Operational considerations and challenges of biochemistry laboratories during the COVID-19 outbreak: an IFCC global survey

Introduction

The relatively recent appearance of coronavirus disease 2019 (COVID-19), a life-threatening infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is now challenging response and resilience of healthcare systems all around the globe [1]. The upgrade of this outbreak to a pandemic by the World Health Organization (WHO) [2] highlights the serious nature of the disease, which has caused unexpected and unprecedented disruption and challenges to laboratory practices [3], [4]. In particular, the highly infectious nature of this novel coronavirus and the risk of progression toward severe, even critical, forms of disease have necessitated measures to limit the risk of nosocomial transmission in clinical laboratories which routinely handle large volumes of specimens from suspected and confirmed COVID-19 cases [5], [6]. Considering the infectiousness and severity of COVID-19, the epidemic will affect laboratories around the world, and there is a need to understand how they are managing the operational challenges.

The Task Force on COVID-19, recently established under the umbrella of the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) (https://www.ifcc.org/executive-board-and-council/eb-task-forces/ifcc-task-force-on-covid-19/), has prepared and undertaken a global survey aimed at elucidating how clinical laboratories manage operational challenges during the COVID-19 outbreak. This article describes the second part of data garnered with this survey. The first part of the survey data is published in a separate companion article [7].

Materials and methods

A survey questionnaire has been conceived and then constructed by three chemical pathologists from Singapore and Australia (see Supplementary material). After a concise presentation aimed at describing the purposes of the survey, an informed consent was asked to survey participants for publicizing the information. This survey has been conducted without requesting identifiable data from responders. Participants were then asked to answer specific questions dealing with some characteristics of their laboratory, as well as with pre-analytical, analytical, post-analytical and operational activities. The original draft of the survey has been pilot tested in seven laboratories in Sydney (Australia) and Singapore, undergoing two refinement cycles.

The questionnaire was then constructed using an enterprise internet survey engine (Verint Systems, Melville, NY, USA), being published in the English language on April 16, 2020. Chinese, Spanish and French translations of the survey were also developed and disseminated on April 22, 2020. The survey was publicized globally through multiple channels, including the IFCC eNewsFlash, the Canadian Society for Clinical Chemistry, the Australasian Association for Clinical Biochemistry and Laboratory Medicine, the European Federation of Clinical Chemistry and Laboratory Medicine, the American Association for Clinical Chemistry, the Spanish Society of Laboratory Medicine, the Korean Society for Clinical Chemistry, the Chinese Society of Laboratory Medicine, the Argentinian National Society and the Latin American Confederation of Clinical Biochemistry. The survey was closed on May 1, 2020.

All responses were retrieved from the survey engine into an Excel file and analyzed using Analyse-It (for Microsoft Excel, Microsoft, Seattle, WA, USA). This study focused on survey responses related to operational considerations and challenges, which were hence summarized only using descriptive statistics.

Results

General characteristics of survey participants

The survey received 1483 valid submissions. A total number of 273 of these submissions ought to be excluded because the responders replied that they were not involved in processing biospecimens from COVID-19 patients at the time of the survey, or failed to reply to this question. Overall, the final analysis was hence based on 1210 valid submissions, 921 in English, 62 in Chinese, 183 in Spanish and 44 in French, respectively, from 86 worldwide regions and countries (Supplementary Table 1). The general aspects of responders are briefly reported in Table 1. Most participants declared to be working in hospital laboratories and more than half declared to be managing between 200 and 2500 biospecimens per day. Nearly half of all clinical laboratories were using partial or total laboratory automation. The responses to operational considerations and challenges during the COVID-19 pandemic are summarized in Figure 1.

Table 1:

General characteristics of survey participants.

Question	Response	Frequency, n (% of total submission)
Which of the following best describes your biochemistry laboratory?	Hospital central/core laboratory	998 (82.4)
	Hospital satellite laboratory	69 (5.7)
	Community-based laboratory	81 (6.7)
	Other	62 (5.1)
Which of the following patient populations are served by your biochemistry laboratory? Please select all that apply	Inpatient	1101 (90.1)
	Outpatient	1085 (89.7)
	Emergency department	1023 (84.5)
	Intensive care units	1007 (83.2)
	Other	171 (14.1)
	Not answered	4 (0.3)
Please indicate the number of patient samples your laboratory processes per day?	<200 samples	301 (24.9)
	200–999 samples	446 (36.9)
	1000–2500 samples	253 (20.9)
	>2500 samples	204 (16.9)
	Not answered	6 (0.5)
Does the biochemistry laboratory use any of the following components of a laboratory automation system? Please select all that apply	Centrifugation	752 (20.3)
	Decapping	652 (53.9)
	Aliquoting	594 (49.1)
	Recapping	508 (42.0)
	Sample storage	593 (49.0)
	Sample conveyance track	466 (38.5)
	We do not use a laboratory automation system	373 (30.8)
	Not answered	12 (1.0)

Figure 1:

Frequency of responses to questions related to operational considerations and challenges in clinical biochemistry laboratories during the COVID-19 pandemic.

The percentages are expressed fractions of the total number of valid submissions (n=1210). *indicates percentages expressed fractions of the total number of positive response of the stem question.

