614
MICROBIOLOGY AND IMMUNOLOGY
Zdrav Vestn | November – December | Volume 89 | https://doi.org/10.6016/ZdravVestn.3103
Institute of Microbiology 
and Immunology, Faculty 
of Medicine, University 
of Ljubljana, Ljubljana, 
Slovenia
Correspondence/
Korespondenca:
Tina Uršič, e: tina.ursic@
mf.uni-lj.si
Key words:
SARS-CoV-2; COVID-19; 
high-priority patients; 
turnaround time
Ključne besede:
SARS-CoV-2; covid-19; 
prioritetni bolniki; čas od 
sprejema do izvida
Received: 4. 6. 2020
Accepted: 14. 9. 2020
eng slo element
en article-lang
10.6016/ZdravVestn.3103 doi
4.6.2020 date-received
14.9.2020 date-accepted
Microbiology and immunology Mikrobiologija in imunologija discipline
Original scientific article Izvirni znanstveni članek article-type
Shortening turnaround time for high-priority 
patients during the COVID-19 epidemic: evalu-
ation of the Xpert Xpress SARS-CoV-2 test
Skrajšanje časa od sprejema vzorca do izvida za 
covid-19 pri prioritetnih bolnikih: evalvacija testa 
Xpert Xpress SARS-CoV-2
article-title
Shortening turnaround time to SARS-CoV-2 
result for high-priority patients
Skrajšanje časa od sprejema vzorca do izvida 
SARS-CoV-2 za prioritetne bolnike
alt-title
SARS-CoV-2, COVID-19, high-priority patients, 
turnaround time
SARS-CoV-2, covid-19, prioritetni bolniki, čas od 
sprejema do izvida
kwd-group
The authors declare that there are no conflicts 
of interest present.
Avtorji so izjavili, da ne obstajajo nobeni 
konkurenčni interesi. conflict
year volume first month last month first page last page
2020 89 11 12 614 625
name surname aff email
Tina Uršič 1 tina.ursic@mf.uni-lj.si
name surname aff
Rok Kogoj 1
Katarina Resman Rus 1
eng slo aff-id
Institute of Microbiology 
and Immunology, Faculty 
of Medicine, University of 
Ljubljana, Ljubljana, Slovenia
Inštitut za mikrobiologijo 
in imunologijo, Medicinska 
Fakulteta, Univerza v Ljubljanai, 
Ljubljana, Slovenija
1
Shortening turnaround time for high-
priority patients during the COVID-19 
epidemic: evaluation of the Xpert Xpress 
SARS-CoV-2 test
Skrajšanje časa od sprejema vzorca do izvida za covid-19 pri 
prioritetnih bolnikih: evalvacija testa Xpert Xpress SARS-CoV-2
Rok Kogoj, Katarina Resman Rus, Tina Uršič
Abstract
Background: Although several molecular tests are now available for detecting SARS-CoV-2 RNA 
in nasopharyngeal swab samples, the number of requested tests exceeds the capacity of many 
diagnostic laboratories. Unfortunately, the available high-throughput platforms exhibit longer 
turnaround times than those required for management of high-priority patients.
Methods: The aim of this study was to evaluate the performance and possible benefits of the 
Cepheid Xpert Xpress SARS-CoV-2 test, focusing mainly on turnaround time when applied to 
high-priority patients. We evaluated the Xpert Xpress SARS-CoV-2 test in comparison to the 
Roche’s cobas 6800 SARS-CoV-2 test by monitoring turnaround times and by retrospectively test-
ing 20 nasopharyngeal swabs from COVID-19 patients with various viral loads. In addition, 50 
patients were tested by both methods prospectively. 
Results: We observed a lower limit of detection of one SARS-CoV-2 genome equivalent/µL and 
100% (95% CI, 92.6−100%) specificity and 95.5% (95% CI, 77.2−99.9%) sensitivity in comparison 
to the cobas SARS-CoV-2 test. When applying the Xpert Xpress SARS-CoV-2 test for high-priority 
patients the turnaround time could be greatly reduced, i.e. from 3 - 5 hours that take our routine 
diagnostics methods to about 1 hour. 
Conclusion: The novel Xpert Xpress SARS-CoV-2 test is a useful, easy to perform tool, valuable 
for rapid and reliable diagnosis of COVID-19, especially in high-priority patients when a short 
turnaround time is of key importance for further patient management.
Izvleček
Izhodišče: Čeprav je danes na voljo že veliko testov za dokaz okuženosti z virusom SARS-CoV-2 
RNA v brisih nosnega dela žrela, je število naročenih preiskav preseglo zmožnosti številnih diag-
nostičnih laboratorijev. Žal sistemi, ki omogočajo sočasno obdelavo velikega števila vzorcev, za 
to potrebujejo daljši čas do rezultata, kot je zaželen za prioritetne bolnike.
