Computer-readable storage medium and data processing device for grouping novel coronavirus infected patients

Abstract

The present invention discloses a computer-readable storage medium and data processing device for grouping patients infected with the novel coronavirus. The present invention provides a device for comparing the risk of a subject developing a severe illness after being infected with SARS-CoV-2, characterized in that the device includes the following modules: M1, a data receiving module: for receiving information on whether the subject carries allele C at the SNP rs186996510 site to obtain sample data; M2, a result output module: for comparing the risk of the subject developing a severe illness after being infected with SARS-CoV-2 based on the sample data. The computer device and computer-readable storage medium provided by the present invention can be used to prevent or reduce the occurrence of severe illness caused by SARS-CoV-2 infection.

Description

Technical Field

[0001] The present invention belongs to the field of healthcare informatics and relates to a computer-readable storage medium and a data processing device for grouping patients infected with the novel coronavirus. Background Art

[0002] Novel coronavirus infection is an acute infectious disease caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 is primarily transmitted through respiratory droplets and close contact. In relatively closed environments, it is spread through aerosols, and contact with contaminated objects can also cause infection. SARS-CoV-2 spreads rapidly, infects a wide range of people, and is difficult to control.

[0003] Clinical symptoms of SARS-CoV-2 infection exhibit significant heterogeneity, ranging from asymptomatic infection to mild to severe disease. Mild cases may present with only mild fever, cough, and fatigue, and typically recover quickly with appropriate isolation and symptomatic treatment. Severe cases often progress rapidly, are highly susceptible to complications such as acute respiratory distress syndrome (ARDS), septic shock, difficult-to-correct metabolic acidosis, and coagulopathy, and have a significantly increased mortality rate. This inter-individual variability in disease severity is not only closely related to factors such as age and underlying medical conditions (such as cardiovascular disease, diabetes, and chronic respiratory illnesses), but a growing body of research suggests that genetic factors also play a crucial role. Therefore, identifying the genetic susceptibility genes underlying severe SARS-CoV-2 infection and dissecting the genetic differences between severe and mild cases are crucial for a deeper understanding of SARS-CoV-2 pathogenicity, accurately predicting the course of disease, implementing proactive interventions, and developing targeted therapeutics. Summary of the Invention

[0004] The purpose of the present invention is to provide a computer-readable storage medium and a data processing device for grouping people infected with the new coronavirus.

[0005] The present invention provides a device for comparing the risk of a subject developing a severe illness after being infected with SARS-CoV-2, characterized in that the device comprises the following modules:

[0006] M1, data receiving module: used to receive information about whether the subject's SNP rs186996510 site carries allele C and obtain sample data;

[0007] M2. Result output module: used to compare the risk of the subject developing severe illness after being infected with SARS-CoV-2 based on the sample data.

[0008] “Comparing the risks of the subjects developing severe illness after being infected with SARS-CoV-2” can mean: subjects carrying allele C at the SNPrs186996510 site have a higher risk of developing severe illness after being infected with SARS-CoV-2 than subjects not carrying allele C at the SNPrs186996510 site.

[0009] The subjects may be two or more subjects.

[0010] The present invention also provides a device for grouping subjects according to their risk of developing severe illness after being infected with SARS-CoV-2, characterized in that the device includes the following modules:

[0011] M3, data receiving module: used to receive information about whether the subject's SNP rs186996510 site carries allele C and obtain sample data;

[0012] M4. Result output module: used to group the risk of the subjects developing severe illness after being infected with SARS-CoV-2 based on the sample data.

[0013] “Clustering the subjects according to the risk of developing severe illness after being infected with SARS-CoV-2” can be: if the subject carries allele C at the SNP rs186996510 site, the subject belongs to a high-risk group for developing severe illness after being infected with SARS-CoV-2; if the subject does not carry allele C at the SNP rs186996510 site, the subject belongs to a low-risk group for developing severe illness after being infected with SARS-CoV-2; the high-risk group has a higher risk of developing severe illness after being infected with SARS-CoV-2 than the low-risk group.

[0014] The subject may be more than one subject.

