviral resistance testing in new york and wisconsin, 2006 to 2008: methodology and surveillance data.

The need for effective influenza antiviral susceptibility surveillance methods has increased due to the emergence of near-universal adamantane resistance in influenza A/H3N2 viruses during the 2005-2006 season and the appearance of oseltamivir resistance in the influenza A/H1N1 virus subtype during the 2007-2008 season. The two classes of influenza antivirals, the neuraminidase inhibitors (NAIs) and the adamantanes, are well characterized, as are many mutations that can confer resistance to these drugs. Adamantane resistance is imparted mainly by a S31N mutation in the matrix gene, while NAI resistance can result from a number of mutations in the neuraminidase gene.

Adult bone marrow-derived cells trans-differentiating into insulin-producing cells for the treatment of type I diabetes.

Recent findings suggest that bone marrow (BM) cells have the capacity to differentiate into a variety of cell types including endocrine cells of the pancreas. We report that BM derived cells, when cultured under defined conditions, were induced to trans-differentiate into insulin-producing cells. Furthermore, these insulin-producing cells formed aggregates that, upon transplantation into mice, acquired architecture similar to islets of Langerhans.