A total of SARS CoV2- RNA RT-PCR-positive and negative patients (n = 1530) were diagnosed at Suez Canal University Hospital from 1st August 2021 to January 2022. The clinical data had been collected from patients’ records. The mean age of patients was 54.97 ± 18.21years old, the median age was 59 (interquartile range 3 – 99). Four hundred thirty-nine (28.7%) came from rural area, 1091 (71.3%) came from urban areas (Table 1). A total of 748 (48.9%) were male while a total of 782 (51.1%) were females. All 1420 (91.3%) patients were conscious at presentation while 133 patients (8.7%) presented with altered level of consciousness. The studied population was 1415 (92.5%) of non-health care workers while 115 (7.5%) were health care worker patients (Table 1).
The classification of samples as positive or negative for SARS-CoV-2 RNA was performed based on the analysis of the obtained values of the cycle threshold (Ct) and amplification curves shapes. Of these patients, 129 (8.4%) had weak positive RT-PCR results while 762 patient (49.8%) had positive RT-PCR. The N gene was represented in 85 patients (9.5%) and the ORF gene was represented in 13 patients (1.5%). Both genes were represented in 793 patients (89.0%) (Table 2).
The severity of disease ranged from mild to severe. Among the 758 patients, 483 (31.6%) had mild disease, 728 (47.6%) had moderate disease, and 319 (20.8%) had severe disease; the severity was determined according to the guidelines for MOHP Egypt, version 1.5/ September 2021(Table 1).
The clinical characteristics of patients were shown in table 3; high temperature, dry cough and breathing difficulty were the most common symptoms among patients while some patients had some neurological sequalae including coma, Cerebro-vascular sinus thrombosis (CVST), large vessel occlusion (LVO) and Guillian Barrie syndrome (GBS) (table 3).
No significant difference was detected between negative and positive patients concerning gender, residence, excessive obesity, cancer, and pregnancy. However, there was a highly statistically significant relation between increasing age and positivity of COVID-19 PCR (p<0.001). Similarly, there was statistically significant relationships between PCR positivity and the presence of each of the following diseases: hypertension (HTN), diabetes mellitus (DM) and stroke (Table 4).
Regarding total leucocytic count and lymphocytic count, the group with positive PCR results had the statistically significant lowest counts (p<0.001) (Table 4).
Among the 762 patients with positive PCR results, death rate was 27.3% which is higher than the group with weak positive PCR results (12.4%) and the group with negative results (0%) (p<0.001) (table 5).
Regarding the neurological sequelae, headache, coma, CVST, GBS, and LVO were significantly higher among the positive PCR results group compared with the weak positive and negative results’ groups (table 5).
Univariate logistic regression analysis showed that both N gene and ORF genes demonstrated significant association with mortality prediction (p<0.001 for both). Age showed highly significant association with mortality through both univariate and multivariate regression analyses (p<0.001 and <0.007 respectively). Similarly, HTN, DM, liver disease, IHD, stroke, CT chest Covid findings as well as presence of some symptoms such as headache, fever, cough, dyspnea, and disturbed level of consciousness, all showed significant association with mortality (table 6).
Table (1): Risk factors and basic Characteristics of the studied population (n = 1530)
|
No. (%)
|
Gender
|
|
Male
|
748 (48.9%)
|
Female
|
782 (51.1%)
|
Age (years)
|
|
Mean ± SD.
|
54.97 ± 18.21
|
Median (Min. – Max.)
|
59 (3 – 99)
|
Residence
|
|
Rural
|
439 (28.7%)
|
Urban
|
1091 (71.3%)
|
Excessive obesity
|
37 (2.4%)
|
Cancer
|
20 (1.3%)
|
Pregnancy
|
9 (0.6%)
|
*Chronic illness
|
782 (51.1%)
|
HTN
|
482 (31.5%)
|
DM
|
406 (26.5%)
|
Liver
|
62 (4.1%)
|
Renal
|
80 (5.2%)
|
IHD
|
103 (6.7%)
|
NCI
|
98 (6.4%)
|
Stroke
|
66 (4.3%)
|
CVS
|
17 (1.20%)
|
|
|
Type of patients
|
|
Non Health care worker
|
1415 (92.5%)
|
Health care worker
|
115 (7.5%)
|
TLC
|
|
Mean ± SD.
|
10449.5 ± 5510.5
|
Median (Min. – Max.)
|
11000 (1000 – 100000)
|
Lymphocytes %
|
|
Mean ± SD.
|
14.05 ± 6.94
|
Median (Min. – Max.)