[0015] The present invention further provides a data processing device comprising a memory, a processor, and a computer program stored in the memory, wherein the processor executes the computer program to implement the following steps:

[0016] S1. Data reception: Receive information about whether the subject carries allele C at the SNP rs186996510 site and obtain sample data;

[0017] S2. Result output: Compare the risk of the subjects developing severe illness after being infected with SARS-CoV-2 based on the sample data.

[0018] The computer flow chart of the above steps is shown in Figure 1 .

[0019] “Comparing the risks of the subjects developing severe illness after being infected with SARS-CoV-2” can mean: subjects carrying allele C at the SNPrs186996510 site have a higher risk of developing severe illness after being infected with SARS-CoV-2 than subjects not carrying allele C at the SNPrs186996510 site.

[0020] The subjects may be two or more subjects.

[0021] The present invention further provides a data processing device comprising a memory, a processor, and a computer program stored in the memory, wherein the processor executes the computer program to implement the following steps:

[0022] S3. Data reception: Receive information about whether the subject carries allele C at the SNP rs186996510 site and obtain sample data;

[0023] S4. Result output: The risk of the subjects developing severe illness after being infected with SARS-CoV-2 is grouped according to the sample data.

[0024] “Clustering the subjects according to the risk of developing severe illness after being infected with SARS-CoV-2” can be: if the subject carries allele C at the SNP rs186996510 site, the subject belongs to a high-risk group for developing severe illness after being infected with SARS-CoV-2; if the subject does not carry allele C at the SNP rs186996510 site, the subject belongs to a low-risk group for developing severe illness after being infected with SARS-CoV-2; the high-risk group has a higher risk of developing severe illness after being infected with SARS-CoV-2 than the low-risk group.

[0025] The subject may be more than one subject.

[0026] The present invention also provides a computer program product, comprising a computer program, characterized in that: when the computer program is executed by a processor, the step S1 and the step S2 are implemented.

[0027] The present invention further provides a computer-readable storage medium storing a computer program, wherein the computer program implements step S1 and step S2 when executed by a processor.

[0028] The present invention further provides a computer program product, comprising a computer program, characterized in that: when the computer program is executed by a processor, the step S3 and the step S4 are implemented.

[0029] The present invention further provides a computer-readable storage medium having a computer program stored thereon, wherein the computer program implements step S3 and step S4 when executed by a processor.

[0030] The present invention also provides a method for comparing the risk of a subject developing severe illness after being infected with SARS-CoV-2, comprising the following steps:

[0031] Receive information about whether the subject carries allele C at the SNP rs186996510 site and obtain sample data;

[0032] Comparing the risk of the subjects developing severe illness after being infected with SARS-CoV-2 based on the sample data;

[0033] The method is not directed towards the diagnosis of disease or health status.

[0034] “Comparing the risks of the subjects developing severe illness after being infected with SARS-CoV-2” can mean: subjects carrying allele C at the SNPrs186996510 site have a higher risk of developing severe illness after being infected with SARS-CoV-2 than subjects not carrying allele C at the SNPrs186996510 site.

[0035] The subjects may be two or more subjects.

[0036] The present invention also provides a method for grouping subjects according to their risk of developing severe illness after being infected with SARS-CoV-2, comprising the following steps:

[0037] Receive information about whether the subject carries allele C at the SNP rs186996510 site and obtain sample data;

[0038] Grouping the subjects according to their risk of developing severe illness after being infected with SARS-CoV-2 based on the sample data;

[0039] The method is not directed towards the diagnosis of disease or health status.

[0040] “Clustering the subjects according to the risk of developing severe illness after being infected with SARS-CoV-2” can be: if the subject carries allele C at the SNP rs186996510 site, the subject belongs to a high-risk group for developing severe illness after being infected with SARS-CoV-2; if the subject does not carry allele C at the SNP rs186996510 site, the subject belongs to a low-risk group for developing severe illness after being infected with SARS-CoV-2; the high-risk group has a higher risk of developing severe illness after being infected with SARS-CoV-2 than the low-risk group.

[0041] The subject may be more than one subject.

[0042] Any of the above methods may not include the step of obtaining a biological sample from an animal. All of the above methods may not be conducted on living human or animal subjects, but only on data. All of the above methods may be information processing methods in which all steps are performed by a data processing device such as a computer.

