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

Abstract

The invention discloses a computer readable storage medium and a data processing device for grouping novel coronavirus infected persons. The invention provides a device which is used for comparing the severe risk of a subject infected with SARS-CoV-2, and is characterized in that the device comprises the following modules: M1, a data receiving module which is used for receiving information that whether an SNP rs186996510 site of the subject carries an allele C or not to obtain sample data; and the result output module is used for comparing the severe risk of the subject infected with the SARS-CoV-2 according to the sample data. The computer device and the computer readable storage medium provided by the invention can be used for avoiding or reducing severe occurrence of SARS-CoV-2 infection.

Description

Technical Field

[0001] The present invention belongs to the field of medical care 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 mainly transmitted through respiratory droplets and close contact, and through aerosols in a relatively closed environment. Contact with objects contaminated by the virus may also cause infection. SARS-CoV-2 spreads quickly, infects a wide range of people, and is difficult to prevent and control.

[0003] The clinical symptoms after SARS-CoV-2 infection show great heterogeneity, covering asymptomatic infection, mild and severe types. Mild patients may only have mild fever, cough, fatigue and other symptoms, and can usually recover quickly after proper isolation and symptomatic treatment. Severe patients often progress rapidly, and are prone to complications such as acute respiratory distress syndrome (ARDS), septic shock, difficult-to-correct metabolic acidosis and coagulation dysfunction, and the mortality rate is significantly increased. This difference in the severity of the disease between individuals is not only closely related to factors such as age and underlying diseases (such as cardiovascular disease, diabetes, chronic respiratory diseases, etc.), but more and more studies have shown that genetic factors also play a vital role in it. Therefore, exploring the genetic susceptibility genes hidden behind severe SARS-CoV-2 infection and analyzing the differences between severe and mild patients at the genetic level are of great practical significance for in-depth understanding of the pathogenic mechanism of SARS-CoV-2, accurately predicting the course of patients' diseases, implementing intervention measures in advance, and developing targeted therapeutic drugs. 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 severe illness of a subject after being infected with SARS-CoV-2, characterized in that the device comprises the following modules: M1, data receiving module: used to receive information about whether the subject's SNP rs186996510 site carries allele C, and obtain sample data; 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.

[0006] "Comparing the risks of developing severe illness after the subjects are infected with SARS-CoV-2" can mean: the risk of developing severe illness after being infected with SARS-CoV-2 by subjects carrying allele C at the SNPrs186996510 site is higher than that of subjects not carrying allele C at the SNPrs186996510 site.

[0007] The subjects may be two or more subjects.

[0008] 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 comprises 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.

[0009] “Grouping the subjects according to their 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.

[0010] The subject may be more than one subject.

[0011] The present invention also provides a data processing device, which includes a memory, a processor, and a computer program stored in the memory, wherein the processor executes the computer program to implement the following steps: S1. Data reception: receiving information on whether the subject's SNP rs186996510 site carries allele C, and obtaining sample data; S2. Result output: Compare the risk of the subjects developing severe illness after being infected with SARS-CoV-2 based on the sample data.

[0012] The computer flow chart of the above steps is shown in Figure 1 .

[0013] "Comparing the risks of developing severe illness after the subjects are infected with SARS-CoV-2" can mean: the risk of developing severe illness after being infected with SARS-CoV-2 by subjects carrying allele C at the SNPrs186996510 site is higher than that of subjects not carrying allele C at the SNPrs186996510 site.

[0014] The subjects may be two or more subjects.

[0015] The present invention also provides a data processing device, which includes a memory, a processor, and a computer program stored in the memory, wherein the processor executes the computer program to implement the following steps: S3, data reception: receiving information on whether the subject's SNP rs186996510 site carries allele C, and obtaining sample data; 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.

[0016] “Grouping the subjects according to their 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.

[0017] The subject may be more than one subject.

[0018] The present invention also provides a computer program product, including a computer program, characterized in that: when the computer program is executed by a processor, the step S1 and the step S2 are implemented.