Metode: Evalvacija testa Cepheid Xpert Xpress SARS-CoV-2 je potekala na 20 retrospektivno iz-
branih za SARS-CoV-2 RNA pozitivnih vzorcih ter na 50 prospektivno vključenih vzorcih. Občut-
ljivost in specifičnost metode smo izračunali glede na test Roche SARS-CoV-2 na sistemu cobas 
6800. Dodatno smo primerjali čas od sprejema vzorca do izvida za obe metodi.
Rezultati: Ugotovili smo, da s testom Xpert Xpress SARS-CoV-2 lahko dokažemo do 1 kopije ge-
Slovenian
Medical
Journal
615
ORIGINAL SCIENTIFIC ARTICLE
Shortening turnaround time to SARS-CoV-2 result for high-priority patients
1 Introduction
The novel severe acute respiratory 
syndrome coronavirus (SARS-CoV-2) 
is a recently emerged member of the 
coronavirus family (1) firstly detected in 
December 2019 in the city of Wuhan in 
China’s, Hubei Province (2). Although 
most patients have a good prognosis, 
in some cases, usually when patients 
have underlying accompanying diseases, 
death may occur (3,4). Fortunately, the 
virus does not seem to be highly patho-
genic, but high human-to-human trans-
mission ability (5) allowed it to spread 
all over the world in less than 3 months 
after its emergence, therefore making it 
a serious global concern and exerting 
an enormous burden on healthcare sys-
tems.
The rapid development and wide 
implementation of reliable diagnostic 
tests plays a key role in controlling the 
pandemic, better understanding the ep-
idemiology of the disease, and allowing 
countries to implement adequate emer-
gency measures (6). To meet diagnostic 
needs as the pandemic grows, the U.S. 
FDA expanded enforcement discretion 
noma SARS-CoV-2 na mikroliter vzorca. V primerjavi s sistemom cobas 6800 pa je test v 100 % (95 
% CI, 92.6−100 %) specifičen in 95,5 % (95 % CI, 77.2−99.9 %) občutljiv. Pri uporabi testa Xpert 
Xpress SARS-CoV-2 za prioritetne bolnike je čas od sprejema vzorca do izvida znašal eno uro, 
medtem ko je s sistemom cobas trajal 3 do 5 ur.
Zaključek: Novi Xpert Xpress SARS-CoV-2 test je visoko specifičen in občutljiv ter preprosto iz-
vedljiv molekularni test. Glavna prednost testa se kaže v kratkem času od sprejema vzorca do 
izvida, kar je ključnega pomena za nadaljnjo obravnavo prioritetnih bolnikov.
Cite as/Citirajte kot: Kogoj R, Resman Rus K, Uršič T. Shortening turnaround time for high-priority patients 
during the COVID-19 epidemic: evaluation of the Xpert Xpress SARS-CoV-2 test. Zdrav Vestn. 2020;89(11–
12):614–25.
DOI: https://doi.org/10.6016/ZdravVestn.3103
Copyright (c) 2020 Slovenian Medical Journal. This work is licensed under a
Creative Commons Attribution-NonCommercial 4.0 International License.
to speed up COVID-19 test access, re-
sulting in granting EUA to 81 different 
SARS-CoV-2 commercial assays and 32 
laboratory developed tests as of 28 May 
2020 (7).
From March 2020 onward, Slovenian 
diagnostics laboratories were faced with 
unforeseen demand for fast and reliable 
COVID-19 testing. Although we were 
able to partially meet these demands by 
quickly switching the diagnostic pro-
tocol from automatic nucleic acid ex-
traction using the MagNA Pure Compact 
system (Roche Applied Science, Mann-
heim, Germany) and manual rtRT-PCR 
preparation (8) to the high-throughput 
cobas 6800 SARS-CoV-2 test (Roche 
Molecular Diagnostics, Pleasanton, CA, 
USA) – cobas SARS-2 test (9), the num-
ber of tests requested per day exceeded 
all expectations. A demand for faster re-
sults arose when dealing with high-pri-
ority patients, from intensive care units 
(ICU), surgical units, transplantation 
wards, oncology and haematology de-
partments, and intensive paediatric care 
units (PICU).
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The aim of this study was to evalu-
ate the performance of the Xpert Xpress 
SARS-CoV-2 (Cepheid, Sunnyvale, CA, 
USA) – Xpert SARS-2 test focusing 
mainly on turnaround time before its 
implementation as a method of choice 
for those high-priority patients who re-
quire a COVID-19 result sooner than 
our usual turnaround time of 3 to 5 
hours.
2 Material and Methods
2.1 Analytical PCR efficiency 
and lower limit of detection
A serial dilution of inactivated SARS-
CoV-2 virus was prepared in fresh RP-
MI−1640 (Sigma-Aldrich, St. Louis, MI, 
USA) medium from 1.0 × 104 copies/µL 
(100 pfu/mL) to one copy/µL (0.01 pfu/
mL). Each dilution was tested in trip-
licate and, from the results obtained, 
mean Ct values and the standard devi-
ation (SD) were calculated. Calibration 
curves were plotted, and PCR efficiency 
for both target genes was calculated.
2.2 Validation on patient 
samples’ panel
In the first validation part, we ret-
rospectively tested 20 nasopharyngeal 
swabs stored at −30°C in Universal 
Transport Medium; UTM (Copan, Bres-
cia, Italy), from patients diagnosed with 
COVID-19 during routine diagnostics 
by using a cobas SARS-2 test performed 
on a cobas 6800 system, which detects 
two genes, ORFab1 as Target 1 and E 
as Target 2, as previously described (9). 