[0043] Specifically, based on SNP rs186996510, the subject's genotype is GG or CG or CC.

[0044] SNP rs186996510 is located in human genomic DNA, corresponding to nucleotide position 301 in SEQ ID NO: 6, and is represented by S. S represents C or G.

[0045] Any of the above subjects may be Chinese.

[0046] Any of the above subjects may be Chinese Han nationality.

[0047] Any of the above subjects may be infected with SARS-CoV-2.

[0048] The inventors of the present invention discovered that, based on the SNP rs186996510, subjects carrying the C allele have a higher risk of developing severe illness after SARS-CoV-2 infection than subjects without the C allele. In Examples 3 and 4, the present invention uses samples from different populations as examples to exemplify genotype distribution frequency data in groups of patients with severe SARS-CoV-2 infection and groups of patients with mild SARS-CoV-2 infection, respectively. Based on these findings, the inventors of the present invention developed the aforementioned computer device and computer-readable storage medium.

[0049] The computer device and computer-readable storage medium provided by the present invention can be used to avoid or reduce the occurrence of severe SARS-CoV-2 infection. BRIEF DESCRIPTION OF THE DRAWINGS

[0050] Figure 1 A computer flow chart. DETAILED DESCRIPTION

[0051] The present invention will be further described in detail below in conjunction with specific embodiments. The examples provided are only for illustrating the present invention and are not intended to limit the scope of the present invention. The examples provided below can serve as a guide for further improvements by those skilled in the art and are not intended to limit the present invention in any way.

[0052] Unless otherwise specified, the experimental methods in the following examples are conventional methods and were performed according to the techniques or conditions described in the literature in this field or according to the product instructions. Unless otherwise specified, the materials and reagents used in the following examples are commercially available. Ethics Statement: Each subject signed an informed consent form, and this study was approved by the Medical Ethics Committee of the PLA General Hospital. Both severe and mild patients were confirmed to be infected with SARS-CoV-2 through nucleic acid testing.

[0053] p-value:Person test. lnBeta=OR, OR: odds ratio.

[0054] Strictly follow the diagnostic criteria for severe COVID-19 issued by the World Health Organization (WHO) and the National Health Commission of my country. Inclusion criteria for severe patients are those who meet at least one of the following: ① tachypnea (respiratory rate ≥ 30 breaths / minute); ② resting oxygen saturation ≤ 93% while breathing air; ③ arterial oxygen partial pressure (PaO2) / inspired oxygen fraction (FiO2) ≤ 300 mmHg (1 mmHg = 0.133 kPa); ④ progressive worsening of clinical symptoms, with lung imaging demonstrating significant lesion progression involving >50% of the lung fields within 24-48 hours; and ⑤ accompanied by at least one of the following complications: respiratory failure requiring mechanical ventilation, shock, or concurrent organ failure requiring ICU admission for monitoring and treatment. At the same time, in order to exclude other interfering factors, the patient's medical history was reviewed in detail to ensure that the selected patients met the following ①, ②, and ③ at the same time: ① No other underlying diseases that could clearly cause similar severe manifestations (such as advanced malignant tumors, severe congenital cardiopulmonary hypoplasia, etc.); ② No special treatments that may affect gene expression (such as radiotherapy and chemotherapy, targeted anti-cancer drug therapy, etc.) in the recent period; ③ No history of long-term alcoholism, drug abuse, or other bad living habits.

[0055] Inclusion criteria for patients with mild disease were those who simultaneously met the following: ① mild clinical symptoms, stable condition during the course of illness, no dyspnea, and no need for respiratory support such as oxygen inhalation or mechanical ventilation; ② lung imaging showed no obvious signs of pneumonia or only a few scattered inflammatory infiltrates; ③ no tendency towards severe disease. To exclude other confounding factors, a detailed review of the patient's medical history ensured that the following ① and ② were met: ① no underlying chronic diseases (such as hypertension, diabetes, and coronary heart disease, which were well controlled and had no recent acute exacerbations) or autoimmune diseases; and ② no recent use of immunomodulators, which could interfere with genetic analysis.