|
12.0 (1.40 – 84.0)
|
No. lymphocytes
|
|
Mean ± SD.
|
1448.6 ± 1088.3
|
Median (Min. – Max.)
|
1320.0 (39.2 – 19068)
|
Risk rating
|
|
Mild
|
483 (31.6%)
|
Moderate
|
728 (47.6%)
|
Severe
|
319 (20.8%)
|
Outcome
|
|
Death
|
224 (14.6%)
|
Improvement
|
1285 (84.0%)
|
Home isolation
|
21 (1.4%)
|
SD: Standard deviation
*Documented comorbidities included hypertension, diabetes mellitus, liver disease, renal, Ischemic heart disease, NCI, stroke, cardiovascular symptoms. CVST (Cerebro vascular sinus thrombosis, GBS (Guillian Barrie syndrome), LVO (Large vessel occlusion)
Table (2): Descriptive analysis of the studied cases according to PCR results of N and ORF genes (n = 1530)
|
Negative 639 (41.8%)
|
Weak positive 129 (8.4%)
|
Positive 762 (49.8%)
|
N gene
|
(n = 639)
|
(n = 116)
|
(n = 762)
|
Mean ± SD.
|
0 ± 0
|
35.13 ± 7.15
|
28.33 ± 5.63
|
Median (Min. – Max.)
|
0 (0 – 0)
|
38.14 (11.98 – 42.57)
|
28.42 (11.14 – 57.52)
|
ORF
|
(n = 639)
|
(n = 44)
|
(n = 762)
|
Low (>37)
|
–
|
44 (100.0%)
|
49 (6.4%)
|
Intermediate (>25 - 37)
|
–
|
0 (0.0%)
|
448 (58.8%)
|
High viral Load (≤25)
|
–
|
0 (0.0%)
|
265 (34.8%)
|
Mean ± SD.
|
0 ± 0
|
39.15 ± 0.53
|
27.92 ± 5.70
|
Median (Min. – Max.)
|
0 (0 – 0)
|
39.15 (38.17 – 39.96)
|
27.71 (14.24 – 39.61)
|
SD: Standard deviation
Table (3): Clinical Characteristics of the studied population (n = 1530)
|
No. (%)
|
Neurological sequalae
|
|
Coma
|
203 (13.3%)
|
CVST
|
10 (0.7%)
|
GBS
|
10 (0.7%)
|
Headache
|
164 (10.7%)
|
LVO
|
33 (2.2%)
|
Symptoms
|
|
High temperature
|
1029 (67.3%)
|
Dry cough
|
1057 (69.1%)
|
Breathing difficulty
|
1037 (67.8%)
|
Fever
|
25 (1.6%)
|
Body aches
|
46 (3.0%)
|
Loss of smell
|
20 (1.3%)
|
Loss of taste
|
19 (1.2%)
|
Consciousness (GCs)
|
205 (13.4%)
|
Motor
|
63 (4.1%)
|
Cranial nerves
|
6 (0.4%)
|
Diarrhea
|
12 (0.8%)
|
Dizziness
|
16 (1.0%)
|
Vomit
|
3 (0.2%)
|
Ataxia
|
3 (0.2%)
|
Sore throat
|
9 (0.6%)
|
Other Symptoms
|
95 (6.2%)
|
CVST (Cerebro vascular sinus thrombosis, GBS (Guillian Barrie syndrome), LVO (Large vessel occlusion)
Table (4): Relation between Stratification of Covid 19 PCR results and risk factors parameters (n = 1530)
|
Result of PCR
|
Test of Sig.
|
P
|
Negative (n = 639)
|
Weak positive (n = 129)
|
Positive (n = 762)
|
Gender
|
|
|
|
|
|
Male
|
330 (51.6%)
|
54 (41.9%)
|
364 (47.8%)
|
χ2=4.873
|
0.087
|
Female
|
309 (48.4%)
|
75 (58.1%)
|
398 (52.2%)
|
Age (years)
|
|
|
|
|
|
Mean ± SD.
|
50.91b ± 20.55
|
56.15a ± 17.99
|
57.69a ± 15.78
|
F= 22.296*
|
<0.001*
|
Median (Min. – Max.)
