Dynamic changes of Ct values of N gene and ORF1ab genes and laboratory parameters in patients with COVID-19 caused by SARS-CoV-2 B.1, BA.2 and BA.5 variants and their correlation with clinical characteristics

doi:10.21203/rs.3.rs-4291017/v1

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Dynamic changes of Ct values of N gene and ORF1ab genes and laboratory parameters in patients with COVID-19 caused by SARS-CoV-2 B.1, BA.2 and BA.5 variants and their correlation with clinical characteristics

https://doi.org/10.21203/rs.3.rs-4291017/v1

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This study investigated the patterns of variation in the Ct values of the ORF1ab and N genes in oropharyngeal swabs of COVID-19 patients with different variants and to evaluate their associations with clinical and laboratory parameters. Total of 259 individuals with COVID-19 from 2021 to 2023 in Jilin Province were retrospectively included. Analysis was performed to compare the Ct values of the gene of SARS-CoV-2 in patients, with negative conversion time of nucleic acid, and the levels of blood tests during the patients' hospitalization.The majority of B.1 variant-infected individuals were asymptomatic; the median ORF1ab gene and N gene Ct values in oropharyngeal swabs from heavy patients were the lowest; and all ORF1ab gene Ct values were lower than N gene Ct values; with the longest negative conversion time of nucleic acid in these patients being 18 days.The median Ct values of the ORF1ab gene and the N gene were the highest in BA. 2 variant infected patients, and the Ct values of the ORF1ab gene and the N gene were higher in male patients than in female patients, and the shortest negative conversion time of nucleic acid was 14 days in patients with this variant, and the negative conversion time of nucleic acid was shorter in vaccinated patients than in unvaccinated patients.While the negative conversion time of nucleic acid was similar between BA.2 patients and BA.5 patients, the median Ct values of the ORF1ab and N genes were considerably lower in BA.5 patients than in BA.2 patients. The CREA, WBC, and NE% were significantly higher, and the ALB and LY% were significantly lower in BA.2 and BA.5 patients compared with B.1 patients. With disease aggravation, CREA, NE%, APTT, PT, and D-D increased, and LY% decreased. In conclusion, The most asymptomatic and longest transitional cycles were shown in patients with the ancestral lineage B.1 variation. Patients with the OmicronBA.2 variant showed the highest Ct values for the ORF1ab and N genes, while patients with the BA.2 and BA.5 variants had more serious coagulation and renal impairment.

COVID-19

SARS-CoV-2 BA.2 variant

SARS-CoV-2 BA.5 variant

SARS-CoV-2 B.1 lineage

cycle threshold

reverse transcription-quantitative polymerase chain reaction

SARS-CoV-2 has undergone genetic diversification since the COVID-19 pandemic caused by it, which has caused the introduction of novel variants [1]. The World Health Organization (WHO) has been regularly monitoring and evaluating the evolution of SARS-CoV-2 [2]. Five variants of concern (VoC) have been detected and labeled with Greek letters to date: Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617), and Omicron (B.1.1.529). The B.1 lineage, which is regarded as the ancestral lineage and is less developed than the VoC above, may have originated during the COVID-19 outbreak in northern Italy in early 2020, as demonstrated [3]. A novel SARS-CoV-2 variant (B.1.1.529) was discovered in South Africa from a patient sample on November 9, 2021, and the WHO named it the Omicron variant on November 26 [4]. Due to a significant number of mutations (particularly in the spike protein), studies have shown that Omicron variants exhibit increased transmissibility, high receptor binding affinity, and evasion of naturally occurring infection or vaccine-induced immunity [5]. This lineage consists of BA.1/21K, BA.2/21L, BA.3, BA.4/22A, BA.5/22B, BA.2.12.1/22C, and BA.2.75/22D; regarding the Omicron BA.5/22B variant, it was reported to have a growth advantage over the Omicron BA.1 and BA.2 variants [4].