Discussion

During the COVID-19 pandemic, clinical laboratories were confronted by two major challenges, encompassing the need to ensure a safe workplace environment and maintaining laboratory activities often without adequate resources. In response to these challenges, some facilities were forced to limit laboratory test availability. The analyses that were restricted for biohazard concerns mostly involved pleural fluid, respiratory samples, and fecal and urine specimens. This choice may be related to reports of viral nucleic acid being detected in fecal and urine samples [8], [9], [10], [11], but the latter is particularly surprising considering its extremely low positivity rate in COVID-19 patients [12], [13]. However, the transmissibility of SARS-CoV-2 in these biospecimens remains uncertain [14], [15]. Similarly, laboratory tests that require manual manipulation or are not testable with automated instruments have been limited. The IFCC Task Force on COVID-19 currently recommends management of these samples in a biosafety cabinet, whenever the risk of aerosolization is high [16]. However, this equipment may be unavailable in many routine laboratories, which may hence expose the laboratory staff to a significant biohazard risk when handling high-risk clinical samples such as pleural fluid.

Resource constraints imposed by COVID-19 have also compelled many clinical laboratories to limit their test menu availability. Although most of the restricted tests also carry biosafety risks (e.g. fecal and urine analyses), others such as endocrine testing, specialized biochemistry testing, as well as services such as outpatient testing and referred-in testing may have impact beyond the care of patients with COVID-19. Prolonged turnaround times may also have an impact. When such tests or services cannot be performed within the laboratory, sample referral to external facilities may be considered, if clinically indicated. However, selection of external laboratories is more challenging during pandemics, as there is shortage of time for addressing the performance of such laboratories or for assessing test result comparability. This lack of validating external laboratories is particularly problematic when patients are regularly monitored by tests that are poorly harmonized, which calls for better preparation of contingency plans for esoteric or specialized testing services.

Beyond the use of PPE, additional operational biosafety precautions can be adopted within the laboratory environment. These include daily temperature monitoring of the staff, which our survey showed many laboratories were unable to perform. This inability may increase the risk of cluster outbreaks from personnel with asymptomatic or undetected COVID-19. This risk is particularly high in regions with high rates of community transmission. However, it is important to remember that temperature monitoring does not guarantee the detection of all potentially infected patients, due to the rate of transmissions occurring during the pre-symptomatic incubation period or due to possible cases of asymptomatic infections [17], [18]. Other biosafety measures, not directly related to the risk posed by the possible transmission from processed samples, should be respected including social distancing, facemask wearing and correct hand hygiene.

Another operational biosafety precaution entails reinforced disinfection practices within the laboratory. In this regard, most laboratories reported an increased frequency of disinfection, with most of them cleaning 3 times or more per day. It is important to adhere to recommended disinfection agents and frequency (at least once every 3 h) to minimize the risk of work bench contamination [16]. About a quarter of laboratories also reported an increase in areas cleaned, which often included high touchpoint areas and ‘non-clinical’ areas, such as administrative and rest rooms.

To reduce the potential risk and proportion of staff being exposed to a colleague with asymptomatic or undetected COVID-19, approximately half of all laboratories split their teams. This allows the staff to isolate at most the members of the same team as the index staff, while preserving the functioning of the alternate team. Indeed, several laboratories shared the challenges in managing the laboratory owing to significant number of staff requiring self-isolation/quarantine after direct exposure to a colleague who was diagnosed as having COVID-19.

Most often, laboratory staff is split into two teams. The implementation of split teams can be highly challenging without adequate staffing level, and may need longer working hours to ensure sufficient service coverage. The different teams should not meet or work in overlapping shifts to minimize contact. This can pose a challenge to communications, handover and continuity of services. A longer stretch of duration of work of each team is probably desirable to further minimize interaction between teams. It may also be easier to plan the roster of such arrangements. The most effective split team arrangement involves all staff. Often-overlooked personnel in split team arrangement is the cleaning staff, who often interacts with multiple areas of the laboratory.

The operational processes in the laboratory are most commonly planned by clinicians, scientists/technologists and laboratory managers. The clinical specialties involved in such planning are biochemistry, microbiology and hospital infection control teams. Inclusion of microbiology and hospital infection control colleagues can be helpful in performing biosafety assessment. Administrative support is often required for vital optimal operations, whilst involvement of hospital administration can help mobilizing resources and provide political buy-in for decisions that may impact wide-ranging stakeholders (e.g. restriction of tests or services).

Finally, the number of challenges facing the laboratory profession during COVID-19 is vast. Foremost amongst these is the lack of testing resources and availability of consumables. Staff rostering and biosafety concerns require longer-term solutions, as they are crucial for continued operation of laboratory during what may well be a prolonged pandemic. Operational challenges require problem-solving and organizational skills in a flexible environment. Adding to the challenge is often the wider imposed public health measures, such as community lockdown for reinforcing social distancing (e.g. public transport limitations), which may have unintended consequences on critical sectors such as healthcare, national security or food delivery. For example, this has resulted in challenges in transporting staff to work, receiving supplies, and convincing vendors to provide repair and servicing to laboratory instruments.

Conclusions

The pandemic has affected the routine work of the clinical laboratory and has manifested in the form of test restriction. The restriction of tests and services may have undesirable clinical consequences, as clinicians are deprived of important laboratory data and information for delivering appropriate care to their patients. Temperature monitoring and splitting staff into teams can reduce the risk of transmission within the laboratory environment but is not practiced widely by the survey participants. The latter is difficult to implement without adequate staffing capacity. A multi-disciplinary approach in planning laboratory operations during times of uncertainty is likely to result in better well-thought-out decisions. The greatest reported challenge faced by laboratories is the lack of testing resources and consumables. The laboratory is an indispensable pillar of clinical care during the COVID-19 pandemic and the profession has risen to the task despite seemingly insurmountable challenges.