Method of discovering specific functional antibodies

Abstract

The invention relates to a method for discovering specific functional antibodies, in particular to a method for discovering specific functional antibodies based on sequence composition and frequency analysis of variable regions of immune host antibodies. Compared with conventional high-throughput antibody sequencing method, this method can quickly and accurately obtain the full-length sequence of the variable region of antibody containing candidate CDR3, the success rate of antibody gene pairing is high and it is suitable for the detection of few samples, and improves the efficiency of obtaining specific functional antibodies.

Claims

1. A method for identifying an influenza virus recombinant antibody comprising, (1) Extracting total RNA from at least one influenza virus immunized host, and constructing an antibody sequence library therefrom; (2) Performing high-throughput sequencing of variable regions of immunoglobulin genes present in said library thereby obtaining sequences of the antibody variable region genes for the target antigen; (3) Selecting a heavy chain CDR3 homologous cluster selected from the group consisting of SEQ ID NOS: 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, and 78, and selecting a light chain CDR3 homologous cluster selected from the group consisting of SEQ ID NOS: 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, and 98; (4) Identifying full length amino acid sequence of highest frequency antibody heavy chain variable region containing the heavy chain CDR3 homology cluster as a first candidate sequence, and identifying full length amino acid sequence of highest frequency antibody light chain variable region containing the light chain CDR3 homology cluster as a second candidate sequence; (5) Determining nucleic acid sequences of the first and second candidate sequences; (6) Expressing said nucleic acid sequences in vitro thereby producing a candidate influenza virus recombinant antibody comprising said CDR3 homologous clusters; and (7) Testing affinity to an antigen for the candidate influenza virus recombinant antibody, to determine if it is a functional antibody.

2. The method as claimed in claim 1, wherein said antibody sequence library is generated by RACE and/or RT library construction.

3. The method according to claim 2, where a RACE library is constructed and cDNA is synthesized by reverse transcription using oligo (dT) as primer and said isolated total RNA as template, said antibody sequence library being produced by using said synthesized cDNA as template.

4. The method according to claim 2, where an RT library is constructed and cDNA is synthesized by reverse transcription using oligo (dT) as primer and said isolated total RNA as template, said antibody sequence library being produced with specific primer separate amplification using said synthesized cDNA as template.

5. The method according to claim 1, wherein the host is selected from the group consisting of a mammal, an amphibian, a fish, a bird, and combinations thereof.

6. The method as claimed in claim 2, wherein the RACE library construction includes a PCR amplicon library construction method.

7. The method as claimed in claim 1, wherein the high-throughput sequencing is performed by one or more of sequencing by synthesis, sequencing by joining, sequencing by hybridization, single molecule DNA sequencing, multiple polymerase community sequencing or nano-pore sequencing.

8. The method of claim 5, wherein the mammal is selected from the group consisting of a human individual, a mouse, a primate, a rabbit, a goat, a sheep, and a pig.

9. The method of claim 8, wherein said total RNA is extracted from at least two of peripheral blood, lymphoid organs, spleen, bone marrow or liver.

10. The method of claim 1, wherein said total RNA is extracted from two or more cells selected from memory B cells, plasma cells, or plasmablasts.

11. The method of claim 6, wherein an antibody gene is amplified by a first round of PCR, and the amplification product is used for DNA library construction.

12. The method of claim 11, wherein the primers for PCR used in the first round of two-step PCR amplification include partial forward primer of SEQ ID NO: 1 and a partial reverse primer selected from SEQ ID NO. 2-4, wherein the partial forward joint sequence optionally includes 5-60 nucleotides of the 3′ end of SEQ ID NO: 5, and the partial reverse joint sequence optionally includes 5-60 nucleotides of the 3′ end of SEQ ID NO: 6.

13. The method of claim 11, wherein said forward joint primer is SEQ ID NO. 5, and the reverse joint primer is SEQ ID NO. 6.

14. The method as claimed in claim 2, wherein the RACE library construction includes a two-step PCR library construction method.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

(1) FIG. 1 is a schematic diagram of the optimized discovery method for antibodies in the invention.