The samples were selected according to 
the cycle threshold value (Ct) with val-
ues between 12 and 40 in order to cover 
the entire analytical range of a real-time 
RT-PCR method. In the second part, 
we prospectively tested 50 nasopharyn-
geal swab samples from high-priority 
patients that were processed in parallel 
on both the Xpert SARS-2 test and cobas 
SARS-2 test. After comparing the results 
to the cobas SARS-2 test as a reference 
method, we calculated the specifici-
ty, sensitivity, positive predictive value, 
negative predictive value, and Cohen’s 
kappa agreement coefficient, and we 
performed a Bland-Altman analysis. In 
addition, we also calculated turnaround 
and hands-on times.
2.3 Xpert Xpress 
SARS-CoV-2 test
The Xpert SARS-2 test detects two 
genes: the E gene and N2 gene. The test 
was performed according to the manu-
facturer’s instructions. Briefly, nasopha-
ryngeal swabs inserted in UTM were 
thoroughly mixed for 30 seconds and 
transferred directly to the test cartridge 
with the accompanying pipette. The pre-
pared cartridges were loaded into a GX-
XVI instrument (Cepheid). Analysis of 
the results was performed automatically 
by using GeneXpert Dx software version 
4.8 (Cepheid). 
2.4 Laboratory testing 
requirements and 
turnaround times
The number of total and high-priority 
tests ordered during the government-de-
clared COVID-19 epidemic (calendar 
weeks 10 through 20) was exported 
from the laboratory information sys-
tem (LIS) and used to analyze the turn-
around times per day for SARS-CoV-2 
RNA detection by LightMix Modular 
617
ORIGINAL SCIENTIFIC ARTICLE
Shortening turnaround time to SARS-CoV-2 result for high-priority patients
Wuhan CoV E-, RdRp- and N-gene Kits 
(TIB Molbiol, Berlin, Germany) – LMM 
or cobas SARS-2 test at the Institute of 
Microbiology and Immunology (IMI), 
Faculty of Medicine, University of Lju-
bljana. The turnaround time’s results 
were compared to those that would have 
been achieved by using the Xpert Xpress 
SARS-CoV-2 test.
2.5 Ethical compliance
In line with the principles expressed 
in the Declaration of Helsinki, the Ovie-
do Convention on Human Rights and 
Biomedicine, and the Slovenian Code of 
Medical Deontology, all human samples 
were anonymized, and data on patient 
sex and age were linked only to random-
ized numerical codes. Because no addi-
tional samples or data were collected, the 
study was deemed low risk and the need 
for additional ethical approval from the 
National Medical Ethics Committee was 
waived.
3 Results
3.1 Limit of detection 
and PCR efficiency
Our results show that the Xpert 
SARS-2 test has a 98.0% (slope: −3.3700) 
and 94.0% (slope: −3.4757) PCR effi-
ciency for the E gene and N2 gene, re-
spectively. We observed the same limit 
of detection (LoD) as stated by the man-
ufacturer; namely, 0.01 pfu/ml (one copy 
of SARS-CoV-2 RNA/µL) (Figure 1).
3.2 Retrospective testing
The results of the retrospective test-
ing show that the Xpert SARS-2 test 
correctly identified 85.0% (17/20) of 
samples which tested positive by cobas 
SARS-2 and 95.0% (19/20) when Xpert 
SARS-2 test presumptive positive results 
were calculated as positive (Table 1). Af-
ter comparing Ct values, a strong posi-
Figure 1: Xpert SARS-2 test results of inactivated SARS-CoV-2 virus serial dilutions in RPMI−1640 
from 1 × 104 copies/µL (100 pfu/mL) down to 1 copy/µL (0.01pfu/mL).
R2 = 0,9972
R2 = 0,9927
25
27
29
31
33
35
37
39
41
43
45
0,00 0,50 1,00 1,50 2,00 2,50 3,00 3,50 4,00 4,50
Log SARS-CoV-2 genome equivalent copy number
Ct
 va
lu
e
y = - 3,37x + 39,613
y = - 3,4757x + 42,148
E gene:
N2 gene:
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tive correlation was observed for the E 
gene / Target 2 (R = 0.89; p < 0.00001) 
and a moderate correlation for the N2 
gene / Target 1 (R = 0.69; p = 0.0008). 
From both Ct comparison plots (Figures 
2 and 3), it can also be observed that the 
decrease in correlation strength is due 
to greater dispersion of high Ct values 
(> 34.0). We did not observe any failed 
results due to internal control status for 
2 and N2 versus Target 1 genes, respec-
tively; however, the difference did not 
reach statistical significance (p = 0.59 
and p = 0.096).
Table 1: Detailed results of the Xpert SARS-2 test in comparison with the reference method 
(cobas SARS-2 test) with respective Ct values for both targets, internal control status, and 
automatic interpretation of the overall result.
IC – internal control; Neg – negative
Patient 
no.
