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HOW TO CHOOSE A SAMPLE COLLECTION DEVICE FOR SELF-COLLECTED

HOW TO CHOOSE A SAMPLE COLLECTION DEVICE FOR SELF-COLLECTED, AT-SCALE TESTING

CONSIDERATIONS FOR DIRECT-TO-CONSUMER SAMPLING APPLICATIONS

There are a lot of considerations when choosing a sample collection device for direct-to-consumer testing. This could mean creating a kit that is shipped to end users, leaving sample collection entirely in the hands of the user. Unsupervised sample collection has become increasingly common with at-home COVID-19 tests as well as ancestry and other DNA tests done without a physician. While this is the new norm for accessible health information, unsupervised sample collection is not without challenges. More than ever before, the sample collection device a direct-to-consumer test uses is one of the most critical components.

The first thing to consider when choosing a sample collection device is the intended application. What biological sample types will be collected? Some common sample types include saliva, nasal, buccal (inner cheek), fecal, and vaginal samples. The sample type required for the test will help narrow down what sample collection devices are able to be used. Saliva applications are becoming more popular due to increased usability and saliva has also shown to yield good results for oral samples. Other applications, like vaginal microbiome testing, will require a swab to be used.

One of the most important components a collection device should have is a liquid stabilizing reagent which quickly preserves the genetic integrity of the sample once collected. This is especially important for tests that require RNA, as it degrades as soon as a sample is taken, creating an impossibly small window for results unless it is stabilized immediately after collection.

If a sample collection device does not include a stabilization solution and only uses saline, it will require costly shipping techniques including shipping on dry ice, expedited shipping, hazard shipping, and additional precautions needed to receive the sample as a biological hazard. In the United States, this adds a minimum cost of $50 to each sample that would need to be priced into the cost of the test or test kit that is sold to users.


As the market for at-home testing grows, it’s crucial to choose safe and reliable methods of sample collection.

PATHOGEN INACTIVATION

Another critical component the reagent in the sample collection device should have is pathogen inactivation. With the ability to render pathogens non-infectious, the receiving lab that processes the sample is only required to be a Bio Safety Level (BSL) 2, and not a BSL-3. BSL-2 labs are more widely available than BSL-3, and less costly, as they do not require enhanced safety measures designed to handle highly infectious samples.

TECHNOLOGY

While there are several sample collection devices on the marketing that offer pathogen inactivation, the design is often what sets them apart. With the intention of the collection device being at-home or unsupervised collection, this presents more opportunities for accidental ingestion and thus the need for safety precautions. Some collection devices are designed with the preservation solution in the cap or as part of the saliva funnel. While this is convenient for users it still poses the safety risk of exposure to the solution as the funnel needs to be taken off and replaced with the cap after the solution is added. Additionally, devices with preservation solution chambers outside of the tube can easily expose users if the film on the chamber is accidentally removed.

USER SAFETY

User safety is perhaps the most critical aspect of a sample collection device, as it limits liability while ensuring sample integrity for accurate results. Opt for a collection device designed around user safety and ease of use, that minimizes collection errors and prevents access to the preservation solution by containing it inside the tube with a safety seal. By sealing the solution inside the tube and only allowing the seal to be punctured after collection, the risk of accidental exposure can be mitigated.

SCALING BUSINESS

As a direct-to-consumer business scales and acquires new customers, a larger volume of samples will need to be processed, requiring increased efficiency only made possible by automation. An important consideration when choosing a sample collection device is how easily it can be integrated into automated workflows such as de-capping, aliquoting, and recapping. Some automation suppliers offer stock automated platforms, such as the Sarstedt DC/RC 900 Flex system, specifically developed to perform some of the steps found in sample accessioning. To facilitate integration into some of the pre-existing accessioning systems there are certain dimension and shape constraints to consider for a collection device. For instance, the DC/RC 900 Flex system only de-caps tubes in the diameter range of 11-16mm, with additional limitations on dimensions for recapping. In blunter terms, a square device will be harder to work with in an industry adapted towards cylindrical tubes.

