Evaluating direct amplification from viral transport medium for SARS-CoV-2 detection, strain typing, and angiotensin-converting enzyme genotyping and expression assays.

OBJECTIVE: The aim of this study was to compare the performance of direct amplification of viral nucleic acid from transport medium to extracted nucleic acid for polymerase chain reaction (PCR), sequencing, and genotyping applications. METHODS: XpressAmp lysate and extracted total nucleic acid from viral transport medium containing nasopharyngeal specimens were evaluated across different molecular applications to determine performance characteristics. RESULTS: SARS-CoV-2 quantitative PCR and angiotensin-converting enzyme (ACE) genotyping assays worked well with XpressAmp lysate, almost equal with or better than extracted nucleic acid in some specimens. However, XpressAmp completely failed to perform in next-generation sequencing for strain typing. Both protocols failed to detect ACE2 expression in viral transport medium. CONCLUSION: Direct amplification of viral nucleic acid from viral transport medium containing nasopharyngeal specimen works well for molecular assays with low thresholds of quality; however, it does have limitations with assays that require high quality nucleic acid for input. Use of the XpressAmp protocol significantly improves turnaround time and allows for easy ramp-up of PCR and genotyping assays.

Respiratory Pathogen Coinfections in SARS-CoV-2-Positive Patients in Southeastern Wisconsin: A Retrospective Analysis.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of coronavirus disease 2019 (COVID-19), has infected all age groups and disproportionately impacted vulnerable populations globally. Polymicrobial infections may play an important role in the development of SARS-CoV-2 infection in susceptible hosts. These coinfections may increase the risk of disease severity and pose challenges to the diagnosis, treatment, and prognosis of COVID-19. There have been limited SARS-CoV-2 coinfection studies. In this retrospective study, residual nucleic acid extracts from 796 laboratory-confirmed COVID-19-positive specimens, collected between March 2020 and February 2021, were analyzed using a Luminex NxTAG respiratory pathogen panel (RPP). Of these, 745 returned valid results and were used for analysis; 53 (7.1%) were positive for one or more additional pathogens. Six different respiratory viruses were detected among the 53 SARS-CoV-2-positive patient specimens, and 7 of those specimens tested positive for more than one additional respiratory virus. The most common pathogens include rhinovirus/enterovirus (RV/EV) (n = 22, 41.51%), human metapneumovirus (hMPV) (n = 18, 33.9%), and adenovirus (n = 12, 22.6%). Interestingly, there were no SARS-CoV-2 coinfections involving influenza A or influenza B in the study specimens. The median age of the SARS-CoV-2-positive patients with coinfections was 38 years; 53% identified as female, and 47% identified as male. Based on our retrospective analysis, respiratory coinfections associated with SARS-CoV-2-positive patients were more common in young children (≤9 years old), with white being the most common race. Our findings will likely prompt additional investigation of polymicrobial infection associated with SARS-CoV-2 during seasonal respiratory pathogen surveillance by public health laboratories. IMPORTANCE This examination of respiratory pathogen coinfections in SARS-CoV-2 patients will likely shed light on our understanding of polymicrobial infection associated with COVID-19. Our results should prompt public health authorities to improve seasonal respiratory pathogen surveillance practices and address the risk of disease severity.

Enhancing the scoping study methodology: a large, inter-professional team's experience with Arksey and O'Malley's framework.

BACKGROUND: Scoping studies are increasingly common for broadly searching the literature on a specific topic, yet researchers lack an agreed-upon definition of and framework for the methodology. In 2005, Arksey and O'Malley offered a methodological framework for conducting scoping studies. In their subsequent work, Levac et al. responded to Arksey and O'Malley's call for advances to their framework. Our paper builds on this collective work to further enhance the methodology. DISCUSSION: This paper begins with a background on what constitutes a scoping study, followed by a discussion about four primary subjects: (1) the types of questions for which Arksey and O'Malley's framework is most appropriate, (2) a contribution to the discussion aimed at enhancing the six steps of Arskey and O'Malley's framework, (3) the strengths and challenges of our experience working with Arksey and O'Malley's framework as a large, inter-professional team, and (4) lessons learned. Our goal in this paper is to add to the discussion encouraged by Arksey and O'Malley to further enhance this methodology. SUMMARY: Performing a scoping study using Arksey and O'Malley's framework was a valuable process for our research team even if how it was useful was unexpected. Based on our experience, we recommend researchers be aware of their expectations for how Arksey and O'Malley's framework might be useful in relation to their research question, and remain flexible to clarify concepts and to revise the research question as the team becomes familiar with the literature. Questions portraying comparisons such as between interventions, programs, or approaches seem to be the most suitable to scoping studies. We also suggest assessing the quality of studies and conducting a trial of the method before fully embarking on the charting process in order to ensure consistency. The benefits of engaging a large, inter-professional team such as ours throughout every stage of Arksey and O'Malley's framework far exceed the challenges and we recommend researchers consider the value of such a team. The strengths include breadth and depth of knowledge each team member brings to the study and time efficiencies. In our experience, the most significant challenges presented to our team were those related to consensus and resource limitations. Effective communication is key to the success of a large group. We propose that by clarifying the framework, the purposes of scoping studies are attainable and the definition is enriched.