Accessioning and automation compatible anterior nares swab design

Abstract

The COVID-19 pandemic has resulted in an unparalleled need for viral testing capacity across the world and is a critical requirement for successful re-opening of economies. The logistical barriers to near-universal testing are considerable. We have designed an injection molded polypropylene anterior nares swab, the Rhinostic, with a screw cap integrated into the swab handle that is compatible with fully automated sample accessioning and processing. The ability to collect and release both human and viral material is comparable to that of several commonly used swabs on the market. SARS-CoV-2 is stable on dry Rhinostic swabs for at least 3 days, even at 42 °C, and elution can be achieved with small volumes. To test the performance of the Rhinostic in patients, 119 samples were collected with Rhinostic and the positive and negative determinations were 100 % concordant with samples collected using Clinical Laboratory Improvement Amendments (CLIA) use approved nasal swabs at a clinical lab. The Rhinostic swab and barcoded tube set can be produced, sterilized, and packaged cost effectively and is designed to be adopted by clinical laboratories using automation to increase throughput and dramatically reduce the cost of a standard SARS-CoV-2 detection pipeline.

Keywords: AN swab; COVID-19; Detection; Nasal swab; SARS-CoV-2.

Fig. 1

96-well format automation and accession compatible AN swab design. (A) Custom injection molded AN swab that can be produced at large scale and is compatible with 96-well format automation. A sample tube compatible with the Rhinostic swab is shown with barcodes on the side and bottom. The Rhinostic swab is 4.9 cm long with a collection head length of 1.6 cm. 1 cm scale bar shown for reference. (B) 96-well rack of swabs and tubes with 2D matrix codes printed on the bottom of the tubes, allows for rapid accessioning.

Fig. 2

Comparison of swab performance. (A) AN swabs tested in this study, from left to right: Rhinostic, Procter & Gamble (P&G) Blue, Wyss Institute flocked prototype, Puritan hydraflock, Puritan foam, Puritan polyester, US Cotton, and Microbrush®. 1 cm scale bar shown for reference. (B) Schematic of swab experiments performed in C-D. Scheme I; SARS-CoV-2 negative volunteer self-collected nasal matrix on a swab. Scheme II; unused swab, without nasal matrix, was either treated with packaged synthetic SARS-CoV-2 virus or left untreated (clean, unused swab). Scheme III; SARS-CoV-2 negative volunteer self-collected nasal matrix on a swab which was then treated with packaged synthetic SARS-CoV-2 or SARS-CoV-2 remnant clinical sample (Methods). All samples were eluted in PBS and used as direct input to RT-qPCR assays. Images were created with BioRender.com. (C) RT-qPCR quantitation of human GAPDH mRNA from used swabs containing nasal matrix (pink bars) or matched unused swabs (grey bars). (D) RT-qPCR quantitation of the SARS-CoV-2 N gene from packaged synthetic virus applied to clean, unused swabs. The grey bar is the negative control, PBS input into RT-qPCR. The pink line is a guideline for complete recovery based on the positive control. (E) RT-qPCR quantitation of SARS-CoV-2 N gene from swabs in the presence of nasal matrix spiked with a lower (∼140 copies/μL, pink bars) or higher (∼1600 copies/μL, green bars) titer remnant clinical sample. The grey bar is the negative control, PBS, and the positive controls are the lower or higher titer remnant clinical samples directly input to RT-qPCR. RT-qPCR data in C-E all show technical replicates of at least 3 biological experiments (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article).

Fig. 3

Stability of SARS-CoV-2 on swabs in the presence of nasal matrix. (A) Schematic of the experimental workflow in B-E. SARS-CoV-2 remnant clinical sample was applied to unused swabs or self-collected AN swabs with nasal matrix, (Methods) and left dry or wet at 25 °C, and dry at 42 °C for up to 72 h. All samples were quantified by direct input of eluent into RT-qPCR. Images were created with BioRender.com. (B,C) The stability of SARS-CoV-2 on Rhinostic swabs with nasal matrix left dry or wet at 25 °C or dry at 42 °C was analyzed over the course of 72 h by RT-qPCR for the SARS-CoV-2 N gene (B) or GAPDH (C). (D,E) The stability of SARS-CoV-2 on Puritan foam swabs with nasal matrix left dry or wet at 25 °C or dry at 42 °C was analyzed over the course of 72 h by RT-qPCR for the SARS-CoV-2 N gene (D) or GAPDH (E). Data points in B-E are technical replicates of 2 biological replicates. The positive control in B-E is the SARS-CoV-2 remnant clinical sample directly added to PBS at time 0. The negative control is an unused Rhinostic (B, C) or Puritan foam (D, E) swab in PBS.

Fig. 4

Rhinostic concordance with control swabs. (A) Determination of SARS-CoV-2 status (positive or negative) based on a Rhinostic swab or a CLIA use approved swab. Rhinostic swabs were used by each patient for a total of 15 positive patient samples and 104 negative patient samples. The CLIA use approved swabs were performed at an independent CLIA lab for RT-qPCR determination; the Rhinostic swabs were self-collected by the patient and assayed by direct RT-qPCR in our lab. Swabs were not taken at the same time; instead Rhinostic swabs were taken within 2 days of CLIA SARS-CoV-2 status determination. (B,C) Fourteen paired clinical patient samples were collected with a Rhinostic swab and a CLIA use approved swab and tested for N gene and GAPDH by direct input of swab eluent into RT-qPCR. Presented are the average of two or three technical replicates for each paired sample tested for N gene (B) or GAPDH (C). Samples that were negative for N gene detection are identified as not determined (ND) in (B).