(2) FIG. 2 is a schematic diagram of concrete steps of the embodiment 1 of the invention.

(3) FIG. 3 is the correlation analysis of antibody gene CDR3 frequency of different RNA inputs: FIG. 3(a) is the comparison of heavy-chain CDR3 when RNA input is 600 ng and 20 ng; FIG. 3(b) is the comparison of heavy chain CDR3 when RNA input is 600 ng and 100 ng; FIG. 3(c) is the comparison of kappa CDR3 when RNA input is 600 ng and 20 ng; FIG. 3(d) is the comparison of kappa CDR3 when RNA input is 600 ng and 100 ng; FIG. 3(e) is the comparison of lambda CDR3 when RNA input is 600 ng and 20 ng; FIG. 3(f) is the comparison of lambda CDR3 when RNA input is 600 ng and 100 ng.

(4) FIG. 4 is a pairing expression result of a candidate dengue virus antibody of the embodiment 2 in the invention.

(5) FIG. 5 is a pairing expression result of a candidate flu virus antibody of the embodiment 3 in the invention.

(6) FIG. 6 is the correlation analysis of CDR3 frequency of RT and RACE libraries: FIG. 6(a) is the correlation analysis of the CDR3 frequency of heavy chain in RT and RACE libraries; FIG. 6(b) is the correlation analysis of CDR3 frequency of Lambda chain in RT and RACE libraries.

SPECIFIC IMPLEMENTATIONS

(7) In order to further elaborate the technical means adopted by the invention and its effect, the technical scheme of the invention is further explained by combining with the drawings and by concrete embodiments, but the invention is not limited to the scope of the embodiment.

Embodiment 1 an Optimized High-Throughput Library Construction Method for Few Samples

(8) The concrete steps to build the library are shown in FIG. 2. Sample preparation and first chain cDNA synthesis: Peripheral blood mononuclear cells (PBMC) are isolated from human or animal peripheral blood by density gradient centrifugation. Total RNAs are isolated from PBMC by Trizol. 20 ng, 100 ng and 600 ng RNAs are used as template and oligo (dT) is used as primer for the synthesis of first-chain cDNA. The concrete operation can be carried out by referring to the manual of SMARTer® RACE 5′/3′ Kit.

(9) The optimized two-step PCR method is used to construct the antibody library. In the first round of PCR amplification, the forward primer is the optimized SMARTer® RACE 5′/3′ Kit UPM with the partial joint primer containing Illumina, the reverse primer containing the sequence of the invariant region of the antibody and the partial joint primer containing Illumina. VH, VK and VL are amplified respectively. The reaction system is as follows:

(10) TABLE-US-00003 Reaction System Component Volume PCR 1 × TransStart ® FastPfu Fly   5 μL reaction Buffer Optimized UPM   5 μL Reverse primer 0.2 μL TransStart ® FastPfu Fly DNA 0.5 μL Polymerase cDNA   5 μL dNTPs  0.2 mM Total volume 50

(11) PCR reaction conditions are as follows:

(12) TABLE-US-00004 Reaction program Cycles number Amplification 95° C. 2 min  1 program 95° C. 30 s 25 67° C.-62° C. 30 s 72° C. 30 s 72° C. 7 min  1

(13) The first round of PCR products are recovered by magnetic beads.

(14) The primer of the second round of PCR is conventional Illumina library construction primer, and the reaction system is as follows:

(15) TABLE-US-00005 Reaction System Component Volume PCR 1 × TransStart ® FastPfu Fly   5 μL reaction Forward primer 0.2 μM Reverse primer 0.2 μM TransStart ® FastPfu Fly DNA 0.5 μL  Polymerase First round PCR recovered product 20 μL dNTPs  0.2 mM Total volume 50

(16) PCR reaction conditions are as follows:

(17) TABLE-US-00006 Reaction program Cycles number Amplification 95° C. 2 min 1 program 95° C. 30 s 6-8 60° C. 30 s 72° C. 30 s 72° C. 7 min 1

(18) The steps of gel cutting and purification of products can be referred to the manual of QIAquick Gel Extraction Kit. After the library is constructed, Bioanalyzer High Sensitivity DNA chip is used for QC, sequencing platform is Illumina Miseq 2×300, the result is shown in FIG. 3(a)-(f).