Patients with COVID-19 typically present with systemic symptoms like fever and muscle pains or respiratory symptoms like cough [6]. The previous SARS-CoV-2 variants appear to affect primarily the upper respiratory tract and cause acute laryngitis without olfactory dysfunction, with clinical manifestations similar to those of epiglottitis in some patients, whereas the Omicron variant appears to affect primarily the lower respiratory tract and causes loss of smell and taste in many patients [7]. In addition, patients with the Omicron variant show lower median ages and a higher proportion of milder and asymptomatic patients than those with the Delta and Beta variants[8].

Real-time reverse transcription polymerase chain reaction (RT-PCR) has been frequently used to identify SARS-CoV-2 nucleic acids in respiratory swabs from patients. When the detection value of the fluorescent signal is above the cycling threshold (Ct), the earlier the cycle, the higher the concentration of the target gene in the sample. The Ct value is typically inversely proportional to the viral load [9], and the Ct value is frequently utilized as a distinct metric of viral load in the research of new coronaviruses [10].

In Jilin Province, China, COVID-19 patients appeared one after the other from 2021 to 2023. The three SARS-CoV-2 variants that predominated during that time all belonged to different genotypes, as revealed by whole genome sequencing and genomics analysis. The BA.2 variant prevalent in 2022 and the BA.5 variant prevalent in 2023 were both members of the Omicron lineage[4], while the B.1 variant prevalent in 2021 belonged to the ancestral lineage [3]. In this study, the Ct values of the ORF1ab gene and the N gene of SARS-CoV-2 in oropharyngeal swabs of patients with COVID-19, the negative conversion time of nucleic acid, clinical performance of patients with COVID-19, and blood test levels were compared and analyzed in order to investigate the characteristics of molecular biological tests and other laboratory tests for different genotypes of SARS-CoV-2, as well as the differences in clinical performance, and to provide a reference for the diagnosis and treatment of COVID-19.

Study Population

A total of 259 patients were included in this study, including 110 patients with B.1 variant infection admitted to Changchun Infectious Disease Hospital from January to February 2021, 82 patients with BA.2 variant infection admitted to Department II of Jilin University Hospital from April to May 2022, and 67 patients with BA.5 variant infection admitted to Mehekou City Hospital from December 2022 to February 2023. The demographic data, clinical and laboratory parameters, and clinical classification were obtained through the hospital's electronic medical record and analyzed by a group of skilled doctors. Clinical data included patient demographics (sex, age), underlying comorbidities (hypertension, diabetes, cardiovascular disease, pulmonary disease, renal disease, liver disease, neurological disease, and prior history of malignancy), signs and symptoms (fever, cough, chest tightness, weakness, palpitations, dyspnea, shortness of breath after activity, dizziness and headache, nausea and vomiting, nausea and diarrhea, asymptomatic), and duration of hospitalization. Laboratory parameters included SARS-CoV-2 nucleic acid test results (ORF1ab gene and N gene Ct values) from the patient's oropharyngeal swab and blood tests (creatinine: CREA, reference interval 41–73 10⁹/L; albumin: ALB, reference interval 40–55×10⁹/L; and white blood cells: WBC, reference interval 3.52–9.50×10⁹/L; neutrophil percentage: NE, reference interval 40–75%; lymphocyte percentage: LY, reference interval 20–50%; platelet count: PLT, reference interval 125–350×10⁹/L; activated partial thromboplastin time: APTT, reference interval 28.0–42.0; prothrombin time: PT, reference interval 11.0–15.0; D dimer: D, reference interval 0.00-0.50).