Cobas 6800 SARS-CoV-2 test Xpert Xpress SARS-CoV-2 test
Target 1 
(ORF1ab)
Target 2 
(E gene)
IC E gene N2 gene IC Interpretation
P1 12.6 16.3 Pass 16.2 18.0 Pass POSITIVE
P2 14.2 17.3 Pass 14.3 16.6 Pass POSITIVE
P3 16.1 18.1 Pass 15.5 17.9 Pass POSITIVE
P4 18.2 19.3 Pass 19.1 21.5 Pass POSITIVE
P5 20.2 20.6 Pass 21.9 24.3 Pass POSITIVE
P6 22.3 22.8 Pass 22.1 25.1 Pass POSITIVE
P7 24.3 25.1 Pass 24.2 26.4 Pass POSITIVE
P8 26.9 26.1 Pass 27.3 29.6 Pass POSITIVE
P9 27.4 27.1 Pass 27.1 29.4 Pass POSITIVE
P10 28.3 28.7 Pass 27.3 30.2 Pass POSITIVE
P11 29.4 30.2 Pass 28.7 31.7 Pass POSITIVE
P12 30.3 31.7 Pass 30.8 33.6 Pass POSITIVE
P13 31.3 31.8 Pass 30.6 34.0 Pass POSITIVE
P14 38.0 32.8 Pass 31.9 35.0 Pass POSITIVE
P15 35.2 33.2 Pass 38.4 41.3 Pass POSITIVE
P16 37.8 34.3 Pass 35.9 38.4 Pass POSITIVE
P17 37.7 35.2 Pass 40.0 Neg Pass Presumptive POSITIVE
P18 39.9 35.2 Pass Neg Neg Pass NEGATIVE
P19 36.3 36.5 Pass 35.0 Neg Pass Presumptive POSITIVE 
P20 35.2 37.6 Pass 36.0 38.7 Pass POSITIVE
Figure 2: Ct value correlation (a) and Bland-Altman comparison plot (b) for the N2 gene (Xpert SARS-2) against Target 1 – 
ORF1ab gene (cobas SARS-2).
(a)
COBAS Target 2
X
p
e
rt
 E
 g
e
n
e
454035302520151050
0
5
10
20
30
40
15
25
35
45
(b)
COBAS Target 2 Xpert E gene
C
T
 v
a
lu
e
10
20
30
40
50
0
Figure 3: Ct value correlation (a) and Bland-Altman comparison plot (b) for the E gene (Xpert SARS-2) against Target 2 – E 
gene (cobas SARS-2).
COBAS Target 1
COBAS Target 1 Xpert N2 gene
C
T
 v
a
lu
e
X
p
e
rt
 N
2
 g
e
n
e
(a) (b)
454035302520151050
0
5
10
20
30
40
15
25
35
45
10
20
30
40
50
0
619
ORIGINAL SCIENTIFIC ARTICLE
Shortening turnaround time to SARS-CoV-2 result for high-priority patients
all samples tested. The Bland-Altman 
analysis revealed that the mean differ-
ence in Ct values for both targets was in 
favour of the Xpert SARS-2 test for −0.5 
and −3.5 (at 95% CI) for E versus Target 
2 and N2 versus Target 1 genes, respec-
tively; however, the difference did not 
reach statistical significance (p = 0.59 
and p = 0.096).
Table 1: Detailed results of the Xpert SARS-2 test in comparison with the reference method 
(cobas SARS-2 test) with respective Ct values for both targets, internal control status, and 
automatic interpretation of the overall result.
IC – internal control; Neg – negative
Patient 
no.
Cobas 6800 SARS-CoV-2 test Xpert Xpress SARS-CoV-2 test
Target 1 
(ORF1ab)
Target 2 
(E gene)
IC E gene N2 gene IC Interpretation
P1 12.6 16.3 Pass 16.2 18.0 Pass POSITIVE
P2 14.2 17.3 Pass 14.3 16.6 Pass POSITIVE
P3 16.1 18.1 Pass 15.5 17.9 Pass POSITIVE
P4 18.2 19.3 Pass 19.1 21.5 Pass POSITIVE
P5 20.2 20.6 Pass 21.9 24.3 Pass POSITIVE
P6 22.3 22.8 Pass 22.1 25.1 Pass POSITIVE
P7 24.3 25.1 Pass 24.2 26.4 Pass POSITIVE
P8 26.9 26.1 Pass 27.3 29.6 Pass POSITIVE
P9 27.4 27.1 Pass 27.1 29.4 Pass POSITIVE
P10 28.3 28.7 Pass 27.3 30.2 Pass POSITIVE
P11 29.4 30.2 Pass 28.7 31.7 Pass POSITIVE
P12 30.3 31.7 Pass 30.8 33.6 Pass POSITIVE
P13 31.3 31.8 Pass 30.6 34.0 Pass POSITIVE
P14 38.0 32.8 Pass 31.9 35.0 Pass POSITIVE
P15 35.2 33.2 Pass 38.4 41.3 Pass POSITIVE
P16 37.8 34.3 Pass 35.9 38.4 Pass POSITIVE
P17 37.7 35.2 Pass 40.0 Neg Pass Presumptive POSITIVE
P18 39.9 35.2 Pass Neg Neg Pass NEGATIVE
P19 36.3 36.5 Pass 35.0 Neg Pass Presumptive POSITIVE 
P20 35.2 37.6 Pass 36.0 38.7 Pass POSITIVE
Figure 2: Ct value correlation (a) and Bland-Altman comparison plot (b) for the N2 gene (Xpert SARS-2) against Target 1 – 
ORF1ab gene (cobas SARS-2).