[0019] The present invention also provides a computer-readable storage medium on which a computer program is stored, characterized in that: when the computer program is executed by a processor, the step S1 and the step S2 are implemented.

[0020] 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.

[0021] The present invention further provides a computer-readable storage medium on which a computer program is stored, characterized in that: when the computer program is executed by a processor, the step S3 and the step S4 are implemented.

[0022] The present invention also provides a method for comparing the risk of severe illness after a subject is infected with SARS-CoV-2, comprising the following steps: Receive information about whether the subject's SNP rs186996510 site carries allele C, and obtain sample data; Comparing the risk of the subjects developing severe illness after being infected with SARS-CoV-2 based on the sample data; The method is not directed toward the diagnosis of disease or health status.

[0023] "Comparing the risks of developing severe illness after the subjects are infected with SARS-CoV-2" can mean: the risk of developing severe illness after being infected with SARS-CoV-2 by subjects carrying allele C at the SNPrs186996510 site is higher than that of subjects not carrying allele C at the SNPrs186996510 site.

[0024] The subjects may be two or more subjects.

[0025] 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: Receive information about whether the subject's SNP rs186996510 site carries allele C, and obtain sample data; Grouping the risk of the subjects developing severe illness after being infected with SARS-CoV-2 according to the sample data; The method is not directed toward the diagnosis of disease or health status.

[0026] “Grouping the subjects according to their 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.

[0027] The subject may be more than one subject.

[0028] Any of the above methods may not include the step of obtaining a biological sample from an animal. The methods may not be based on living human or animal bodies, but only on data. The methods may be information processing methods in which all steps are implemented by a data processing device such as a computer.

[0029] Specifically, based on SNP rs186996510, the subject's genotype is GG or CG or CC.

[0030] SNP rs186996510 is located in human genomic DNA, and its position corresponds to the 301st nucleotide in SEQ ID NO: 6, and is represented by S. S represents C or G.

[0031] Any of the above subjects may be Chinese.

[0032] Any of the above-mentioned subjects may be Chinese Han nationality.

[0033] Any of the above subjects may be infected with SARS-CoV-2.

[0034] The inventors of the present invention found that based on SNP rs186996510, subjects carrying allele C have a higher risk of developing severe illness after being infected with SARS-CoV-2 than subjects not carrying allele C. In Example 3 and Example 4, the present invention uses samples from different populations as examples to exemplarily show the genotype distribution frequency data in the group of patients with severe SARS-CoV-2 infection and the group of patients with mild SARS-CoV-2 infection. Based on the above findings, the inventors of the present invention developed the above-mentioned computer device and computer-readable storage medium.

[0035] 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

[0036] Figure 1 A computer flow chart. DETAILED DESCRIPTION

[0037] The present invention is further described in detail below in conjunction with specific embodiments, and the examples provided are only for illustrating the present invention, rather than for limiting the scope of the present invention. The examples provided below can be used as a guide for further improvements by those of ordinary skill in the art, and do not constitute a limitation of the present invention in any way.

[0038] The experimental methods in the following examples, unless otherwise specified, are conventional methods, and are carried out according to the techniques or conditions described in the literature in this field or according to the product instructions. The materials, reagents, etc. used in the following examples, unless otherwise specified, can be obtained from commercial channels. Ethics Statement: Each subject signed an informed consent form, and this study was approved by the Medical Ethics Committee of the General Hospital of the People's Liberation Army. Both severe and mild patients have been confirmed to be infected with SARS-CoV-2 by nucleic acid testing.

[0039] p-value:Person test. lnBeta=OR, OR: odds ratio.