[0056] Example 1: Screening for SNPs associated with the risk of severe illness from SARS-CoV-2 infection

[0057] The paired groups consist of patients with severe SARS-CoV-2 infection and patients with mild SARS-CoV-2 infection.

[0058] Multiple paired populations were established, and extensive whole-genome sequencing and sequence alignment analysis were performed to obtain a large number of differentially expressed single nucleotide polymorphisms (SNPs). The allele and genotype frequencies of each differentially expressed SNP were then verified in both the severe and mild SARS-CoV-2 infection populations for association analysis.

[0059] SNP rs186996510, also known as rs186996510 in the NCBI database, is located at position 231421877 on human chromosome 1 (GRCh38.p14) and has a G / C polymorphism. In human genomic DNA, SNP rs186996510 and its surrounding nucleotides are set forth in SEQ ID NO:6 (SNP rs186996510 is nucleotide position 301 in SEQ ID NO:6, represented by S).

[0060] Existing technologies have not found that SNP rs186996510 is associated with SARS-CoV-2 infection.

[0061] Through the aforementioned extensive work, the inventors found that SNP rs186996510 is correlated with the risk of severe illness in patients infected with SARS-CoV-2, and subjects carrying allele C have a higher risk of severe illness after being infected with SARS-CoV-2.

[0062] Example 2: Establishing a method for detecting the genotype of a subject based on SNP rs186996510

[0063] 1. Take peripheral blood from the subjects and extract genomic DNA.

[0064] 2. Using the genomic DNA extracted in step 1 as a template, perform PCR amplification using specific primer pairs.

[0065] The specific primer pair consists of primer F1 and primer R1.

[0066] Primer F1 (SEQ ID NO: 1): 5′-ACGTTGGATGTCCTTGCAGCAGTAGAAGGAG-3′;

[0067] Primer R1 (SEQ ID NO: 2): 5′-ACGTTGGATGCAGTAACGGCCCCTATCTCTC-3′.

[0068] PCR amplification was performed in a 384-well plate, with one reaction system per well.

[0069] The PCR amplification reaction mixture (5 μL) consists of: 0.5 μL 10× PCR buffer (Agena Bioscience, Cat. No. 11327), 0.4 μL 25 mM MgCl₂ solution, 0.1 μL 25 mM dNTP mix, genomic DNA, HotStart Taq DNA polymerase, primers F1 and R1. The volume was made up to volume with ultrapure water. In a 5 μL reaction, the genomic DNA content was 20–50 ng, the HotStart Taq DNA polymerase content was 0.5 U, the primers F1 and R1 content were 0.5 pmol, and the primers R1 content were 0.5 pmol.

[0070] The PCR amplification reaction program was as follows: 94°C for 4 minutes; 45 cycles of 94°C for 20 seconds, 56°C for 30 seconds, and 72°C for 1 minute; 72°C for 3 minutes; and hold at 4°C.

[0071] 3. Perform alkaline phosphatase treatment (to remove free dNTPs in the system).

[0072] Take the 384-well plate prepared in step 2, prepare the reaction system, and then carry out the reaction.

[0073] The composition of the reaction system (7 μL): 5 μL of the product solution obtained in step 2, 0.3 μL of SAP, 0.17 μL of 10× SAP buffer, and 1.53 μL of ultrapure water.

[0074] SAP (shrimp alkaline phosphatase): product specification is 1.7 U / μl; Agena, product number is 10002.1. 10× SAP buffer is the matching buffer for SAP.

[0075] Reaction conditions: 37°C for 40 minutes; 85°C for 5 minutes; maintain at 4°C.

[0076] 4. Perform single base extension.

[0077] Take the 384-well plate prepared in step 3, prepare the reaction system, and then perform the single base extension reaction.

[0078] The single-base extension reaction system (10 μL) consists of: 7 μL of the product solution from step 3, 0.3 μL of single-base extension enzyme, 0.17 μL of 10× single-base extension reaction buffer, 1 μL of single-base extension primer, and 1.53 μL of ultrapure water. The single-base extension primer content in the single-base extension reaction system is 5 μmol.