(19) The results of FIG. 3(a)-(f) show that the frequency correlation R2 values of heavy chain, Kappa chain and Lambda chain CDR3 are 0.83, 0.90 and 0.98 respectively at the 20 ng RNA input, comparing with 600 ng RNA input, it shows a high correlation. And the figure shows the ranking of high frequency CDR3, For example, CDR3, which ranks the top 10 in the gene spectrum of the variable region of antibody, also shows a high consistency at 600 ng, 100 ng and 20 ng RNA inputs. The comparison of CDR3 frequency correlation explains that the RACE library constructed with 20 ng RNA input can meet the requirements of antibody library sequencing in terms of antibody gene coverage and CDR3 region bias.

Embodiment 2 an Optimized Antibody Gene Screening Method for Dengue Virus Monoclonal Antibody

(20) Use the method of RACE antibody library construction described in embodiment 1, total RNAs are isolated from PBMC of dengue patients in acute stage and convalescence stages, and construct the RACE libraries of heavy chain, Kappa chain and Lambda chain respectively. Use Illumina Miseq 2×300 system to sequence the library: the heavy chain library is sequenced alone, and the Kappa and Lambda chain libraries are combined and sequenced. The sequencing results are processed by software Trimmomatic-0.30, the parameters are set as follows: phred33, LEADING:20, TRAILING:20, SLIDINGWINDOW:20:20, MINLEN:200). Remove poor quality data. The following improvements are made to data analysis. Comparing the data amount in the antibody library after removing and preserving Singleton sequence, it is found that the data amount changes greatly after Singleton is removed, so Singleton sequence cannot be removed. And the way of repeated sequence normalization can reduce the occupation of server resources: first, find out each sequence and its repeat times, then analyze each sequence by IgBlast, and obtain each CDR3 frequency by counting the repeat times.

(21) TABLE-US-00007 TABLE 1 Comparison of data amount of antibody library before and after removing Singleton sequence Reads amount before Reads amount after removing singleton removing singleton 6H-R1 30179 4573 6H-R2 30179 471 6K-R1 574845 141848 6L-R1 6K-R2 574845 16785 6L-R2

(22) TABLE-US-00008 TABLE 2 Comparison of data amount of antibody library before and after repeated sequence normalization Reads amount before Reads amount after repeated sequence repeated sequence normalization normalization 6H-R1 30179 27278 6H-R2 30179 29913 6K-R1 574845 463091 6L-R1 6K-R2 574845 563921 6L-R2

(23) TABLE-US-00009 TABLE 3 Comparison of library quality of dengue patients in acute and convalescent stages Sequence amount Q30 index Sequence after after Library amount organization organization Convalescent 2365300  812294 81.90 stage H Convalescent 1569720  647412 82.88 stage K Convalescent stage L Acute stage H 4721106   60358 83.98 Acute stage K 1726272 1149690 82.45 Acute stage L

(24) Because CDR3 sequences are almost unique markers for different antibody genes, the abundance of CDR3 sequences can be evaluated in the gene spectrum of the variable region of antibodies according to the number of obtained CDR3 sequences. The sequences of FR region and CDR region are determined according to IgBlast website, but the sequence of CDR3 region is not determined by IgBlast website, so we use characteristic sequence of FR4 region to determine CDR3 amino acid sequence, and the characteristic sequence of heavy chain FR4 initiation region is WG*G (SEQ ID NO.199) or GQG (SEQ ID NO.200), characteristic sequences of Kappa and Lambda chains are FG*GT (SEQ ID NO:201). Run IgBlast respectively for the Read1 and Read2 sequences and merge the results, and select the pairing candidate CDR3 sequence based on one or all of the following principles: 1) High frequency sequence after CDR3 clustering; 2) Select the CDR3 sequences which have significantly higher frequency in after-immunization or outbreak stage than in the pre-immunization or convalescent stage; 3) The V gene family corresponding to CDR3 is significantly different between that of after-immunization or outbreak stage and that of pre-immunization or convalescent stage.