|
53 (3 – 99)
|
61 (9 – 89)
|
61 (3 – 98)
|
Residence
|
|
|
|
|
|
Rural
|
165 (25.8%)
|
35 (27.1%)
|
239 (31.4%)
|
χ2= 5.387
|
0.068
|
Urban
|
474 (74.2%)
|
94 (72.9%)
|
523 (68.6%)
|
Excessive obesity
|
16 (2.5%)
|
6 (4.7%)
|
15 (2.0%)
|
χ2=3.399
|
0.183
|
Cancer
|
10 (1.6%)
|
3 (2.3%)
|
7 (0.9%)
|
χ2= 2.258
|
0.323
|
Pregnancy
|
5 (0.8%)
|
2 (1.6%)
|
2 (0.3%)
|
χ2= 4.144
|
MCp=0.102
|
Chronic illness
|
|
|
|
|
|
HTN
|
134 (21.0%)
|
45 (34.9%)
|
303 (39.8%)
|
χ2=57.632*
|
<0.001*
|
DM
|
114 (17.8%)
|
46 (35.7%)
|
246 (32.3%)
|
χ2=43.205*
|
<0.001*
|
Liver
|
25 (3.9%)
|
9 (7.0%)
|
28 (3.7%)
|
χ2= 3.149
|
0.207
|
Renal
|
39 (6.1%)
|
5 (3.9%)
|
36 (4.7%)
|
χ2= 1.854
|
0.396
|
IHD
|
33 (5.2%)
|
10 (7.8%)
|
60 (7.9%)
|
χ2= 4.298
|
0.117
|
NCI
|
23 (3.6%)
|
7 (5.4%)
|
68 (8.9%)
|
χ2=16.661*
|
<0.001*
|
Stroke
|
12 (1.9%)
|
8 (6.2%)
|
46 (6.0%)
|
χ2=15.779*
|
<0.001*
|
CVS
|
6 (0.9%)
|
2 (1.6%)
|
7 (0.9%)
|
χ2= 0.473
|
0.789
|
CMR
|
0 (0.0%)
|
1 (0.8%)
|
0 (0.0%)
|
χ2= 5.315
|
MCp=0.079
|
Type of patients
|
|
|
|
|
|
Non Health care worker
|
571 (89.4%)
|
119 (92.2%)
|
725 (95.1%)
|
χ2= 16.749*
|
<0.001*
|
Health care worker
|
68 (10.6%)
|
10 (7.8%)
|
37 (4.9%)
|
Total Leucocytes Count
|
|
|
|
|
|
Mean ± SD.
|
11480.3 ± 7015.6
|
10615.5 ± 4596.8
|
9557 ± 3807.8
|
H= 38.096*
|
<0.001*
|
Median (Min. – Max.)
|
11000a (2000 – 100000)
|
11000a (1600 – 23400)
|
10250b (1000 – 29900)
|
Lymphocytes %
|
|
|
|
|
|
Mean ± SD.
|
13.88 ± 6.21
|
14.40 ± 6.99
|
14.15 ± 7.50
|
H= 2.059
|
0.357
|
Median (Min. – Max.)
|
12 (3 – 43)
|
12 (3 – 43)
|
12 (1.40 – 84)
|
No. lymphocytes
|
|
|
|
|
|
Mean ± SD.
|
1573.1 ± 1162.4
|
1536.7 ± 1071.7
|
1329.3 ± 1012.6
|
H= 27.163*
|
<0.001*
|
Median (Min. – Max.)
|
1380a(75 – 13000)
|
1430a(192 – 7740)
|
1210b(39.2 – 19068)
|
Risk rating
|
|
|
|
|
|
Mild
|
258 (40.4%)
|
37 (28.7%)
|
188 (24.7%)
|
χ2= 44.015*
|
<0.001*
|
Moderate
|
260 (40.7%)
|
72 (55.8%)
|
396 (52.0%)
|
Sever
|
121 (18.9%)
|
20 (15.5%)
|
178 (23.4%)
|
Means or Medians in the same raw with small common letters are not significant (Different letters are significant
SD: Standard deviation H: H for Kruskal Wallis test, Pairwise comparison bet. each 2 groups was done using Post Hoc Test (Dunn's for multiple comparisons test)
F: F for One way ANOVA test, Pairwise comparison bet. each 2 groups was done using Post Hoc Test (Tukey)
c2: Chi square test MC: Monte Carlo
p: p value for comparing between the different result of PCR *: Statistically significant at p ≤ 0.05