The disease is divided into four categories in clinical practice: mild, moderate, severe, and critical. Mild cases are those with mild clinical symptoms and no imaging signs of pneumonia; moderate cases are those with fever and respiratory symptoms and imaging signs of pneumonia; and severe cases are those with one of the following criteria: (a) dyspnea with respiratory rate ≥ 30/min; (b) pulse oximetry at rest ≤ 93%; (c) oxygenation index (arterial partial pressure of oxygen/inhalation oxygen fraction, PaO₂/FiO₂) ≤ 300 mmHg; (d) progressive clinical symptoms with significant progression of lesions > 50% on lung imaging within 24–48 hours; critical cases are those that meet one of the following criteria: (a) respiratory failure requiring mechanical ventilation; (b) shock; (c) combined with other organ failure requiring ICU monitoring and treatment. All diagnostic and clinical classifications of COVID-19 above are based on the "Diagnosis and Treatment Protocol for Novel Coronavirus Pneumonia (8th Trial Version)" published by the National Health Commission of the People’s Republic of China[11].

Methods

In this study, pharyngeal swabs from patients with COVID-19 were collected for routine COVID-19 diagnosis, and the inclusion criterion was a Ct value of < 38 for nucleic acid testing in patients in 2021–2022, and < 35 for nucleic acid testing in 2023. The negative criteria for nucleic acid testing in 2021–2022 were established as two consecutive nucleic acid tests for the ORF1ab gene and the N gene with a Ct value of ≥ 38 (fluorescence quantitative PCR method, two sampling intervals of at least 24 hours); the negative criteria for nucleic acid testing in 2023 were established as two consecutive nucleic acid tests for the ORF1ab gene and the N gene with a Ct value of ≥ 35 (fluorescence quantitative PCR method, two sampling intervals of at least 24 hours). When patients were admitted to the hospital, blood tests were conducted every three days for mild

patients and as often as the dynamics of the disease permitted until the patients were discharged for severe patients. Four clinical classification were present in the cases included in this study, but there were not enough patients with the moderate or critical types to form separate groups. As a result, the text has referred to the combination of mild and moderate patients as "mild" and the combination of severe and critical patients as "severe."

Quality Control

Laboratory parameters included ORF1ab gene and N gene Ct value testing for SARS-CoV-2 in patient oropharyngeal swabs and blood tests. Oropharyngeal swab sample collection and RT-qPCR assays were performed by trained medical personnel according to to standardized procedures and traceability of sample results. "Guidelines for the Implementation of Regional 2019-nCoV Nucleic Acid Detection (2nd Edition)" and "Working Manual of Novel Coronavirus Nucleic Acid Detection for Medical Institutions (second trial Edition)" were strictly followed during the sample collection procedure[12, 13]. RNA extraction was performed using a nucleic acid extraction (NAE) system and accompanying NAE or purification reagents, and the operating procedures strictly followed the manufacturer's protocol. Nucleic acid amplification was performed on a RT-qPCR detection system. The PCR reaction system configuration, reaction parameters, and program settings were set according to the kit's instructions, respectively. Each run was subjected to quality control, which included three weakly positive and one weakly negative controls to detect false positive and false negative results. At the three hospitals, the blood testing equipments were put through stringent quality control testing. The Jilin Clinical Laboratory Center accredited all three of the study's participating labs for inter-laboratory quality evaluation and proficiency. The Health Commission of Jilin Province provided standardized training to all of the doctors, technicians, and nurses involved in this study. For common biochemical analytes and blood cell analysis in Chinese adults, reference interval standards have been issued by the National Health Commission of the People’s Republic of China[14]. Reference intervals that met the requirements were used by the three hospitals. There was no influence of different instruments on the test results.

Statistical analysis

IBM SPSS version 22 (IBM Corporation, Chicago) was used for all statistical analyses. The Shapiro-Wilk test was used to determine the normality of the distribution of continuous variables; Ct values, negative conversion time of nucleic acid, and blood test levels were compared between groups using the unpaired Student’s t test if they were normally distributed and the Mann-Whitney U test if they were not normally distributed, and the results were expressed as M (P25, P75). Frequencies and rates were used to express the patients' fundamental traits and clinical performance, and the X² test or Fisher's exact probability method was used to compare the groups. The Perason test, the Spearman test, and binary logistic regression were used to examine the correlation between continuous numerical data, the correlation between dichotomous variables, and the regression between variables.Graphpad Prism 8 and Origin Pro were used to create the figures.