(25) The CDR3 frequency changes of heavy chain and light chain of dengue patients in acute and convalescent stages are shown in tables 4, 5 and 6. The results show that the concentration of CDR3 in acute stage is significantly higher than that in convalescent stage, indicating that it may be related to specific antigen.

(26) TABLE-US-00010 TABLE 4  Analysis of the CDR3 frequency of heavy chain of dengue patients in the acute and convalescent stages Frequency of Frequency convalescent CDR3 Heavy chain of acute stage Cluster CDR3 sequence stage (%) (%) (%) ARALSEKSLTTSYLDC 8.53 0.11 9.76 (SEQ ID NO. 7) VKDASTTSIGAAPFDY 5.97 0.03 10.04 (SEQ ID NO. 8) THRRPSLRYPDV 5.45 0.15 5.62 (SEQ ID NO. 9) ASLGGTVTDAFDL 3.13 0.03 5.55 (SEQ ID NO. 10) AKDASTTSKGAAPFDY 2.49 0 3.14 (SEQ ID NO. 11) ARGFTYGHYFDY 2.23 0 2.24 (SEQ ID NO. 12) VKDASTTSIGAAPFDN 2.05 0 10.04 (SEQ ID NO. 13) AKTVVTAPGVFDY 1.86 0 2.15 (SEQ ID NO. 14) ASDILDAFDV 1.84 0 1.85 (SEQ ID NO. 15) VKDASTTSIGAAPFDS 1.72 0 10.04 (SEQ ID NO. 16) ASLGGTVTDAFDV 1.21 0 5.55 (SEQ ID NO. 17) ASLGGTVTDAFDI 1.15 0 5.55 (SEQ ID NO. 18) ATGYTYGYYFDY 1.00 0 1.01 (SEQ ID NO. 19)

(27) TABLE-US-00011 TABLE 5  Analysis of CDR3 frequency of Kappa chain of dengue patients in the acute and convalescent stages Frequency Frequency of CDR3 Kappa chain of acute convalescent Cluster CDR3 sequence stage (%) stage (%) (%) QQANSFPWT 5.94 0.06 6.31 (SEQ ID NO. 20) HQYSSWPPGGT 4.87 0.18 5.22 (SEQ ID NO. 21) HQYNSWPPGGT 2.83 0 3.04 (SEQ ID NO. 22) HQYNAWPPGGT 2.81 0 3.78 (SEQ ID NO. 23) MQGTHWRS 2.63 0 2.68 (SEQ ID NO. 24) QQYSFWPWT 2.45 0 2.56 (SEQ ID NO. 25) QQYDSFPLT 1.68 0 1.75 (SEQ ID NO. 26) QQANNFPWT 1.57 0 1.66 (SEQ ID NO. 27) HQYTSWPPGGT 1.28 0 1.37 (SEQ ID NO. 28) QQRSNWPRT 1.24 0.01 1.3 (SEQ ID NO. 29) QQISNFPIT 1.17 0 1.2 (SEQ ID NO. 30) QQSFSPPWT 1.09 0.07 1.17 (SEQ ID NO. 31) QQSGSSLH 1.02 0 1.27 (SEQ ID NO. 32) QQRSTWPYT 1 0.07 1.09 (SEQ ID NO. 33)