While custom automated solutions are always an option for unique device designs, it is an added complication and cost for companies seeking to rapidly expand their throughput without the hassle of having to develop new equipment from scratch. There can also be some overlooked characteristics that are problematic in automation; for example, brittle collection device materials will be more prone to cracking when exposed to grip or torque forces. Given these constraints, companies should only consider sample collection devices that can be reliably integrated into automated accessioning systems even if manual processing is relied upon early on so manual processing does not inhibit business growth.

SUPPLY CHAIN CONTROL

It’s no secret that the global supply chain has become a concern for businesses in most industries. Considering the reliability of a sample collection device manufacturer should not be overlooked, as backordered components for sample collection devices can bring a company’s growth to a halt. A sample collection device manufacturer should control the entirety of their supply chain to ensure consistent production, so they are not inhibited by relying on components from other suppliers. Additionally, a sample collection device manufacturer should have the flexibility and production capacity to scale with the growth of the businesses they supply to.

THE BEST SAMPLE COLLECTION DEVICES FOR DIRECT-TO-CONSUMER APPLICATIONS

With all of these considerations, finding a sample collection device may seem like a daunting task, but there are two options that meet all of the above criteria. Zymo Research’s SafeCollect Saliva Collection Kit and SafeCollect Swab Collection Kit were designed specifically for unsupervised sample collection and at-home testing applications.

SafeCollect devices come in two formats: one for swabs and one for saliva (Figure 2). Both formats feature DNA/RNA Shield in the sealed tube chamber, a solution that inactivates infectious agents, stabilizes DNA and RNA for up to 30 days at ambient temperature (or indefinitely when frozen), and an automation-compatible tube and cap. Spills are prevented by a safety seal that isolates the DNA/RNA Shield reagent from user contact.

With the SafeCollect Swab Collection Kit, the sample is brought into contact with DNA/RNA Shield by puncturing the safety seal with a swab after sample collection. The swab is then broken to fit within the collection tube, and the tube is capped. A variety of swabs are compatible to accommodate a variety of applications and sample types.

The SafeCollect Saliva Collection Kit allows users to deposit saliva into the tube with a user-friendly funnel. Once enough saliva is collected, the funnel is removed and replaced with a tube cap featuring a Safe Puncture Cap Tip™. Capping the tube punctures the safety seal, allowing DNA/RNA Shield to mix with the saliva sample once the cap is screwed onto the tube.

Zymo Research is the preferred supplier of sample collection devices for many direct-to-consumer testing companies. With virtually unlimited production capacity and as the sole manufacturer of all components in SafeCollect Collection Kits, Zymo Research can scale production to match any business’s growth and sustain supply through the rapidly evolving era of modern biological testing.

LEARN MORE ABOUT ZYMO RESEARCH’S SAFECOLLECT SWAB AND SALIVA COLLECTION KITS

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HOW TO EXTRACT RNA FROM HARD-TO-LYSE SAMPLES IN TRIZOL®

HOW TO EXTRACT RNA FROM HARD-TO-LYSE SAMPLES IN TRIZOL®

LEARN THE BEST EXTRACTION METHODS FOR CHALLENGING SAMPLE TYPES

THE CHALLENGE OF RNA ISOLATION

RNA isolation is a challenging procedure. Unlike DNA, which is highly stable, RNA is very unstable, quickly digested by RNase enzymes if their activity isn’t immediately inhibited. Traditional RNA isolation protocols are also tedious, time-consuming, and unscalable. Since RNA isolation is critical to many scientific enterprises, researchers have optimized protocols and reagents to speed up and simplify the process.

One popular reagent in RNA isolation protocols is TRIzol®. Composed of phenol and guanidine thiocyanate in a mono-phase solution, TRIzol® (or TRI Reagent®) is a cell lysis and RNase-inhibiting solution used for the simultaneous isolation of RNA, DNA, and proteins from biological samples. The components of TRI Reagent® facilitate immediate and effective inhibition of RNase activity and isolate RNA from human, animal, plant, yeast, bacterial, and viral samples with consistent performance on all quantities of tissues or cultured cells.