[0040] Strictly follow the COVID-19 diagnosis criteria issued by the World Health Organization (WHO) and my country's National Health Commission. The inclusion criteria for critically ill patients are to meet at least one of the following ① to ⑤: ① shortness of breath (respiratory rate ≥ 30 times / minute); ② oxygen saturation ≤ 93% when breathing air at rest; ③ arterial oxygen partial pressure (PaO2) / oxygen concentration (FiO2) ≤ 300mmHg (1mmHg=0.133kPa); ④ progressive worsening of clinical symptoms, lung imaging shows significant progression of lesions within 24-48 hours, > 50% lung field involvement; ⑤ accompanied by at least one of the following complications: respiratory failure and need for mechanical ventilation, shock, combined with other organ failure requiring admission to the ICU 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 dysplasia, 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 and other bad living habits.

[0041] The inclusion criteria for mild patients are to meet the following ①, ② and ③ at the same time: ① Mild clinical symptoms, stable condition during the course of the disease, no dyspnea, no need for oxygen inhalation, mechanical ventilation and other respiratory support treatments; ② No obvious signs of pneumonia or only a small number of scattered inflammatory exudates in lung imaging examinations; ③ No tendency to severe illness. 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 and ② at the same time: ① No chronic underlying diseases (such as hypertension, diabetes, coronary heart disease is well controlled and has no recent acute attacks) and no autoimmune diseases; ② No recent use of immunomodulators and other conditions that may interfere with genetic analysis.

[0042] Example 1: Screening for SNPs associated with the risk of severe illness due to SARS-CoV-2 infection The paired groups consist of patients with severe SARS-CoV-2 infection and patients with mild SARS-CoV-2 infection.

[0043] Multiple paired groups were established, and a large number of whole genome sequencing and sequence comparison analysis were performed to obtain a large number of differential SNPs. The allele frequency and genotype frequency of each differential SNP in the SARS-CoV-2 infection severe patient group and the SARS-CoV-2 infection mild patient group were verified in turn for association analysis.

[0044] SNP rs186996510, i.e., the SNP numbered rs186996510 in NCBI, is specifically located at position 231421877 (GRCh38.p14) of human chromosome 1, and the polymorphic form is G / C. In human genomic DNA, SNP rs186996510 and its surrounding nucleotides are shown in SEQ ID NO: 6 (SNP rs186996510 is the 301st nucleotide in SEQ ID NO: 6, represented by S).

[0045] SNP rs186996510 has not been found to be associated with SARS-CoV-2 infection in the existing technology.

[0046] Through the aforementioned extensive work, the inventors found that SNP rs186996510 is correlated with the risk of severe illness in SARS-CoV-2 infected individuals, and subjects carrying allele C have a higher risk of severe illness after being infected with SARS-CoV-2.

[0047] Example 2: Establishment of a method for detecting the genotype of a subject based on SNP rs186996510 1. Take peripheral blood from the subjects and extract genomic DNA.

[0048] 2. Using the genomic DNA extracted in step 1 as a template, perform PCR amplification using specific primer pairs.

[0049] The specific primer pair consists of primer F1 and primer R1.

[0050] Primer F1 (SEQ ID NO: 1): 5′-ACGTTGGATGTCCTTGCAGCAGTAGAAGGAG-3′; Primer R1 (SEQ ID NO: 2): 5'-ACGTTGGATGCAGTAACGGCCCCTATCTCTC-3'.

[0051] PCR amplification was performed in a 384-well plate, with one reaction system in each well.

[0052] The composition of the PCR amplification reaction system (5 μL): 0.5 μL 10× PCR buffer (Agena Bioscience, catalog number 11327), 0.4 μL 25 mM MgCl2 solution, 0.1 μL 25 mM dNTP mix, genomic DNA, HotStart Taq DNA polymerase, primer F1, primer R1, and the volume is made up with ultrapure water. In the 5 μL system, the content of genomic DNA is 20-50 ng, the content of HotStart Taq DNA polymerase is 0.5 U, the content of primer F1 is 0.5 pmol, and the content of primer R1 is 0.5 pmol.

[0053] The reaction program of PCR amplification was as follows: 94°C for 4 minutes; 94°C for 20 seconds, 56°C for 30 seconds, 72°C for 1 minute, 45 cycles; 72°C for 3 minutes; and 4°C hold.