Table (5): Relation between result of PCR and clinical outcome parameters (n = 1530)
|
Result of PCR
|
χ2
|
P
|
Negative (n = 639)
|
Weak positive (n = 129)
|
Positive (n = 762)
|
Outcome
|
|
|
|
|
|
Death
|
0 (0.0%)
|
16 (12.4%)
|
208 (27.3%)
|
229.93*
|
<0.001*
|
Improvement
|
639 (100.0%)
|
111 (86.0%)
|
535 (70.2%)
|
Home isolation
|
0 (0.0%)
|
2 (1.6%)
|
19 (2.5%)
|
Neurological sequelae
|
|
|
|
|
|
Coma
|
0 (0.0%)
|
15 (11.6%)
|
188 (24.7%)
|
184.169*
|
<0.001*
|
CVST
|
0 (0.0%)
|
0 (0.0%)
|
10 (1.3%)
|
9.777*
|
MCp=0.004*
|
GBS
|
0 (0.0%)
|
0 (0.0%)
|
10 (1.3%)
|
9.777
|
MCp=0.004*
|
Headache
|
12 (1.9%)
|
19 (14.7%)
|
133 (17.5%)
|
90.477*
|
<0.001*
|
LVO
|
0 (0.0%)
|
4 (3.1%)
|
29 (3.8%)
|
24.448*
|
<0.001*
|
Symptoms
|
|
|
|
|
|
High temperature
|
353 (55.2%)
|
98 (76.0%)
|
578 (75.9%)
|
71.896*
|
<0.001*
|
Dry cough
|
343 (53.7%)
|
94 (72.9%)
|
620 (81.4%)
|
125.69*
|
<0.001*
|
Breathing difficulty
|
328 (51.3%)
|
94 (72.9%)
|
615 (80.7%)
|
139.02*
|
<0.001*
|
Fever
|
6 (0.9%)
|
5 (3.9%)
|
14 (1.8%)
|
6.151*
|
0.046*
|
Body aches
|
23 (3.6%)
|
2 (1.6%)
|
21 (2.8%)
|
1.872
|
0.392
|
Loss of smell
|
9 (1.4%)
|
1 (0.8%)
|
10 (1.3%)
|
0.334
|
0.846
|
Loss of taste
|
9 (1.4%)
|
1 (0.8%)
|
9 (1.2%)
|
0.397
|
0.820
|
Consciousness (GCs)
|
2 (0.3%)
|
15 (11.6%)
|
188 (24.7%)
|
178.105*
|
<0.001*
|
Motor
|
2 (0.3%)
|
14 (10.9%)
|
47 (6.2%)
|
46.363*
|
<0.001*
|
Cranial nerves
|
3 (0.5%)
|
0 (0.0%)
|
3 (0.4%)
|
0.219
|
MCp=1.000
|
Diarrhea
|
9 (1.4%)
|
0 (0.0%)
|
3 (0.4%)
|
5.713
|
0.057
|
Dizziness
|
5 (0.8%)
|
1 (0.8%)
|
10 (1.3%)
|
1.043
|
0.594
|
Vomit
|
2 (0.3%)
|
0 (0.0%)
|
1 (0.1%)
|
0.863
|
MCp=0.688
|
Ataxia
|
0 (0.0%)
|
0 (0.0%)
|
2 (0.3%)
|
1.774
|
MCp=0.585
|
Sore throat
|
6 (0.9%)
|
1 (0.8%)
|
2 (0.3%)
|
3.141
|
MCp=0.169
|
Other Symptoms
|
59 (9.2%)
|
3 (2.3%)
|
33 (4.3%)
|
17.992*
|
<0.001*
|
c2: Chi square test MC: Monte Carlo
p: p value for comparing between the different result of PCR
*: Statistically significant at p ≤ 0.05
Table (6): Univariate and multivariate Logistic regression analysis for the parameters affecting mortality (n = 224 vs. 1306)
|
Univariate
|
#Multivariate
|
P
|
OR (95%C.I)
|
p
|
OR (95%C.I)
|
N gene (n = 1517)
|
<0.001*
|
1.070 (1.057 – 1.084)
|
0.183
|
1.171 (0.928 – 1.478)
|
ORF (n = 1445)
|
<0.001*
|
1.068 (1.055 – 1.082)
|
0.627
|
0.944 (0.748 – 1.192)
|
Consciousness
|
0.246
|
1.318 (0.826 – 2.101)
|
|
|
Male
|
0.130
|
1.246 (0.938 – 1.655)
|
|
|
Age (years) (n = 1390)
|
<0.001*
|
1.045 (1.034 – 1.055)
|
0.007*
|
1.072 (1.019 – 1.127)
|
Rural
|
0.019*
|
1.432 (1.061 – 1.932)