(a)
COBAS Target 2
X
p
e
rt
 E
 g
e
n
e
454035302520151050
0
5
10
20
30
40
15
25
35
45
(b)
COBAS Target 2 Xpert E gene
C
T
 v
a
lu
e
10
20
30
40
50
0
Figure 3: Ct value correlation (a) and Bland-Altman comparison plot (b) for the E gene (Xpert SARS-2) against Target 2 – E 
gene (cobas SARS-2).
COBAS Target 1
COBAS Target 1 Xpert N2 gene
C
T
 v
a
lu
e
X
p
e
rt
 N
2
 g
e
n
e
(a) (b)
454035302520151050
0
5
10
20
30
40
15
25
35
45
10
20
30
40
50
0
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3.3 Prospective testing
For the prospective part of the study, 
we tested 50 consecutive symptomatic 
patients. The study population was com-
posed of 42.0% (21/50) males and 58.0% 
(29/50) females, with a mean age of 50 
years (< 1 to 97). Twenty-eight percent 
(14/50) were children under 18 years 
of age, 42.0% (21/50) were working-age 
adults, and 30.0% (15/50) were people 
over the age of 65. Four percent of the 
patients (2/50) were positive and 96.0% 
(48/50) were negative (Table 2). For one 
sample, we were unable to obtain the re-
sult with the Xpert SARS-2 test due to 
internal control amplification failure. 
However, after retesting the same sam-
ple, the result was negative. In conclu-
sion, no discrepancies were observed 
between the Xpert SARS-2 and cobas 
SARS-2 tests in the prospective part of 
the study.
3.4 Specificity, sensitivity 
and method agreement with 
the cobas 6800 SARS-2 test
After combining the results from the 
retrospective and prospective testing, 
we calculated the Xpert SARS-2 test 
specificity (including presumptive posi-
tive results) in comparison to the cobas 
SARS-2 test to be 100% (92.6–100% at 
95% CI), sensitivity 95.5% (77.2–99.9% 
at 95% CI). Cohen’s kappa agreement 
coefficient was 98.6% (86.8–99.9% at 
95% CI). If the presumptive positive 
samples were omitted from the calcu-
Table 2: Detailed results of prospective 
testing.
Test Positive Negative
Xpert Xpress SARS-CoV-2 2 48
Cobas 6800 SARS-CoV-2 2 48
lation, the specificity value remains the 
same, whereas the sensitivity lowers to 
95% (75.1%-99.9% at 95% CI).
3.5 High-priority testing 
requirements and turnaround 
times during the epidemic
The analysis of data from our LIS 
shows that after the detection of the first 
COVID-19 case in Slovenia on 4 March 
2020 (in calendar week 10), the number 
of tests ordered per day has increased 
rapidly (Table 3). Despite our efforts, 
turnaround times started to increase 
mainly due to infrastructure and human 
resources limitations. Nevertheless, we 
were able to provide results for 89.6% 
(31997/35723) of tested samples in time-
frame of 6 hours. Similarly, the number 
of high-priority tests ordered from ICUs, 
surgical units, transplantation wards, 
oncology and haematology departments 
and PICUs, followed the same trend. A 
more detailed analysis reveals that in 
weeks 10 and 11 only 1 ± 1 and 5 ± 3 
tests on average per day were request-
ed respectively by the units mentioned 
above. In the following weeks, a decisive 
increase in the number of high-priority 
tests requested was observed (Table 3, 
Figure 4). Average weekly turnaround 
times after an initial increase from 3:13 
(in week 10) to 3:44 (in week 11) actually 
started to decrease in week 13, when we 
switched our diagnostics approach to a 
combination of LMM and cobas SARS-2 
test. Consequently, in week 17, for the 
high-priority samples the shortest aver-
age turnaround time was about 3 hours 
(2:59). However, such turnaround time 
was not sustained until the end of the 
study period mainly due to a complete 
testing switch to the cobas SARS-2 test 
as the primary COVID-19 diagnostic 
method.
Table 3: Average number of total tests ordered per day during respective weeks, high-priority tests ordered per day 
during respective week, and total weekly percentage of high-priority tests from the announcement of the COVID-19 
epidemic until it was declared over in Slovenia.