(28) TABLE-US-00012 TABLE 6  Analysis of CDR3 frequency of Lambda chain of dengue patients in the acute and convalescent stages Frequency of Frequency convalescent CDR3 Lambda chain of acute stage Cluster CDR3 sequence stage (%) (%) (%) CSYAASYYDTGV 10.08 1.06 10.96 (SEQ ID NO. 34) SSYRSISPFYV 5.2 0.64 5.45 (SEQ ID NO. 35) SSYRSSSPFYV 5.06 0.52 5.18 (SEQ ID NO. 36) QVWDRSTNHRV 4.49 0.97 4.53 (SEQ ID NO. 37) QVWDRSSDHRL 3.69 0.61 3.82 (SEQ ID NO. 38) QSYDTSLRAGV 3.58 0.65 3.67 (SEQ ID NO. 39) SSYTGSSTV 2.06 0.19 2.06 (SEQ ID NO. 40) LLSYGGAPCV 1.5 0.27 1.58 (SEQ ID NO. 41) CSYAGRSTWV 1.48 0.04 1.53 (SEQ ID NO. 42) QSFDDSLSGWV 1.38 0.24 1.4 (SEQ ID NO. 43) QVWDRSTNHRL 1.26 0.15 1.28 (SEQ ID NO. 44) CSYAGSNTWI 1.24 0.21 2.55 (SEQ ID NO. 45) CSYAGSNTWV 1.16 0.17 2.55 (SEQ ID NO. 46)

(29) Anchor candidate CDR3 sequences, take the heavy-chain CDR3 sequence THRRPSLRYPDV (SEQ ID NO.9) as an example, run all Read2 and corresponding Read1 containing the CDR3 homology cluster respectively by IgBlast to obtain the amino acid sequences of CDR region and FR region, such as CDR1, CDR2, CDR3, FR1, FR2, FR3 and FR4. The results of IgBlast analysis are combined into the R12 file. In parallel, the sequencing results of R1 and R2 are spliced, and the amino acid and nucleotide sequences of each domain are determined by running IgBlast with the spliced sequences, and the Contig file is obtained.

(30) The selection of the full length sequence of the variable region follows the following steps: taking the heavy chain CDR3-THRRPSLRYPDV (SEQ ID NO.9) homologous cluster as an example, the highest frequency variable region of the antibody gene is screened and obtained from the R12 file. The amino acid sequences of each domain are as follows, as shown in Table 7:

(31) TABLE-US-00013 (SEQ ID NO. 48) FR1(QITLKESGPMLVKPTQTLTLTCTFS)- (SEQ ID NO. 47) CDR1(GFSLSTSGVG)- (SEQ ID NO. 51) FR2(VGWIRQPPGEALEWLAI)- (SEQ ID NO. 52) CDR2(IYWDDDK)- (SEQ ID NO. 49) FR3(RYSPSLRSRLTISKDTSKNQVVLTMTNLDPVDTATYFC) (SEQ ID NO. 50) FR4(WGQG).

(32) Further, the corresponding nucleotide sequences are selected in turn from the Contig file according to the sequence of nnFR4-nnCDR3-nnFR3-nnCDR2-nnFR2-nnCDR1-nnFR1-contig. The corresponding full-length nucleotide sequence of the antibody variable region of the highest frequency nucleotide sequence is obtained, which should contain the complete FR and CDR regions and the signal peptide sequence.

(33) TABLE-US-00014 TABLE 7  Heavy chain CDR3 THRRPSLRYPDV (SEQ ID NO. 9) homologous clusters corresponding to combinations of the highest frequency FR and CDR regions Heavy chain-THRRPSLRYPDV-R12 highest frequency amino acid sequence CDR1 GFSLSTSGVG (SEQ ID NO. 47) FR1 QITLKESGPMLVKPTQTLTLTCTFS (SEQ ID NO. 48) FR3 RYSPSLRSRLTISKDTSKNQVVLTMTNLDPVDTATYFC (SEQ ID NO. 49) FR4 WGQG (SEQ ID NO. 50) FR2 VGWIRQPPGEALEWLAI (SEQ ID NO. 51) CDR2 IYWDDDK (SEQ ID NO. 52) 

(34) Take Kappa chain -HQYSSWPPGGT (SEQ ID NO.21) homologous cluster as an example, the most abundant sequence combinations of FR and CDR regions ae screened and obtained from the R12 file. The amino acid sequence of each region is as follows: FR1(EIVMTQSPATLSVSPGERATLSCRAS) (SEQ ID NO.54)-FR2(LAWYQHKPGQAPRLLLY) (SEQ ID NO.57)-FR3 (TRAAGIPDRF SGSGSGTEFTLTIS SLQSEDFAVYFC) (SEQ ID NO.55)-CDR2(GAS) (SEQ ID NO.58)-CDR1(QSVSSN) (SEQ ID NO.53)-FR4(FGQGT) (SEQ ID NO.56), refer to FIG. 8. The corresponding highest frequency nucleotide sequence is selected in turn from the Contig file according to the sequence of nnFR4-nnCDR3-nnFR3-nnCDR2-nnFR2-nnCDR1-nnFR1-contig, the corresponding highest frequency full-length DNA sequence of the antibody variable region is obtained.