TRIZOL® FOR ISOLATING RNA FROM A RANGE OF SAMPLES

TRIzol® was specifically formulated to isolate total RNA from any sample type in the modern research laboratory, whether in academia or industry: cells, hard to lyse or solid tissue, and infectious biological samples.

CELLS

TRIzol® permits efficient RNA isolation from cells, because it quickly breaks down cell structures and inactivates RNases in the sample, protecting RNA from degradation.

HARD-TO-LYSE SAMPLES OR SOLID TISSUE

The chemical makeup of TRIzol® also facilitates the release of RNA from hard-to-lyse cells and tissue samples with the aid of mechanical homogenization and/or Proteinase K treatment.

INFECTIOUS BIOLOGICAL SAMPLES

TRIzol® inactivates pathogens in plasma, serum, stool, blood, and other biological sample types, eliminating infection risk for researchers and simplifying RNA extraction.

TIPS FOR EFFICIENT RNA EXTRACTION WITH TRIZOL®

RNA extraction with TRIzol® combines phenol and guanidine thiocyanate in a mono-phase solution, facilitating immediate and effective inhibition of RNase activity. However, when preparing biological samples for RNA isolation, certain considerations should be taken into account for an optimal outcome. Here are some sample preparation tips to ensure efficient RNA extraction from cells, hard-to-lyse/solid tissue, and infectious biological samples:

CELLS

Due to their cellular structure, mammalian cells are the easiest to lyse in TRIzol®, typically needing no additional chemical lysis or mechanical homogenization. To maximize RNA isolation efficiency, adhere to the following while preparing cells in TRIzol®:

  1. Add 1 ml TRIzol® to 5-10 x 106 fresh, pelleted mammalian cells. Pipette up and down until cells are fully lysed and homogenous.
  2. Tip 1: If the lysate remains cloudy, opaque, and/or viscous, increase the volume of TRIzol® until clear.
  3. Tip 2: After lysis with TRIzol®, centrifuge the lysate at max speed for 1-2 minutes and transfer the supernatant into a new tube prior to processing. Leave at least 50 μl at the bottom of the old tube to avoid transferring part of the pellet.

HARD-TO-LYSE/SOLID TISSUE AND INFECTIOUS BIOLOGICAL SAMPLES

Solid tissues, including heart, lung, liver, muscle, and cartilage, are more difficult to lyse than cells. Additionally, gram-positive bacteria and yeast cells (ex: Bacillus, Listeria, Saccharomyces) are also considered hard-to-lyse due to polysaccharides in their cell walls.

Infectious biological samples, such as plasma, serum, stool, and whole blood, are complex, highly proteinated samples with a mixture of easy and tough-to-lyse components, and therefore should be handled like hard-to-lyse samples. To maximize RNA isolation efficiency, adhere to the following while preparing tough-to-lyse samples, solid tissue, and infectious biological samples in TRIzol®:

  • Tip 1: Unlike cells, these sample types require additional chemical lysis and/or mechanical homogenization.
    • We recommend mechanical homogenization as the optimal approach for lysing these samples. For high-speed homogenization (e.g., Bertin Precellys), add 1 ml TRIzol® to a fresh tissue sample (10% w/v) and bead beat at maximum speed for 30-60 seconds. For low-speed homogenization (e.g., Disruptor Genie), bead beat at maximum speed for 5-10 minutes. The exact amount of time is sample type-dependent.
    • Chemical lysis with Proteinase K treatment can also be performed, either with or without mechanical homogenization. If mechanical homogenization was performed, treat the sample in Proteinase K for 30 minutes. If not, increase Proteinase K treatment time to 2-5 hours.
  • Tip 2: After homogenization and/or Proteinase K treatment, centrifuge down any debris and transfer the supernatant into a new tube prior to purification.
  • Tip 3: If the supernatant/lysate is still cloudy, opaque and/or viscous, increase the volume of TRIzol® until clear.