|
0.490
|
1.526 (0.459 – 5.077)
|
Excessive obesity
|
0.458
|
1.372 (0.595 – 3.163)
|
|
|
Cancer
|
0.497
|
1.466 (0.486 – 4.426)
|
|
|
Pregnancy
|
0.523
|
1.672 (0.345 – 8.100)
|
|
|
Chronic illness
|
|
|
|
|
HTN
|
<0.001*
|
2.270 (1.702 – 3.029)
|
0.054
|
0.243 (0.057 – 1.026)
|
DM
|
<0.001*
|
2.104 (1.566 – 2.828)
|
0.789
|
0.832 (0.216 – 3.204)
|
Liver
|
<0.001*
|
3.192 (1.848 – 5.512)
|
0.968
|
0.951 (0.082 – 11.090)
|
Renal
|
0.089
|
1.620 (0.930 – 2.824)
|
|
|
IHD
|
0.024*
|
1.754 (1.077 – 2.854)
|
0.015*
|
7.324 (1.480 – 36.252)
|
NCI
|
0.282
|
1.339 (0.786 – 2.280)
|
|
|
Stroke
|
<0.001*
|
17.987 (10.320 – 31.348)
|
0.002*
|
24.487 (3.326 – 180.296)
|
CVS
|
0.557
|
1.464 (0.410 – 5.229)
|
|
|
Non Health care worker
|
0.002*
|
21.327 (2.963 – 153.502)
|
0.519
|
11.514 (0.007 – 19318.4)
|
SO2% (n = 1528)
|
<0.001*
|
0.946 (0.931 – 0.961)
|
0.842
|
0.993 (0.925 – 1.065)
|
TLC
|
0.291
|
1.000 (1.000 – 1.000)
|
|
|
Lymphocytes %
|
0.837
|
1.002 (0.982 – 1.023)
|
|
|
No. lymphocytes
|
0.477
|
1.000 (1.000 – 1.000)
|
|
|
Risk rating
|
|
|
|
|
Mild®
|
|
1.000
|
|
|
Moderate
|
0.003*
|
1.732 (1.199 – 2.503)
|
0.653
|
0.688 (0.134 – 3.520)
|
Sever
|
<0.001*
|
2.686 (1.789 – 4.033)
|
0.930
|
1.083 (0.185 – 6.351)
|
Respiratory symptoms
|
0.839
|
1.096 (0.453 – 2.652)
|
|
|
CT findings
|
0.001*
|
1.651 (1.237 – 2.205)
|
0.904
|
1.080 (0.308 – 3.787)
|
Neurological sequelae
|
|
|
|
|
Coma
|
0.993
|
–
|
|
|
CVST
|
0.999
|
–
|
|
|
GBS
|
0.999
|
–
|
|
|
Headache
|
0.001*
|
0.031 (0.004 – 0.226)
|
0.995
|
0.0 (0.0 – .)
|
LVO
|
0.997
|
–
|
|
|
Symptoms
|
|
|
|
|
Fever
|
<0.001*
|
2.069 (1.467 – 2.917)
|
0.990
|
0.989 (0.188 – 5.218)
|
Dry cough
|
<0.001*
|
2.830 (1.930 – 4.148)
|
0.116
|
11.637 (0.548 – 247.323)
|
Dyspnea
|
<0.001*
|
4.445 (2.889 – 6.841)
|
0.629
|
0.598 (0.074 – 4.813)
|
Body aches
|
0.063
|
0.258 (0.062 – 1.074)
|
|
|
Loss of smell
|
0.247
|
0.304 (0.040 – 2.280)
|
|
|
Loss of taste
|
0.612
|
0.683 (0.157 – 2.977)
|
|
|
Consciousness (GCs)
|
<0.001*
|
6302.7(1466.8 – 27083)
|
<0.001*
|
2101 (135.07 – 32677)
|
Motor
|
0.034*
|
0.282 (0.088 – 0.907)
|
0.030*
|
0.089 (0.010 – 0.789)
|
Cranial nerves
|
0.888
|
1.167 (0.136 – 10.034)
|
|
|
Diarrhea
|
0.999
|
0.0 (0.0 – .)
|
|
|
Dizziness
|
0.358
|
0.386 (0.051 – 2.936)
|
|
|
Vomit
|
0.999
|
0.0 (0.0 – .)
|
|
|
Ataxia
|
0.999
|
0.0 (0.0 – .)
|
|
|
Chronic abscesses
|
1.000
|
0.0 (0.0 – .)
|
|
|
Sore throat
|
0.999
|
0.0 (0.0 – .)
|
|
|
Other Symptoms
|
<.0.001*
|
92.961 (47.082 – 183.55)
|
<0.001*
|
23.310 (4.005 – 135.688)
|