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.

COVID-19 Pandemic Spurs Evolution of an Academic Pathology Department and Laboratory.

The COVID-19 pandemic has caused much suffering through disease and death, disruption of daily life, and economic havoc. Global health infrastructure has been challenged, in some cases failing. In the United States, the inability of laboratories to provide adequate testing for the causative pathogen, severe acute respiratory syndrome coronavirus 2, has been the subject of negative press and national debate. Even so, these challenges have prompted pathology practices and clinical labs to change their organizations and operations for the better. The natural positive evolution of the University of Oklahoma Department of Pathology and OU Health Laboratories has been greatly accelerated by the global pandemic. While developing a substantial COVID testing response, our department of pathology and laboratories have evolved a much nimbler organizational structure, established an important research partnership, built a translational research resource, created a significant reference lab capability, and completed many key hires against a national background of hiring freezes and pay cuts. Also, the high visibility of the clinical lab and pathologists during the outbreak has reinforced the value of lab medicine to patient care across our health system. In the midst of significant ongoing changes to the structure and financing of our underlying organizations, high trust among departmental, hospital, health system, and medical school leadership during the pandemic has promoted these positive changes, allowing us to emerge much stronger from this crisis.

Factors Influencing US Allopathic Medical Students to Choose Pathology as a Specialty.

The SARS-CoV-2 pandemic has highlighted the crucial role of pathologists in the health care system at a time of significant decline in the number of US medical students matching to pathology residency positions. To understand this decline, a national survey of fourth-year US allopathic medical students was conducted to assess experiences, knowledge, and attitudes of pathology and factors that impact specialty choice. Participating in a separate pathology course did not increase the probability of choosing pathology. Experiences significantly associated with choosing pathology included clinical or research opportunities in pathology during the last 2 years of medical school, autopsy observation/participation, and participation in pathology interest groups. Many respondents felt they were not sufficiently exposed to pathology to consider it as a specialty. Those who considered pathology but did not choose it were less likely to report understanding the activities of pathologists and being recruited by pathology faculty and more likely to express a preference for more direct patient contact as compared to those entering pathology. In general, respondents agreed that pathology has a good work-life balance and a satisfying degree of intellectual challenge. On the other hand, respondents generally agreed that information on social media and perception of the pathology job market do not seem to be positive and few agreed that pathology is a highly regarded specialty. We identify steps to address these issues and increase the number of US medical students choosing pathology as a specialty crucial to the future of medicine and public health.