Ethics

The data set was entirely anonymous and did not include any personally identifiable health information that might be used to violate the subjects' rights or interests. The study was carried out in accordance with the approved guidelines and was approved by the ethics committees of the hospitals: Ethics Committee of Changchun Infectious Diseases Hospital(No. 2020-001) and First Hospital of Jilin University(No. K2022028). The Ethics Committee of the First Hospital of Jilin University(No. K2022028) and the Ethics Committee of Changchun Infectious Diseases Hospital(No. 2020-001) waived written informed consent for this study for it was a retrospective study.

Basic characteristics of the data

Table 1 summarized the basic characteristics of the included data: patients with the three variants did not differ by sex; patients with the B.1 variant were significantly younger than those with the BA.2 and BA.5 variants (56 vs. 65 vs. 72, P < 0.01); and significantly fewer patients with combined underlying disease than with the BA.2 and BA.5 variants (46.36%vs. 67.07% vs. 76.12%, P < 0.01). Compared to those infected with the B.1 and BA.2 variants, the BA.5 variant showed the highest number of severe patients (8.18% vs. 0 vs. 50.75%, P < 0.01). None of the patients with the B.1 variant were vaccinated, and neither the BA.2 nor the BA.5 variant showed any significant difference in the number of vaccinated patients.

Comparisons of Ct values and trends of the ORF1ab gene and the N gene of patients with the three variants

In this study, the median Ct values of ORF1ab gene and N gene in all subgroups of patients with B.1 variant were significantly lower than those in patients with BA.2 variant (P < 0.01), and the Ct values of N gene were always significantly lower than those of ORF1ab gene (P < 0.01). The Ct values of the ORF1ab gene and the N gene in severe patients with the B.1 variant were significantly lower than those in mild patients (P < 0.01). The median Ct values of both ORF1ab and N genes were significantly higher in patients with the BA.2 variant than in patients with the BA.5 variant (P < 0.01), and the median Ct values of both ORF1ab and N genes were significantly higher in vaccinated patients than in vaccinated patients with the BA.5 variant (P < 0.05), and the Ct values of both ORF1ab and N genes were significantly higher in male patients with this variant than in female patients (P < 0.05). The Ct values of the ORF1ab gene and the N gene in vaccinated patients with the BA.5 variant were significantly lower than those in unvaccinated patients (P < 0.05)(Table 2). In addition, with increasing days of infection, the Ct values of the ORF1ab gene and the N gene in patients with all three variants showed a gradual increase (Fig. 1).

Comparison of the negative nucleic acid conversion time of patients with the three variants

The median negative nucleic acid conversion time was 18 days for patients with the B.1 variant, 14 days for patients with the BA.2 variant, and 15 days for patients with the BA.5 variant (Fig. 1), and the negative nucleic acid conversion time was significantly longer for patients with the B.1 variant than for patients with the Omicron variant in all subgroups (P < 0.01). Sex, age, clinical classification, combined underlying disease, and vaccination or not showed no significant effect on the negative nucleic acid conversion time of B.1 and BA.5 variants. In the BA.2 variant, the elderly the age, the longer the negative nucleic acid conversion time (P < 0.05), and the negative nucleic acid conversion time was significantly longer in unvaccinated patients than in vaccinated patients (P < 0.01) (Fig. 2). No significant differences were found between the BA.2 and BA.5 variants in other subgroups.

Comparison of the clinical performance of the three variants

Patients with all three variants showed the most common symptoms of fever and cough. The highest number of patients with the B.1 variant were asymptomatic (91 vs. 14 vs. 3, P < 0.01), while patients with the BA.2 and BA.5 variants were more likely to suffer from chest tightness, fatigue, muscle aches, headaches, and dyspnea. Compared with BA.2 variant patients, BA.5 variant patients were more likely to suffer from shortness of breath after activity and nausea and vomiting (Table. 3).