W – Week, SD – Standard deviation
Calendar week W10 W11 W12 W13 W14 W15 W16 W17 W18 W19 W20
Tests per day, n (SD) 92 (59)
92 
(110)
495 
(94)
571 
(146)
487 
(136)
558 
(223)
460 
(145)
578 
(167)
449 
(168)
533 
(173)
488 
(133)
(daily min–max 
in resp. W) 0–3
263–
549
354–
603
290–
735
280–
685
214–
818
292–
621
345–
798
244–
655
270–
722
290–
606
Priority tests per day, 
n (SD) 1 (1) 5 (3) 22 (8) 29 (10) 41 (5) 50 (11) 50 (9) 53 (11) 34 (27) 41 (16) 41 (8)
(daily min–max 
in resp. W) 0–3 2–10 12–33 14–42 33–47 33–62 33–60 31–65 6–60 18–58 27–50
% of priority tests per 
week 1.1% 1.3% 4.4% 5.0% 8.3% 9.0% 10.8% 9.1% 8.3% 7.8% 8.5%
Figure 4: Number of SARS-CoV-2 RNA detection tests requested by ICUs, surgical units, transplantation wards, oncology 
and haematology departments and PICUs per day with the weekly average of tests requested and weekly average 
turnaround times. Red: first confirmed COVID-19 case in Slovenia. Yellow: platform switch for low-priority samples from 
LightMix to cobas 6800. Green: switch to cobas 6800 as the sole platform for SARS-CoV-2 RNA detection.
 
03:13
03:26
03:44
03:18 03:12
03:30
03:09 02:59
03:32
05:21 05:14
00:00
00:28
00:57
01:26
01:55
02:24
02:52
03:21
03:50
04:19
04:48
05:16
05:45
06:14
06:43
0
5
10
15
20
25
30
35
40
45
50
55
60
65
2-
M
ar
3-
M
ar
4-
M
ar
5-
M
ar
6-
M
ar
7-
M
ar
8-
M
ar
9-
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ar
11
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ar
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ar
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17
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ar
19
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ar
20
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ar
21
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22
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ar
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ar
24
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ar
25
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ar
26
-M
ar
27
-M
ar
28
-M
ar
29
-M
ar
30
-M
ar
31
-M
ar
1-
A
pr
2-
A
pr
3-
A
pr
4-
A
pr
5-
A
pr
6-
A
pr
7-
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8-
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9-
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10
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11
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12
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13
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14
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15
-A
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16
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17
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18
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pr
19
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20
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pr
21
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pr
22
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23
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pr
24
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pr
25
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26
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pr
27
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28
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29
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30
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pr
1-
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ay
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ay
3-
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ay
14
-M
ay
15
-M
ay
16
-M
ay
17
-M
ay
10 11 12 13 14 15 16 17 18 19 20
Number of high-priority tests requested
Average number of high-priority tests requested - weekly
Average turnaround time - weekly
60
65
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:
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:
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r f i - riority tests requested - weekly
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621
ORIGINAL SCIENTIFIC ARTICLE
Shortening turnaround time to SARS-CoV-2 result for high-priority patients
lation, the specificity value remains the 
same, whereas the sensitivity lowers to 
95% (75.1%-99.9% at 95% CI).
3.5 High-priority testing 
requirements and turnaround 
times during the epidemic
The analysis of data from our LIS 
shows that after the detection of the first 
COVID-19 case in Slovenia on 4 March 
2020 (in calendar week 10), the number 
of tests ordered per day has increased 
rapidly (Table 3). Despite our efforts, 
turnaround times started to increase 
mainly due to infrastructure and human 
resources limitations. Nevertheless, we 
were able to provide results for 89.6% 
(31997/35723) of tested samples in time-
frame of 6 hours. Similarly, the number 
of high-priority tests ordered from ICUs, 
surgical units, transplantation wards, 
oncology and haematology departments 
and PICUs, followed the same trend. A 
more detailed analysis reveals that in 
weeks 10 and 11 only 1 ± 1 and 5 ± 3 
tests on average per day were request-
ed respectively by the units mentioned 
above. In the following weeks, a decisive 
increase in the number of high-priority 
tests requested was observed (Table 3, 
Figure 4). Average weekly turnaround 
times after an initial increase from 3:13 
(in week 10) to 3:44 (in week 11) actually 
started to decrease in week 13, when we 
switched our diagnostics approach to a 
combination of LMM and cobas SARS-2 
test. Consequently, in week 17, for the 
high-priority samples the shortest aver-
age turnaround time was about 3 hours 
(2:59). However, such turnaround time 
was not sustained until the end of the 
study period mainly due to a complete 
testing switch to the cobas SARS-2 test 
as the primary COVID-19 diagnostic 
method.
Table 3: Average number of total tests ordered per day during respective weeks, high-priority tests ordered per day 
during respective week, and total weekly percentage of high-priority tests from the announcement of the COVID-19 
epidemic until it was declared over in Slovenia.