EXTRACT RNA FROM TRIZOL IN 7 MINUTES WITH DIRECT-ZOL RNA KITS

Traditional TRIzol® RNA extraction is an elaborate, time-consuming protocol. Once cells are lysed, then the homogenate must be phase-separated by adding bromochloropropane or chloroform and centrifuging the sample. After centrifugation, three phases are visible: the aqueous phase (RNA), the organic phase (DNA), and the interphase (proteins).

RNA is precipitated from the aqueous phase by adding isopropanol, washing with ethanol, and solubilizing the final RNA pellet. Each step in this process is tedious and time consuming, taking more than an hour for the entire process, and must be performed with care. RNA yields and purity are often compromised due to incomplete cell lysis, contamination of the aqueous phase by the phenol phase, or incompletely dissolved final RNA pellets.

The Direct-zol RNA kits by Zymo Research, designed to work with TRIzol®, TRI Reagent®, or similar acid-guanidinium-phenol based reagent, achieves total RNA extraction, including small/miRNAs, from any sample in only seven minutes. With the Direct-zol RNA kit, you’ll achieve consistent results, higher RNA yields (up to four-fold more), and a quicker processing time compared to the conventional RNA isolation method. No chloroform or phase separation is necessary, and there are no precipitation steps, eliminating aqueous phase contamination and incompletely dissolved RNA pellets.

To isolate RNA with the Direct-zol RNA kit, simply add sample lysed in TRIzol® directly to the Zymo-Spin Column and then bind, wash, and elute the RNA. The resulting DNA-free RNA is ready for any downstream application, including next-generation sequencing (NGS), RT/qPCR, northern blots, and other protocols requiring pure RNA.

The Direct-zol method can also be scaled up and automated with the Direct-zol-96 MagBead RNA kit, which is compatible with any robotic sample processor (e.g., Hamilton, Kingfisher, and Tecan) — making high-throughput, rapid extraction of high-quality RNA accessible to any research laboratory.

THE EXPERIENCE OF RAPID, EFFICIENT RNA EXTRACTION

RNA extraction doesn’t have to be a dreaded part of your scientific protocols. The Direct-zol RNA kit makes RNA isolation from any sample type — including hard to lyse/solid tissue samples — a breeze. Due to its unsurpassed speed and ability to isolate high-yield, pure RNA from a variety of cell and tissue types, the Direct-zol RNA kit is the optimal solution for RNA extraction from samples in TRIzol®. If you’d like to experience for yourself the power of rapid, scalable RNA extraction, 

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New SARS-CoV-2 Recombinant Virus Lineages

New SARS-CoV-2 Recombinant Virus Lineages

Three SARS-CoV-2 recombinant lineages have been designated by Pangolin as of March 2022, two a combination of Delta and BA.1 (designated XD and XF), and the third a combination of Omicron BA.1 and Omicron BA.2 with a few additional mutations in NSP3 and NSP12 (designated XE).

Below is a graphical representation of the recombinant lineages as compared to the genome schematic, courtesy of the UK Health Security Agency.

SARS-CoV-2 XD, XE, and XF Epidemiology

As mentioned, XD is a combination of Delta and Omicron BA.1. More specifically, it is comprised of Delta AY.4 with an Omicron BA.1 Spike. Recombination of two different strains combines features of both parent viruses, potentially causing different phenotypic expressions than either parent virus. In this case potentially the infectivity of Omicron and the disease severity of Delta. The earliest samples were collected in December 2021 and to date, samples have been identified in France, Denmark, and Belgium.

XE, however, is a combination of two Omicron sub-strains, BA.1 and BA.2, first detected on January 19, 2022. This variant contains NSP1-6 from BA.1 with the remainder of the genome from BA.2 with the recombination occurring at nucleotide 11,537. According to the WHO, it currently has an estimated community growth rate advantage of 1.1 as compared to BA.2, which represents a 10% increase in transmissibility.

XF, while also recombination of Delta and Omicron BA.1, is instead comprised of the first part of the genome up until nucleotide 5386, near the end of NSP3. This variant appears to be unique to the UK with samples found between January 7, 2022, and February 14, 2022, and no current evidence of growth.

While it is too early to tell if these recombinant variants will cause a public health concern, it is to be expected as viruses recombine all the time.