[0054] 3. Perform alkaline phosphatase treatment (to remove free dNTPs in the system).

[0055] Take the 384-well plate that has completed step 2, prepare the reaction system and then carry out the reaction.

[0056] 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.

[0057] SAP (shrimp alkaline phosphatase): product specification is 1.7U / μl; Agena company, product number is 10002.1. 10×SAP buffer is the matching buffer for SAP.

[0058] Reaction conditions: 37°C for 40 minutes; 85°C for 5 minutes; maintain at 4°C.

[0059] 4. Perform single base extension.

[0060] Take the 384-well plate that has completed step 3, prepare the reaction system, and then perform a single base extension reaction.

[0061] The composition of the single base extension reaction system (10 μL): 7 μL of the product solution obtained in step 3, 0.3 μL of the single base extension reaction enzyme, 0.17 μL of 10× single base extension reaction buffer, 1 μL of the single base extension primer, and 1.53 μL of ultrapure water. In the single base extension reaction system, the content of the single base extension primer is 5 μmol.

[0062] Single base extension reaction enzyme: product specification is 1.7U / μl; Agena Company, item number is 1432. 10× single base extension reaction buffer is the matching buffer for single base extension reaction enzyme.

[0063] Single base extension primer (SEQ ID NO: 3): 5'-GTGGGCCGGGCCCGCCGCT-3'.

[0064] The reaction procedure for single base extension is as follows: ①94℃ 30 seconds; ②94℃ 5 seconds; ③52℃ 5 seconds, 80℃ 5 seconds, 5 cycles; ④94℃ 5 seconds, 52℃ 5 seconds, 80℃ 5 seconds, 40 cycles; ⑤72℃ 3 minutes; ⑥Maintain at 4℃.

[0065] 5. Perform resin purification.

[0066] Take the 384-well plate that has completed step 4, add 16 μl of water to each well, then add Clean Resin resin (Sequenom, USA) to each well, seal the film, rotate vertically at low speed for 30 minutes to allow the resin to fully contact with the reactants, then centrifuge to allow the resin to sink to the bottom of the well. The supernatant is the extension product after resin purification.

[0067] 6. Chip spotting.

[0068] The MassARRAY Nanodispenser RS1000 sample dispensing device (SEQUENOM) was started to transfer the extension product after resin purification to a 384-well SpectroCHIP (Sequenom) chip (SEQUENOM).

[0069] 7. Mass spectrometry detection.

[0070] The spotted SpectroCHIP chip was analyzed using MALDI-TOF, and the detection results were typed and output using TYPER 4.0 software (sequenom).

[0071] Example 3. Correlation analysis between SNP rs186996510 and the risk of severe illness in patients infected with SARS-CoV-2 Peripheral blood samples were collected from the PLA General Hospital from January 2023 to December 2024. 32 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.

[0072] The method of Example 2 was followed. The genotype of the subject based on SNP rs186996510 was detected.

[0073] Among the 32 patients with severe SARS-CoV-2 infection, 24 had genotype GG, 8 had genotype CG, and 0 had genotype CC, that is, 8 carried allele C (frequency 25.00%), and 24 did not carry allele C (frequency 75.00%). Among the 36 patients with mild SARS-CoV-2 infection, 34 had genotype GG, 2 had genotype CG, and 0 had genotype CC, that is, 2 carried allele C (frequency 5.56%), and 34 did not carry allele C (frequency 94.44%).

[0074] The experimental data were processed and counted using R 4.0.5 statistical software. After correction by generalized linear model test, the significant P value of SNP rs186996510 and the population was <0.05 (p=0.0376), and Beta was 1.73. The results showed that SNPrs186996510 was a SNP associated with severe illness in SARS-CoV-2 infected people, and the risk of severe illness after SARS-CoV-2 infection in subjects carrying allele C was higher than that in subjects not carrying allele C.