[0079] Single-base extension reaction enzyme: product specification is 1.7U / μl; Agena Company, product number is 1432. 10× single-base extension reaction buffer is the matching buffer for single-base extension reaction enzyme.

[0080] Single base extension primer (SEQ ID NO: 3): 5'-GTGGGCCGGGCCCGCCGCT-3'.

[0081] The reaction procedure for single base extension is as follows:

[0082] ①94℃ 30 seconds;

[0083] ②94℃ 5 seconds;

[0084] ③52℃ for 5 seconds, 80℃ for 5 seconds, 5 cycles;

[0085] ④94℃ 5 seconds, 52℃ 5 seconds, 80℃ 5 seconds, 40 cycles;

[0086] ⑤72℃ for 3 minutes;

[0087] ⑥Maintain at 4℃.

[0088] 5. Perform resin purification.

[0089] Take the 384-well plate prepared in step 4 and add 16 μl of water to each well. Then add Clean Resin resin (Sequenom, USA) to each well. Seal the plate and rotate vertically at low speed for 30 minutes to allow full contact between the resin and the reactants. Then centrifuge the plate to allow the resin to sink to the bottom of the wells. The supernatant is the extension product after resin purification.

[0090] 6. Chip spotting.

[0091] The MassARRAY Nanodispenser RS1000 sample dispenser (SEQUENOM) was started to transfer the resin-purified extension product to a 384-well SpectroCHIP (Sequenom) chip (SEQUENOM).

[0092] 7. Mass spectrometry detection.

[0093] The spotted SpectroCHIP chip was analyzed using MALDI-TOF, and the detection results were typed and output using TYPER 4.0 software (sequenom).

[0094] Example 3. Correlation analysis between SNP rs186996510 and the risk of severe illness in patients infected with SARS-CoV-2

[0095] Peripheral blood samples were collected at the PLA General Hospital between January 2023 and December 2024. Thirty-two peripheral blood samples were obtained from 32 patients with severe SARS-CoV-2 infection, and another 36 peripheral blood samples were obtained from 36 patients with mild SARS-CoV-2 infection. All 32 patients with severe SARS-CoV-2 infection and 36 patients with mild SARS-CoV-2 infection were unrelated Chinese Han people.

[0096] The procedure was performed according to Example 2. The genotype of the subject based on SNP rs186996510 was detected.

[0097] Among the 32 patients with severe SARS-CoV-2 infection, 24 had the GG genotype, 8 had the CG genotype, and 0 had the CC genotype. This means that 8 individuals carried the C allele (frequency: 25.00%), while 24 did not carry the C allele (frequency: 75.00%). Among the 36 patients with mild SARS-CoV-2 infection, 34 had the GG genotype, 2 had the CG genotype, and 0 had the CC genotype. This means that 2 individuals carried the C allele (frequency: 5.56%), while 34 did not carry the C allele (frequency: 94.44%).

[0098] The experimental data were processed and analyzed using R 4.0.5 statistical software. After correction using a generalized linear model test, the significance P value for SNP rs186996510 compared with the general population was <0.05 (p=0.0376), with a beta of 1.73. These results suggest that SNP rs186996510 is associated with severe disease in SARS-CoV-2 infection. The risk of severe disease after SARS-CoV-2 infection is higher in subjects with allele C than in those without allele C.

[0099] Example 4. Analysis of SNP rs186996510 and Susceptibility to Severe SARS-CoV-2 Infection

[0100] Peripheral blood samples were collected at the PLA General Hospital between January 2023 and December 2024. Sixty-four peripheral blood samples were obtained from 64 patients with severe SARS-CoV-2 infection, and another 36 peripheral blood samples were obtained from 36 patients with mild SARS-CoV-2 infection. All 64 patients with severe SARS-CoV-2 infection and 36 patients with mild SARS-CoV-2 infection were unrelated Chinese Han people.

[0101] 1. Take peripheral blood from the subjects and extract genomic DNA.

[0102] 2. Using the genomic DNA extracted in step 1 as a template, perform PCR amplification using specific primer pairs.

[0103] The specific primer pair consists of primer F2 and primer R2.

