In this study, a total of 188 COVID-19 suspected patients were enrolled and a throat swab sample was collected from September 25 to October 15/2020 referred to EPHI for SARS-CoV-2 testing. Of the total, 108 (57.4%) participants were male and the rest 80 (42.6%) were female. The mean age of the study participants was 32.2 ± 13.1 years. Out of the total samples without heat-inactivated at 56°C for 30 minutes (untreated group), 117 (62.2 %) and 118 (62.8%) were positive for ORF1a/b gene and N gene respectively. A total of 117 ORF1a/b gene-positive samples were also positive for N gene. Only one sample (0.5 %) that treated without heat inactivation was single gene-positive during the original test and also after re-tested. While out of the samples with heat-inactivated at 56°C for 30 minutes, 111 (59%) were ORF1a/b positive and 116 (61.7%) were N gene positive. Out of the total N gene-positive, 111 were ORF1a/b gene also positive. Only one sample (0.5%) that treated with heat inactivation was turned to completely double target gene negative after re-tested; while five samples (5/188=2.65%) was a consistent single gene-positive after re-tested.
Of the total samples, 7 (3.7%) had discordant result between those heat-inactivated and without heat-inactivated matched Oropharyngeal specimen (Table 1). Out of the discordant samples; 5 (71.4 %) Oropharyngeal specimen were double gene negative after the heat-inactivated procedure, but either double or single gene-positive in those treated without heat inactivation procedure. Interestingly, out of the discordant samples; 1 (14.3%) sample was N gene-positive during heat-inactivated, but double gene negative in those treated without the heat-inactivated procedure. Those discordant samples having with single or double gene-positive had more than 35 CT value (Table 1). Based on the DAAN gene assay result interpretation after Chi-square McNemar test indicated that the qualitative detection of SARS-CoV-2 (negativity or positivity) between heat-inactivated at 56 °C for 30 min and non-inactivated group result had no statistically significant difference (x2 =1.584; p = 0.208).
Table 1: Discordant result between inactivated and non-inactivated Oropharyngeal specimen in COVID 19 testing, Ethiopia, 2020
Sample number
|
Heat Inactivated result
|
Non-heat inactivated result
|
ORF1a/b gene (CT value)
|
N gene (CT value)
|
ORF1a/b gene (CT value)
|
N gene (CT value)
|
ES 020
|
Negative
|
Negative
|
Positive (36.71)
|
Positive (36.22)
|
ES 073
|
Negative
|
Negative
|
Positive (37.84)
|
Negative
|
ES 086
|
Negative
|
Negative
|
Negative
|
Positive (36.62)
|
ES 150
|
Negative
|
Negative
|
Positive (38.2)
|
Negative
|
ES 171
|
Negative
|
Positive (36.61)
|
Positive (39.81)
|
Positive (36.93)
|
ES 067
|
Negative
|
Positive (37.28)
|
Negative
|
Negative
|
ES 068
|
Negative
|
Negative
|
Negative
|
Positive (36.38)
|
The effects of heat inactivation at 56℃ for 30 min on the SARS-CoV-2 RT-PCR CT value were assessed. Out of 188 Oropharyngeal swab samples the ORF1a/b gene average CT value of the inactivation group and non-inactivation group were 25.43 (95% CI; 24.369-26.521) and 25.39 (95 % CI; 24.336-26.438) respectively. The range, median and standard deviation of CT value of ORF1a/b gene in the inactivation group were 26.37 (13.83-41.20), 24.73, and 5.96 respectively. Similarly, the range, median and standard deviation of CT value in the non-inactivation group were 27.1 (12.9-40), 25.13 and 5.74 respectively.
Out of the total sample, 32/188 (17.02 %) of samples had low ORF1a/b gene RNA copies, which had the CT values were greater than 30. While 22 (11.7 %) N gene CT values were greater than 30. The mean non-inactivated ORF1a/b and N gene CT values greater than 30 were 33.37 (95 % CI; 32.43 - 34.32) and 32.52 (95 % CI; 31.65 - 33.34) respectively. On the other hand, the inactivated ORF1a/b and N gene CT values greater than 30 were 34.63 (95 % CI; 33.46 - 35.85) and 33.52 (95 % CI; 32.68 - 34.29) respectively (Table: 2).
As shown in table 2, there is no significant difference between the ORF1a/b CT of inactivated and non-inactivated results. The mean difference between the two groups of CT value was 0.042 (95 % CI, - 0.247 to 0.331) and this difference was not statistically significant (t= 0.28; p = 0.774). On the other hand, the range of N gene CT value in both inactivated and non-treated samples was 29.17 (10.83- 40.0) and 30 (10.0-40.0) respectively. The mean CT value for N gene of the heat-treated group was 24.1585 (95 % CI; 22.925 - 25.301) and the non-inactivated mean CT value was 23.768 (95 % CI; 22.609 - 24.863). The paired t-test analysis showed that the mean difference between both groups of N gene CT was 0.38 (95% CI, 0.097 to 0.682). This difference was indicated that the inactivated and non-inactivated group had a significant difference in CT value (t =2.638; p = 0.010). In addition, as indicated in paired T-test analysis, high CT value (> 30) samples significantly affected with heat inactivation at 56°C for 30 minutes. The mean CT value difference of ORF1a/b and N gene in both inactivated and non-inactivated groups were significantly different (p < 0.05) (Table: 2).
Table 2: Analysis of CT value difference between heat inactivated and non-inactivated Oropharyngeal specimen in COVID 19 testing, Ethiopia, 2020
Variables
|
Mean (95% CI)
|
Paired T-test differences
|
Non-parametric Wilcoxon test
|
Mean difference (95 % CI)
|
T-test
|
P-value
|
p-value
|
Inactivated sample ORF1a/b gene CT
|
25.4397
(24.369,26.521)
|
0.042
(-0.247 , 0.331)
|
0.288
|
0.774
|
0.871
|
Non-inactivated sample ORF1a/b gene CT
|
25.3978
(24.336, 26.438)
|
Inactivated sample N gene CT
|
24.1585
(22.925, 25.301)
|
0.389
(0.097, 0.682)
|
2.638
|
0.010
|
0.000
|
Non-inactivated sample N gene CT
|
23.7689
(22.609, 24.863)
|
Inactivated sample ORF1a/b gene CT > 30
|
34.6269
(33.455, 35.852)
|
1.262
(0.435, 2.088
|
3.114
|
0.004
|
0.001
|
Non-inactivated sample ORF1a/b gene CT > 30
|
33.3650
(32.427, 34.321)
|
Inactivated sample N gene CT > 30
|
33.5155
(32.6796, 34.293)
|
1.00
(0.439, 1.561)
|
3.709
|
0.001
|
0.000
|
Non-inactivated sample N gene CT > 30
|
32.5155
(31.646, 33.3397)
|
In this experimental study the concordance between inactivated and non-inactivated sample results was compared and the, Pearson correlation analysis showed that, the ORF1a/b gene CT values of inactivated sample and non-inactivated sample had excellent correlation (r = 0.978; p < 0.001); (figure 2). Similarly as figure 3 shows, the N gene CT of inactivated and non-inactivated group had excellent correlation (r= 0.969; 95% CI, 0 .934 - 0.991; P<0.001). According to figure 3 and 4 revealed that the ORF1a/b gene CT value correlation between inactivated and non-inactivated groups had high positive correlation (r = 0.749; 95% CI, 0.434 - 0.935; p= 0.000).The N gene correlation between two groups also had strong positive correlation (r= 0.824; 95% CI, 0.634 - 0.962; p = 0.000).