[0075] Example 4. Analysis of SNP rs186996510 and Susceptibility to Severe SARS-CoV-2 Infection Peripheral blood samples were collected from the PLA General Hospital from January 2023 to December 2024. 64 peripheral blood samples were obtained from 64 severe patients with SARS-CoV-2 infection, and another 36 peripheral blood samples were obtained from 36 mild patients with SARS-CoV-2 infection. All 64 severe patients with SARS-CoV-2 infection and 36 mild patients with SARS-CoV-2 infection were unrelated Chinese Han people.

[0076] 1. Take peripheral blood from the subjects and extract genomic DNA.

[0077] 2. Using the genomic DNA extracted in step 1 as a template, perform PCR amplification using specific primer pairs.

[0078] The specific primer pair consists of primer F2 and primer R2.

[0079] Primer F2 (SEQ ID NO: 4): 5'-GCAGCAGGTTCTCCATCTTC-3'; Primer R2 (SEQ ID NO: 5): 5'-CGCACAGGCCCTATTCTCT-3'.

[0080] 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.

[0081] Among the 64 severe SARS-CoV-2 infected patients, 51 had genotype GG, 13 had genotype CG, and 0 had genotype CC, that is, 13 carried allele C (frequency 20.31%), and 51 did not carry allele C (frequency 79.69%). Among the 36 mild SARS-CoV-2 infected patients, 35 had genotype GG, 1 had genotype CG, and 0 had genotype CC, that is, 1 carried allele C (frequency 2.78%), and 35 did not carry allele C (frequency 97.22%).

[0082] The experimental data were processed and counted using R 4.0.5 statistical software. After correction by generalized linear model test, the significant P value of SNP rs186996510 and the population was <0.05 (p=0.039), and Beta was 2.19. Consistent with the results of Example 3, the risk of severe illness after SARS-CoV-2 infection in subjects carrying allele C was higher than that in subjects not carrying allele C.

[0083] The results of this example further illustrate that SNP rs186996510 is a risk site associated with severe SARS-CoV-2 infection, and 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.

[0084] 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 implemented in a wide range under equivalent parameters, concentrations and conditions without departing from the spirit and scope of the present invention and without the need for unnecessary experimentation. Although the present invention provides specific embodiments, it should be understood that further improvements may be made to the present invention. In short, according to the principles of the present invention, this application intends to include any changes, uses or improvements to the present invention, including changes made by conventional techniques known in the art that depart from the scope disclosed in this application. Applications of some of the basic features may be made within the scope of the following appended claims.

Claims

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

2. 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 comprises 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.

3. 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: S1. Data reception: receiving information on whether the subject's SNP rs186996510 site carries allele C, and obtaining sample data; S2. Result output: Compare the risk of the subjects developing severe illness after being infected with SARS-CoV-2 based on the sample data.

4. 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: receiving information on whether the subject's SNP rs186996510 site carries allele C, and obtaining sample data; 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.

5. A computer program product, comprising a computer program, characterized in that: When the computer program is executed by a processor, step S1 and step S2 described in claim 3 are implemented.

6. A computer-readable storage medium having a computer program stored thereon, characterized in that: When the computer program is executed by a processor, step S1 and step S2 described in claim 3 are implemented.

7. A computer program product comprising a computer program, characterized in that: When the computer program is executed by a processor, step S3 and step S4 described in claim 4 are implemented.

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

9. A method for comparing the risk of developing severe illness after a subject is infected with SARS-CoV-2, comprising the following steps: Receive information about whether the subject's SNP rs186996510 site carries allele C, and obtain sample data; Comparing the risk of the subjects developing severe illness after being infected with SARS-CoV-2 based on the sample data; The method is not directed toward the diagnosis of disease or health status.

10. A method for grouping subjects at risk of developing severe illness after being infected with SARS-CoV-2, comprising the following steps: Receive information about whether the subject's SNP rs186996510 site carries allele C, and obtain sample data; Grouping the risk of the subjects developing severe illness after being infected with SARS-CoV-2 according to the sample data; The method is not directed toward the diagnosis of disease or health status.

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