Assessment of risk factors for clinical classification and clinical performance

All patients with the three variants combined in this study were analyzed by logistic regression of the factors influencing clinical classification (sex, age, combination of underlying diseases, and vaccination or not), and elderly age was found to be a risk factor for the diagnosis of severe disease (OR = 5.919, P < 0.01) (Fig. 3A). A logistic regression analysis of the factors influencing clinical performance (sex, age, clinical classification, combination of underlying diseases, and vaccination or not) revealed that combination of underlying diseases was a risk factor for clinical performance (OR = 6.607, p < 0.01) (Fig. 3B).

Comparison of blood test levels for patients with the three variants

Compared with patients with the B.1 variant, patients with the BA.2 and BA.5 variants showed significantly higher CREA, WBC, and NE% (P < 0.01) and significantly lower ALB and LY%.Blood tests such as CREA, WBC, APTT, PT, NE%, PLT, and LY% fluctuated within the reference interval throughout the course of the disease in patients infected with the B.1 variant, but only three blood tests—WBC, PT, and PLT—did so in patients with the three variants (Fig. 4).Patients with B.1 and BA.5 variants displayed a significant decline in LY% and a significant increase in CREA, NE%, APTT, PT, and D-D as disease severity increased (Table 4.). In this investigation, all patients with the three variants were combined, and Pearson correlation analysis revealed a positive association between the number of infection days and ALB, NE%, and PT and a negative correlation with LY% (P < 0.01), (Table 5). Additionally, the correlation analysis of patients' sex, age, underlying disease, vaccination, clinical classification, and blood test levels revealed that age, combined underlying disease, and clinical classification were negatively correlated with ALB and LY% and positively correlated with WBC, NE%, and D-D, and age was also positively correlated with underlying disease and clinical classification. Age was also positively correlated with underlying disease and clinical classification, and underlying disease was positively correlated with clinical classification. The correlation between other indicators is shown in Fig 5.

This study had the following innovative findings: This study pioneered a direct comparison of the B.1 ancestral lineage with the BA.2 and BA.5 variants of the Omicron lineage, integrating clinical manifestations and laboratory findings, used data from three consecutive years of COVID-19 patients in Jilin Province from 2021 to 2023 to investigate the patterns of variants in the Ct values of the ORF1ab and N genes in oropharyngeal swabs of SARS-CoV-2 patients with different variants and to explore their associations with clinical performance, blood test levels, and the negative conversion time of nucleic acid.

Basic characteristics of clinical data

In order to effectively reduce the number of infections when the B.1 and BA.2 variants emerged in Jilin Province, the province implemented quarantine and isolation along with social distancing measures from the start of the outbreak in 2019 until December 2022. While the BA.5 variant outbreak occurred between December 2022 and February 2023, Jilin Province enforced the national policy of no more quarantine and isolation along with social distance for individuals during that time. As a result, the age and clinical history of the inpatients included in this study were different from those from the previous two years. It is believed that most young patients infected with the BA.5 variant do not show co-morbid underlying diseases and suffer mild clinical symptoms; therefore, they are at low risk of hospitalization, whereas older patients with more co-morbid underlying diseases have an increased risk of hospitalization [15]. According to studies, people infected with the Omicron BA.5 variant exhibit modest symptoms and less severe disease, and their average age is lower than that of patients infected with the preceding variants [16]. Holding other variables constant, the results of logistic regression analysis in the current study also revealed that there was a difference in the severity grading of COVID-19 patients in different age groups, patients aged > 60 years were 5.919 times more likely to be classified as severe than those aged 60 years, corroborating the findings of other studies [8, 17]. Therefore, this can be one of the factors contributing to the high proportion of BA.5 variant-severe patients in this study.

