Effectiveness of Self-Collected, Ambient Temperature-Preserved Nasal Swabs Compared to Samples Collected by Trained Staff for Genotyping of Respiratory Viruses by Shotgun RNA Sequencing: Comparative Study

BACKGROUND

The SARS-CoV-2 pandemic has underscored the need for field specimen collection and transport to diagnostic and public health laboratories. Self-collected nasal swabs transported without dependency on a cold chain have the potential to remove critical barriers to testing, expand testing capacity, and reduce opportunities for exposure of health professionals in the context of a pandemic.

OBJECTIVE

We compared nasal swab collection by study participants from themselves and their children at home to collection by trained research staff.

METHODS

Each adult participant collected 1 nasal swab, sampling both nares with the single swab, after which they collected 1 nasal swab from 1 child. After all the participant samples were collected for the household, the research staff member collected a separate single duplicate sample from each individual. Immediately after the sample collection, the adult participants completed a questionnaire about the acceptability of the sampling procedures. Swabs were placed in temperature-stable preservative and respiratory viruses were detected by shotgun RNA sequencing, enabling viral genome analysis.

RESULTS

In total, 21 households participated in the study, each with 1 adult and 1 child, yielding 42 individuals with paired samples. Study participants reported that self-collection was acceptable. Agreement between identified respiratory viruses in both swabs by RNA sequencing demonstrated that adequate collection technique was achieved by brief instructions.

CONCLUSIONS

Our results support the feasibility of a scalable and convenient means for the identification of respiratory viruses and implementation in pandemic preparedness for novel respiratory pathogens.

Accuracy of State-Level Surveillance during Emerging Outbreaks of Respiratory Viruses: A Model-Based Assessment

It is long perceived that the more data collection, the more knowledge emerges about the real disease progression. During emergencies like the H1N1 and the severe acute respiratory syndrome coronavirus 2 pandemics, public health surveillance requested increased testing to address the exacerbated demand. However, it is currently unknown how accurately surveillance portrays disease progression through incidence and confirmed case trends. State surveillance, unlike commercial testing, can process specimens based on the upcoming demand (e.g., with testing restrictions). Hence, proper assessment of accuracy may lead to improvements for a robust infrastructure. Using the H1N1 pandemic experience, we developed a simulation that models the true unobserved influenza incidence trend in the State of Michigan, as well as trends observed at different data collection points of the surveillance system. We calculated the growth rate, or speed at which each trend increases during the pandemic growth phase, and we performed statistical experiments to assess the biases (or differences) between growth rates of unobserved and observed trends. We highlight the following results: 1) emergency-driven high-risk perception increases reporting, which leads to reduction of biases in the growth rates; 2) the best predicted growth rates are those estimated from the trend of specimens submitted to the surveillance point that receives reports from a variety of health care providers; and 3) under several criteria to queue specimens for viral subtyping with limited capacity, the best-performing criterion was to queue first-come, first-serve restricted to specimens with higher hospitalization risk. Under this criterion, the lab released capacity to subtype specimens for each day in the trend, which reduced the growth rate bias the most compared to other queuing criteria. Future research should investigate additional restrictions to the queue.

Detection of the first appearance of SARS-CoV-2 virus in Hungary based on retrospective testing of respiratory samples

INTRODUCTION

In Hungary, SARS-CoV-2 was first detected in the swab samples of two Iranian patients on March 4, 2020. After finding the first positive cases, the question arose whether the virus had entered Hungary and caused infections before this date. Before March 4, 2020, except for the two above-mentioned samples, none of the 224 swab samples received specifically for SARS-CoV-2 tested positive.

AIM

The National Reference Laboratory for Respiratory Viruses of the National Public Health Center aimed to carry out a retrospective study of the swab and other samples taken for testing respiratory virus infections between January 1, and April 19, 2020 sent by sentinel physicians within the influenza surveillance for diagnostic purposes.

METHOD

For the study, we used swab samples taken weekly by sentinel physicians of the influenza surveillance service, and other samples received for diagnostic purposes. Tests were performed using real-time PCR.

RESULTS

All the 465 swab samples sent by sentinel physicians were found to be SARS-CoV-2 negative. Also, of the 551 samples collected for diagnostic reasons of other respiratory viruses, no SARS-CoV-2 positive was found among those taken before March 4.

CONCLUSION

Based on our data, it is very likely that prior to the first cases diagnosed on March 4, 2020, SARS-CoV-2 did not cause clinically symptomatic infections in Hungary. Orv Hetil. 2020; 161(38): 1619-1622.