Viral Recombination

Recombination occurs in many viruses, including other coronaviruses, HIV, and influenza. Results of recombination vary from being innocuous to potentially generate more infectious virions.

How do viruses recombine? This phenomenon occurs when two strains of virus infect the same host cells and interact to generate another strain during replication that contains genes from both original strains.

RNA viruses undergo two forms of recombination. One is copy choice recombination, which occurs during viral replication when the RNA polymerase switches from one RNA to another, creating a new RNA strand that is a combination of the two. The other is reassortment, occurring in viruses with segmented genomes, where different segments of different genomes are packaged into a new virion.

Further your Research with ProSci

To date, ProSci has developed variant-specific reagents by focusing on unique point mutations in the spike protein. Cat. No. 9793 targets the G142D Δ143-145VYY mutation and deletion combination found in BA.1 and Cat. No. 9805 targets the Q493R G496S Q498R N501Y Y505H region currently unique to BA.1 (4 mutations shared with BA.2).

To further research, recombinant proteins for BA.1 (RBD Cat. No. 95-128 and Spike S1 Cat. No. 95-129) are available as well as a BA.1 variant pseudovirus  (Cat. No. 95-201). For additional variant-specific research reagents and wild-type controls, visit our Variants Research Reagents.

At the onset of the COVID-19 pandemic, ProSci developed antibodies against SARS-CoV-2 and has continued to expand its catalog of antibodies and recombinant proteins. Explore the comprehensive catalog of ProSci SARS-CoV-2 Research Reagents.

References:

  1. New SARS-CoV-2 Recombinant Virus Lineages | ProSci Incorporated (prosci-inc.com)
  2. UK Health Security Agency, Technical briefing 39, https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1063424/Tech-Briefing-39-25March2022_FINAL.pdf
  3. https://twitter.com/PeacockFlu/status/1504158922675998723
  4. Weekly epidemiological update on COVID-19 – 5 April 2022, Edition 86. https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports
  5. Fleischmann, Robert. Medical Microbiology. Galveston, TX, Univ of Texas Medical Branch, 1996. https://www.ncbi.nlm.nih.gov/books/NBK8439/
  6. Simon-Loriere, E., Holmes, E. Why do RNA viruses recombine? Nat Rev Microbiol9, 617–626 (2011). https://doi.org/10.1038/nrmicro2614
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Product Change Notification

Product Change Notification

This notice is to inform you Product Change for the items listed below. The change affects the appearance of the plate (images of plates below) which is a component in certain competent cell products as well as the S6002-96-2 and S6002-96-3 lysis racks which are in in various kits (listed below). The change will not affect the fit or function of the products. The change will take place immediately to minimize disruption in supply of the affect products.

List of Affected Products:

  • S6002-96-2 (ZR-96 BashingBead Lysis Rack (2 mm) (1 Rack))
  • S6002-96-3 (ZR-96 BashingBead Lysis Rack (0.5 mm & 0.1 mm) (1 Rack))
  • D4302 – ZymoBIOMICS™-96 MagBead Kit (2 x 96 Preps.)
  • D4303 – ZymoBIOMICS™-96 DNA Kit (2 x 96 Preps.)
  • D6006 – Quick-DNA™ Fungal/Bacterial 96 Kit (2 x 96 Preps.)
  • D6011 – Quick-DNA™ Fecal/Soil Microbe 96 Kit (2 x 96 Preps.)
  • D6017 – Quick-DNA™ Tissue/Insect 96 Kit (2 x 96 Preps.)
  • D6021 – Quick-DNA™ Plant/Seed 96 Kit (2 x 96 Preps.)
  • D6010-FM – Quick-DNA™ Fecal/Soil Microbe 96 Magbead Kit
  • T3005: Mix & Go! Competent Cells – JM109 (96 x 50 ml)
  • T3009: Mix & Go! Competent Cells – Zymo 5a (96 x 50 ml)
  • T3013: Mix & Go! Competent Cells – HB101 (96 x 50 ml)
  • T3020: Mix & Go! Competent Cells – Zymo 10B (96 x 50 ml)