Ct values of the ORF1ab and the N gene and negative conversion time of nucleic acid of patients with the three variants

In this study, the Ct values of the ORF1ab and N genes of patients with the three variants were evaluated, and the relationship between the Ct values and disease development was examined.Firstly, in this study, we found that the Ct values of the ORF1ab gene and N gene of all patients with the three variants reached a plateau on the second day of infection and then gradually increased, and the mean Ct values of the ORF1ab gene and N gene of patients with the BA.2 and BA.5 variants maintained almost all above 35 after the median days of the transient cycle but fluctuated more, which may be attributed to the instability of the Ct values of pharyngeal swabs during the recovery period and easy false negatives occur [18]. Secondly, in all subgroups of patients with the B.1 variant, the Ct value of the N gene was discovered to be significantly lower than that of the ORF1ab gene in this investigation.,validating the findings that the detection limit of the N gene was lower than that of the ORF1ab gene [19]. Third, research has revealed that COVID-19 individuals have a tendency to gradually decrease viral load, lower clinical symptoms, and decrease the severity of disease as SARS-CoV-2 variants continue to arise[2]. Although the median Ct values of the ORF1ab and N genes of the patients with the BA.5 variant were not statistically different from those of the B.1 variant, it was proven in the current investigation that the viral load and negative conversion time of nucleic acid of the patients with the BA.2 variant were significantly lower than those of the B.1 variant. The results of the current investigation also showed that the median Ct values of the ORF1ab and N genes of the patients with the BA.5 variant were much lower than those of the BA.2 variant, supporting previous studies' findings that the BA.5 variant had a greater replication ability than the BA.2 variant [20]. Last but not least, related studies have confirmed that receiving three doses of vaccination within 180 days can reduce the Ct value, shorten the length of the disease, and protect patients [21]. Among those infected with the BA.2 variant, the negative conversion time of nucleic acid in patients vaccinated was indeed shorter than that of unvaccinated patients, but the efficacy of the vaccine was not fully confirmed in this study.In patients with BA.5 variant, the Ct values of ORF1ab gene and N gene in vaccinated patients were instead lower than in unvaccinated patients, probably due to the number of cases included in this study was limited and the study of vaccine effectiveness against COVID-19 was based on a certain amount of data [22], and also due to most of the patients with BA.5 variant received the last dose of vaccine more than 6–8 months from the time of infection with SARS-CoV-2, so the data may not be sufficient for the results obtained to be reliable.

Clinical performance and blood test levels

Patients with co-morbidities were discovered to be 6.607 times more likely to be symptomatic than those without co-morbidities, as judged by risk variables for clinical presentation, and the BA.5 variant was proven to be more pathogenic than the BA.2 variant in mouse research [23]. As a result, there may be more symptomatic patients with the BA.5 variant than with the B.1 and BA.2 variants due to the higher pathogenicity and the significant proportion of infected patients who also have an underlying condition.

Age, combined underlying disease, and clinical classification were shown to be negatively connected with ALB and LY% and positively correlated with NE% and D-D in the correlation analysis of blood test levels. These patients with the three variants also varied greatly in age, combined underlying disease, and clinical classification. This may be one of the factors influencing the variability of the three variants of ALB, NE%, LY%, and D-D. LY%, WBC, D-D, and NE% can all be used to determine the degree of inflammatory response in a patient. The significant increases in NE%, D-D, and WBC as the disease's severity increases and the significant decreases in LY% are evidence of the inflammatory response becoming more pronounced as the patient's condition deteriorates. Lymphocyte levels are typically higher during viral infection[23], but in the current study, it was shown that lymphocyte levels were decreased in patients infected with Omicron BA.2 and BA.5 variations. On the one hand, this finding may be related to the large percentage of elderly Omicron patients, and on the other hand, low lymphocyte levels may be a sign of how severe Omicron variants were.