[0104] Primer F2 (SEQ ID NO: 4): 5'-GCAGCAGGTTCTCCATCTTC-3';

[0105] Primer R2 (SEQ ID NO: 5): 5'-CGCACAGGCCCTATTCTCT-3'.

[0106] 3. After completing step 2, the PCR amplification products were recovered and sequenced, and the genotype of the subject based on SNPrs186996510 was obtained according to the sequencing results.

[0107] Among the 64 patients with severe SARS-CoV-2 infection, 51 had the GG genotype, 13 had the CG genotype, and 0 had the CC genotype. This means 13 individuals carried the C allele (frequency: 20.31%), while 51 did not carry the C allele (frequency: 79.69%). Among the 36 patients with mild SARS-CoV-2 infection, 35 had the GG genotype, 1 had the CG genotype, and 0 had the CC genotype. This means 1 carried the C allele (frequency: 2.78%), while 35 did not carry the C allele (frequency: 97.22%).

[0108] The experimental data were processed and analyzed using R 4.0.5 statistical software. After correction using a generalized linear model test, the significance P value for SNP rs186996510 compared with the population was <0.05 (p=0.039), with a beta of 2.19. Consistent with the results of Example 3, the risk of severe illness after SARS-CoV-2 infection was higher in subjects with allele C than in subjects without allele C.

[0109] The results of this example further illustrate that SNP rs186996510 is a risk site associated with severe SARS-CoV-2 infection, which can be used to screen individuals at high risk of severe SARS-CoV-2 infection, predict the risk of severe SARS-CoV-2 infection in subjects, screen subjects carrying SARS-CoV-2 infection risk alleles, and evaluate the risk of severe SARS-CoV-2 infection.

[0110] The present invention has been described in detail above. It will be apparent to those skilled in the art that the present invention may be practiced over a wide range of parameters, concentrations, and conditions without departing from the spirit and scope of the present invention and without unnecessary experimentation. Although specific embodiments have been given herein, it should be understood that further modifications may be made to the present invention. In summary, this application is intended to encompass any variations, uses, or improvements to the present invention, including those made by conventional techniques known in the art that depart from the scope of the present invention. Applications of the essential features may be made within the scope of the following claims.

Claims

1. A device for grouping subjects based on their risk of developing severe illness after being infected with SARS-CoV-2, characterized in that: The device includes the following modules: M3, data receiving module: used to receive information about whether the subject's SNP rs186996510 site carries allele C and obtain sample data; M4, result output module: used to group the risk of the subjects developing severe illness after being infected with SARS-CoV-2 according to the sample data; "Clustering the subjects according to the risk of developing severe illness after being infected with SARS-CoV-2" means: if the subject carries allele C at the SNPrs186996510 site, the subject belongs to the high-risk group for developing severe illness after being infected with SARS-CoV-2; if the subject does not carry allele C at the SNP rs186996510 site, the subject belongs to the low-risk group for developing severe illness after being infected with SARS-CoV-2; the high-risk group has a higher risk of developing severe illness after being infected with SARS-CoV-2 than the low-risk group.

2. A data processing device comprising a memory, a processor, and a computer program stored in the memory, characterized in that: The processor executes the computer program to implement the following steps: S3. Data reception: Receive information about whether the subject carries allele C at the SNP rs186996510 site and obtain sample data; S4. Result output: grouping the subjects according to their risk of developing severe illness after being infected with SARS-CoV-2 based on the sample data; "Clustering the subjects according to the risk of developing severe illness after being infected with SARS-CoV-2" means: if the subject carries allele C at the SNPrs186996510 site, the subject belongs to the high-risk group for developing severe illness after being infected with SARS-CoV-2; if the subject does not carry allele C at the SNP rs186996510 site, the subject belongs to the low-risk group for developing severe illness after being infected with SARS-CoV-2; the high-risk group has a higher risk of developing severe illness after being infected with SARS-CoV-2 than the low-risk group.

3. A computer program product comprising a computer program, characterized in that: When the computer program is executed by a processor, steps S3 and S4 described in claim 2 are implemented.

4. A computer-readable storage medium having a computer program stored thereon, characterized in that: When the computer program is executed by a processor, steps S3 and S4 described in claim 2 are implemented.

Images