W – Week, SD – Standard deviation
Calendar week W10 W11 W12 W13 W14 W15 W16 W17 W18 W19 W20
Tests per day, n (SD) 92 (59)
92 
(110)
495 
(94)
571 
(146)
487 
(136)
558 
(223)
460 
(145)
578 
(167)
449 
(168)
533 
(173)
488 
(133)
(daily min–max 
in resp. W) 0–3
263–
549
354–
603
290–
735
280–
685
214–
818
292–
621
345–
798
244–
655
270–
722
290–
606
Priority tests per day, 
n (SD) 1 (1) 5 (3) 22 (8) 29 (10) 41 (5) 50 (11) 50 (9) 53 (11) 34 (27) 41 (16) 41 (8)
(daily min–max 
in resp. W) 0–3 2–10 12–33 14–42 33–47 33–62 33–60 31–65 6–60 18–58 27–50
% of priority tests per 
week 1.1% 1.3% 4.4% 5.0% 8.3% 9.0% 10.8% 9.1% 8.3% 7.8% 8.5%
Figure 4: Number of SARS-CoV-2 RNA detection tests requested by ICUs, surgical units, transplantation wards, oncology 
and haematology departments and PICUs per day with the weekly average of tests requested and weekly average 
turnaround times. Red: first confirmed COVID-19 case in Slovenia. Yellow: platform switch for low-priority samples from 
LightMix to cobas 6800. Green: switch to cobas 6800 as the sole platform for SARS-CoV-2 RNA detection.
 
03:13
03:26
03:44
03:18 03:12
03:30
03:09 02:59
03:32
05:21 05:14
00:00
00:28
00:57
01:26
01:55
02:24
02:52
03:21
03:50
04:19
04:48
05:16
05:45
06:14
06:43
0
5
10
15
20
25
30
35
40
45
50
55
60
65
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3-
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5-
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25
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26
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27
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28
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31
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13
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14
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15
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ay
16
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ay
17
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ay
10 11 12 13 14 15 16 17 18 19 20
Number of high-priority tests requested
Average number of high-priority tests requested - weekly
Average turnaround time - weekly
60
65
:
:
:
:
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r f i - riority tests requested - weekly
Average turnaround time - weekly
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MICROBIOLOGY AND IMMUNOLOGY
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4 Discussion
More than a month before the first 
COVID-19 case in Slovenia, our in-
stitution already implemented an in-
house rtRT-PCR method, proposed by 
the WHO, as described previously (8). 
The first positive case was detected on 4 
March. The government declared a SARS-
CoV-2 epidemic on 12 March. Slovenian 
authorities decided to almost completely 
shut down public life: public gatherings 
were forbidden, and preschools, schools, 
restaurants, hotels, and almost all stores 
except grocery stores were closed. No 
public transport was available, and trav-
el between municipalities was prohibit-
ed. Because the numbers of tests ordered 
per day were growing and due to human 
resource limitations, in calendar week 13 
we switched our diagnostics approach 
to the high-throughput cobas 6800 sys-
tem, as described previously (9). The 
switch resulted in extended turnaround 
times from approximately 3 hours to 5 
hours, but it significantly decreased the 
labour required for testing samples. At 
the same time, the demand for shorter 
turnaround time for high-priority pa-
tients arose due to need for COVID-19 
testing before hospitalization or elective 
surgery. Consequently, a steady increase 
in the number of high-priority tests re-
quested was observed; from an average 
of 1 ± 1 to 22 ± 8 tests per day in weeks 
10 through 12 and later constantly over 
40 ± SD with the exception of week 18, 
when an average of 34 ± 27 high-prior-
ity tests were ordered per day. Based on 
the fact that the number rose again to an 
average of over 40 ± SD in the follow-
ing weeks, the most probable reason is 
the lower number of patients and med-
ical doctors on duty. This observation is 
also supported by a similar drop in the 
number of overall tests ordered, for an 
average of approximately 100 tests per 
day during week 18.
Thus the need for faster diagnostic 
approach for high-priority patients like 
the Xpert SARS-2 test was urgent and in-
evitable. In the retrospective part of the 
study, the Xpert SARS-2 test correctly 
identified 95% (19/20) of samples previ-
ously found positive by the cobas SARS-2 
test, and a strong positive correlation 
was observed for the E gene Ct values / 
Target 2 Ct values and a moderate cor-
relation for the N2 gene Ct values / Tar-
get 1 Ct values. In the prospective part 
of the study, 50 consecutive symptom-
atic patients were tested and no discrep-
ancies were observed. Four percent of 
patients (2/50) were positive and 96.0% 
(48/50) were negative. When comparing 
the results of the Xpert SARS-2 test to 
cobas SARS-2 test, which has previous-
ly been shown to have a 100% analyti-
cal specificity and sensitivity (9,10), the 
overall Xpert SARS-2 test specificity and 
sensitivity (including presumptive pos-
itive results) were 100% (92.6–100% at 
95% CI) and 95.5% (77.2–99.9% at 95% 
CI), respectively. We have chosen to de-
termine the presumptive positive results 
as positive and incorporate them in the 
calculation because we already knew the 
samples were positive by our reference 
method. However, we must stress that 
in a routine setting such results should 
be interpreted with caution. We advise 
that presumptive positive results should 
be confirmed by another (possibly refer-
ence) method before reporting the result. 