The results of the current study revealed that the CREA of the B.1 variant fell within the reference interval, whereas the CREA of the BA.2 and BA.5 variants exceeded the top limit of the reference interval(Fig. 5). The research determined that serum CREA only increased when kidney function was moderately impaired, and the total CREA indices of all three variants, notably the BA.5 variant, tended to increase with the progression of the disease. This finding is consistent with other studies [24], and suggests that COVID-19 patients had mild early renal impairment and that there was a risk of growing renal impairment with the progression of the disease.Furthermore, there was no correlation between CREA and age, vaccination status, or underlying disease, and the CREA of the patients with the Omicron BA.2 and BA.5 variations was considerably higher than that of the patients with the B.1 variant. These findings suggest that Omicron BA.2 and BA.5 variants cause more severe kidney injury.

The impact of SARS-CoV-2 on the body is also shown in coagulation; an overactive inflammatory response can lead to a hypercoagulable condition and damage to the vascular endothelium, which results in microcirculatory thrombosis and affects the function of multiple organs [25]. Some SARS-CoV-2 patients will experience thrombocytopenia, and related research has shown that this condition may be brought on by one of the following: (1) reduced platelet synthesis: ① the virus directly infects bone marrow cells, inhibiting platelet synthesis; ② cytokine storm, which kills bone marrow progenitor cells and reduces platelet formation; ③ lung damage, which indirectly reduces platelet synthesis; (2) increased platelet destruction: during SARS-CoV-2 infection, the immune system activates, leading to increased platelet destruction by the immune system, resulting in thrombocytopenia; (3) increased platelet consumption: COVID-19 patients have large numbers of platelets aggregating in the lungs, leading to microthrombosis and platelet depletion [26]. This study also discovered that APTT and PT were considerably delayed in severe patients compared to mild patients, and PLT was lowered, supporting the preceding findings that severe COVID-19 aggravates vascular endothelial cell injury, consumes a lot of platelets, induces intravascular mixed thrombus, and causes coagulation dysfunction. Additionally, PLT levels were noticeably lower in patients with the BA.2 and BA.5 variants of Omicron than in those with the B.1 variant, leading to a more serious coagulation impairment and a poor prognosis.

limitation

Missing data: Due to the extensive time period, admission to many hospitals, and shifting epidemic prevention and control policies, the patient data obtained in this study may contain missing clinical case data. For instance, the vaccine was not yet widely accessible when the first epidemic wave hit Jilin Province in 2021, hence, none of the patients with the B.1 variant received vaccination. Additionally, due to a number of complicating variables, vaccination records for 27 patients with the BA.5 variant were not available; the daily clinical manifestations of the patients were absent from the case records. Further research is required to validate the vaccine's protective impact in COVID-19 patients, explore the relationship between clinical performance and Ct values, and predict the clinical performance of patients based on the variation pattern of Ct values.
Improper subgroup: The protective effect of COVID-19 vaccination depends on the number of vaccinations and the time gap between the previous vaccination and the SARS-CoV-2 infection. Although studies have indicated a modest benefit of the vaccine on viral load and length of detoxification [27, 28], it is still regarded as unreliable to simply split patients into vaccinated and unvaccinated groups for comparison due to the influence of numerous confounding factors.

Patients with ancestral lineage B.1 showed longer turnaround cycles than Omicron BA.2 and BA.5 variants, and most infected patients are asymptomatic. Omicron BA.2 variants showed the highest ORF1ab gene and N gene Ct values, and patients with BA.2 and BA.5 variants suffered most commonly from fever and cough, and their renal and coagulation functions were more severely impaired. Patients of elderly age are more likely to develop severe disease. In conclusion, the changes in SARS-CoV-2 genotype should be closely monitored so that appropriate measures can be taken in time.

Data availability

The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.

Acknowledgements

The authors extend their sincere gratitude to all participants.

Funding

This work was supported by the Jilin Science and Technology Development Program (Grant numbers 20220401085YY).

Ethics

Confict of interest: The authors declare no conficts of interest.

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Tables 1 to 5 are available in the Supplementary Files section.

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Dynamic changes of Ct values of N gene and ORF1ab genes and laboratory parameters in patients with COVID-19 caused by SARS-CoV-2 B.1, BA.2 and BA.5 variants and their correlation with clinical characteristics

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