Mobile SARS‑CoV‑2 screening facilities for rapid deployment and university-based diagnostic laboratory

Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has created a public crisis. Many medical and public institutions and businesses went into isolation in response to the pandemic. Because SARS-CoV-2 can spread irrespective of a patient's course of disease, these institutions' continued operation or reopening based on the assessment and control of virus spread can be supported by targeted population screening. For this purpose, virus testing in the form of polymerase chain reaction (PCR) analysis and antibody detection in blood can be central. Mobile SARS-CoV-2 screening facilities with a built-in biosafety level (BSL)-2 laboratory were set up to allow the testing offer to be brought close to the subject group's workplace. University staff members, their expertise, and already available equipment were used to implement and operate the screening facilities and a certified diagnostic laboratory. This operation also included specimen collection, transport, PCR and antibody analysis, and informing subjects as well as public health departments. Screening facilities were established at different locations such as educational institutions, nursing homes, and companies providing critical supply chains for health care. Less than 4 weeks after the first imposed lockdown in Germany, a first mobile testing station was established featuring a build-in laboratory with two similar stations commencing operation until June 2020. During the 15-month project period, approximately 33,000 PCR tests and close to 7000 antibody detection tests were collected and analyzed. The presented approach describes the required procedures that enabled the screening facilities and laboratories to collect and process several hundred specimens each day under difficult conditions. This report can assist others in establishing similar setups for pandemic scenarios.

Keywords: COVID‐19; HIS & LIMS; PCR; SARS‐CoV‐2; screening.

FIGURE 1

Processes displayed by material and data workflow. (A): Representation of material and data flow. Prepared test‐kits for PCR and antibody testing (a) were provided to screening facilities, where subject data was entered and samples (oropharyngeal swabs or blood samples) were collected (b). Swabs were handed to a BSL‐2 laboratory for RNA isolation (c), followed by PCR analysis (d). Serum samples were used for antibody detection analysis (e). Lab processes were controlled by the LIMS, which also stored raw analysis data (f). Raw analysis data was evaluated and confirmed results (g) were sent to the HIS, upon which sample result and subject data were merged (h). Positive PCR test results were submitted to the health department and a medical staff member informed the subject, whereas all other test results were sent to the subject via e‐mail (i). (B): Implementation of the laboratory and digital infrastructure processes. Subject and sample admissions started with manually entering or recalling a subject's personal information (e.g., name, address) from a previously handed‐out QR code. Subsequently, the acquisition of voluntarily given answers to medical study questionnaires in the HIS data entry software occurred. Subjects were then given printed handouts with their QR code for future visits and a consent form to be signed before taking either an oropharyngeal swab or a blood sample. The collected sample was pseudonymized with an identifier label from a pre‐assembled test kit, and the completed dataset was stored in the HIS database. Depending on the type of specimen, samples were then handed to the appropriate laboratory for analysis. Upon retrieval, the arrival of samples was documented. For PCR and antibody analysis, plate and rack information were created by scanning and sorting samples. Analysis results were evaluated and confirmed by lab managers. If no valid result was achieved and a reserve sample was available, analysis was performed again. Confirmed results (including the need for sample recollection) for each pseudonymized sample were sent to the HIS database for report generation and informing subjects. In case of a positive PCR test result, a medical staff member received the subject and sample information to contact the subject directly. At the same time, the report was sent to the public health department

FIGURE 1

Processes displayed by material and data workflow. (A): Representation of material and data flow. Prepared test‐kits for PCR and antibody testing (a) were provided to screening facilities, where subject data was entered and samples (oropharyngeal swabs or blood samples) were collected (b). Swabs were handed to a BSL‐2 laboratory for RNA isolation (c), followed by PCR analysis (d). Serum samples were used for antibody detection analysis (e). Lab processes were controlled by the LIMS, which also stored raw analysis data (f). Raw analysis data was evaluated and confirmed results (g) were sent to the HIS, upon which sample result and subject data were merged (h). Positive PCR test results were submitted to the health department and a medical staff member informed the subject, whereas all other test results were sent to the subject via e‐mail (i). (B): Implementation of the laboratory and digital infrastructure processes. Subject and sample admissions started with manually entering or recalling a subject's personal information (e.g., name, address) from a previously handed‐out QR code. Subsequently, the acquisition of voluntarily given answers to medical study questionnaires in the HIS data entry software occurred. Subjects were then given printed handouts with their QR code for future visits and a consent form to be signed before taking either an oropharyngeal swab or a blood sample. The collected sample was pseudonymized with an identifier label from a pre‐assembled test kit, and the completed dataset was stored in the HIS database. Depending on the type of specimen, samples were then handed to the appropriate laboratory for analysis. Upon retrieval, the arrival of samples was documented. For PCR and antibody analysis, plate and rack information were created by scanning and sorting samples. Analysis results were evaluated and confirmed by lab managers. If no valid result was achieved and a reserve sample was available, analysis was performed again. Confirmed results (including the need for sample recollection) for each pseudonymized sample were sent to the HIS database for report generation and informing subjects. In case of a positive PCR test result, a medical staff member received the subject and sample information to contact the subject directly. At the same time, the report was sent to the public health department

FIGURE 2

Floorplan of the container‐based screening facility. The setup consisted of two containers, of which the lower one comprised the main staff entrance, storage, server rack, and changing areas. The specimen collection as well as data entry area comprised half of the other container, with two similar working stations and windows facing outsides for subjects to line up. The second half was occupied by a BSL‐2 laboratory used for RNA isolation and was connected to the sampling area via a transfer hatch

FIGURE 3

Views of the container‐based screening facility. Displayed are the two stations for subject admission and specimen collection from the outside (A) and the respective workstations inside (B). The BSL‐2 laboratory is connected to the sampling area via a transfer hatch (C). Sampling area and laboratory can be reached through the changing and storage area (D)

FIGURE 4

System setup and network diagram. The system setup on campus (“local site”) consisted of three hypervisor servers with shared storage over SSD to establish an HA cluster running the separate VMs for LIMS and HIS database applications. For the OS and storage using HDDs on single servers, a redundant array of independent disks was used. Hypervisor servers were hosted at protected and different locations. A dedicated server handled backups of VMs and data. The separate networks for LIMS, HIS, storage, and server management were governed and protected by an HA firewall. External sites (i.e., container‐based screening facilities with build‐in BSL‐2 laboratories or reduced setups for sample collection) were connected using encrypted VPN connections. CPU, central processing unit; NIC, network interface card; RAM: random access memory

FIGURE 5

Number of PCR tests and subjects tested positive for SARS‐CoV‐2 per week. PCR tests and subjects with a PCR confirmed acute SARS‐CoV‐2 infection recorded at a mobile screening facility are displayed per week for the time period between April 2020 and November 2020