If these samples were omitted from the 
calculation, the sensitivity value dropped 
to 95% (75.1%-99.9% at 95% CI). Ad-
ditionally, we must point out, that our 
study sample selection does not reflect 
the true sensitivity and specificity of the 
Xpert SARS-2 test as the study was de-
signed to compare the Xpert SARS-2 test 
623
ORIGINAL SCIENTIFIC ARTICLE
Shortening turnaround time to SARS-CoV-2 result for high-priority patients
to the cobas SARS-2 test and not to clin-
ically confirmed COVID-19 cases. Since 
data on clinically confirmed COVID-19 
cases were not available to us, such cal-
culation was not possible. Therefore, our 
results reflect only the performance of 
the Xpers SARS-2 test in comparison to 
the cobas SARS-2 test. The CI interval of 
the sensitivity calculation is rather wide, 
since a relatively small number of posi-
tive samples were included in the study. 
We were unable to include more posi-
tive samples from high-priority patients 
since, at that time, more such patients 
have not been identified. Therefore, this 
limitation must be taken into account 
when looking at our results. The lower 
sensitivity with the wider CI interval 
implies that false negative results occa-
sionally occur. Nevertheless, based on 
our results, it would appear that the false 
negative results occur for samples with a 
very low concentration of SARS-CoV-2. 
At this point in time, it is still question-
able whether such low concentrations of 
SARS-CoV-2 in samples are clinically 
significant, as such patients might not 
be infectious at all. Specialized studies 
to determine the infectivity of such cas-
es might be considered in the future to 
shed more light on this matter. Finally, 
during our validation we did not observe 
Xpert SARS-2 test false positive results. 
Similar performance results of the 
Xpert SARS-2 test were observed in 
a previous study (11), which showed 
a 100% agreement with a Centers for 
Disease Control and Prevention (CDC) 
laboratory-developed test. In contrast to 
our results, that study was able to detect 
a positive sample with an Xpert SARS-2 
test Ct result of 42.6 and 42.7 for the E 
and N2 genes, respectively; however, 
this occurred in two separate runs after 
repeating the test. In our case, we ob-
served a Ct value of 40.0 ± 1.1 (E gene) 
and 41.4 ± 1.0 (N2 gene) for one SARS-
CoV-2 genome copy per µL of sample. 
Judging from the previously published 
results (11) it would seem that the Xpert 
SARS-2 test can occasionally detect even 
lower amounts of target RNA per µL of 
sample. Another performance evalu-
ation of the Xpert SARS-2 test was re-
cently published (12) where the discrep-
ancies between the cobas SARS-CoV-2 
test and Panther Fusion (Hologic, USA) 
were described. After testing 14 discrep-
ant low-viral-burden samples (Ct > 35), 
more of them agreed with the cobas 
SARS-2 test (nine samples) than with 
Panther Fusion (five samples), thus in-
directly showing a very low detection 
limit of the Xpert SARS-2 test. Finally, in 
a study dedicated completely to the eval-
uation of the Xpert SARS-2 test (13) the 
results are similar to ours. The study al-
so showed high agreement between the 
Xpert SARS-2 and the cobas SARS-2 test 
(99%) and a similar lower mean Ct value 
for both target genes (−1.57 and −5.34 at 
95% CI). Moreover, an excellent agree-
ment with the cobas SARS-2 test was al-
so demonstrated before (14), with a total 
of 98.9% (92.9-99.9%) agreement which 
was mainly due to one low positive sam-
ple wrongly identified as negative by the 
Xpert SARS-2 test. 
When comparing the cobas SARS-2 
test to the Xpert SARS-2 test, the hands-
on time per sample is merely a few 
minutes for both methods. On the oth-
er hand, a greater difference can be ob-
served in turnaround time: 3 hours for 
the cobas SARS-2 and less than an hour 
for the Xpert SARS-2 test. The cobas 
6800 system can process up to 94 sam-
ples in 3 hours (and up to 1,400 sam-
ples in 24 hours) whereas for the Xpert 
SARS-2 test the number depends on the 
size of the GeneXpert Dx system. It must 
be pointed out, that such system de-
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MICROBIOLOGY AND IMMUNOLOGY
Zdrav Vestn | November – December 2020 | Volume 89 | https://doi.org/10.6016/ZdravVestn.3103
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5 Conclusion
In conclusion, due to the Gene Xpert 
system design, the throughput of the 
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testing from a new respiratory sample 
would be highly recommended.
6 Acknowledgements
The authors would like to express 
their gratitude to the whole Institute 
of Microbiology and Immunology’s 
COVID-19 diagnostics team for their 
dedicated work, positive attitude and 
maintaining a friendly work environ-
ment during the SARS-CoV-2 epidem-
ic in Slovenia. A special thanks goes to 
Dr. Miša Korva for brainstorming ideas, 
Prof. Mario Poljak, Prof. Tatjana Avšič-
Županc and Prof. Miroslav Petrovec for 
the original idea and manuscript proof 
reading. 
This research was supported by the 
Slovenian Research Agency (grant no. 
P3-0083) and by the European Virus 
Archive - GLOBAL (EVAg) project that 
received funding from the European 
Union Horizon 2020 research and inno-
vation program under grant agreement 
no. 871029. 
European Union Horizon 2020 re-
search and innovation program - Euro-
pean Virus Archive - GLOBAL (EVAg) 
grant no. 871029.
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