(35) TABLE-US-00015 TABLE 8  Kappa chain CDR3 HQYSSWPPGGT (SEQ ID NO. 21) homologous clusters corresponding to combinations of the highest frequency FR and CDR regions Kappa-HQYSSWPPGGT-R12 highest frequency amino acid sequence CDR1 QSVSSN (SEQ ID NO. 53) FR1 EIVMTQSPATLSVSPGERATLSCRAS (SEQ ID NO. 54) FR3 TRAAGIPDRFSGSGSGTEFTLTISSLQSEDFAVYFC (SEQ ID NO. 55) FR4 FGQGT (SEQ ID NO. 56) FR2 LAWYQHKPGQAPRLLLY (SEQ ID NO. 57) CDR2 GAS (SEQ ID NO. 58)

(36) This selecting method of sequence of antibody variable region has the following benefits: while sequencing data are processed, Singleton reads are retained; the splicing rates of variable regions of antibody genes corresponding to different high frequency CDR3 are significantly different, the full length splicing rate of heavy chain high frequency CDR3 sequences in the following table ranges from 34% to 91% (Table 9). If the splicing sequence analysis is used directly, in some cases the data loss may be huge and the CDR3 frequency analysis may even be biased. For current process, R1 and R2 sequences are used for CDR3 composition analysis at first, which avoids the risk of effective data loss and also helpful to obtain accurate frequency of CDR3 sequences; for current process, the highest frequency amino acid sequences information of FR and CDR regions are obtained from R1 and R2 files, and the highest frequency nucleotide sequences of variable region of antibody gene are selected from Contig sequence file, it can effectively guarantee the sequences of variable regions are the highest frequency sequences, and guarantee the integrity and accuracy of the sequence information. A separate selection of sequences of FR and CDR regions in the R12 file also verifies the accuracy of the current process as shown in FIG. 4.

(37) TABLE-US-00016 TABLE 9  Analysis of sequencing and splicing of variable region of antibody Splicing Heavy chain Reads Reads Splicing CDR3_Seq amount amount rate(%) ARALSEKSLTTSYLDC  2394 810 33.8 (SEQ ID NO. 7) VKDASTTSIGAAPFDY 1676 730 43.6 (SEQ ID NO. 8) THRRPSLRYPDV 1531 1387 90.6 (SEQ ID NO. 9) ARGFTYGHYFDY 628 415 66.1 (SEQ ID NO. 12)

(38) Analysis of antibody gene pairing and expressing: an expression frame is constructed by overlapping PCR, and the expression frame includes promoter, variable region and antibody constant region. The selected antibody heavy chain gene and light chain gene are combined and paired, then transfected 293FT cells for expression. The supernatant is obtained for Elisa assay and tested for its affinity to antigen. Concrete implementation steps are as follows: The variable regions of candidate heavy chain and light chain are constructed expression frame by using the method of bridging PCR. The expression frame includes promoter, variable region and constant region of human antibody. The plasmids containing heavy chain and light chain expression frames are paired and transfected 293FT cells for vitro expression and antibody analysis. 293T cells are collected, adjusted cell density and inoculated with 48-hole plate to 1.2×10.sup.5/hole; after cultivation in an incubator at 37° C. and 5% CO.sub.2 for overnight, the cells are transfected when the cell density reaches 60-80%. The plasmids of 0.25 ug heavy chain and 0.75 ug light chain are incubated at room temperature for 5 minutes, mixed with the transfection reagent then cultivated at room temperature for 20 min to form the transfection complex. The transfection complex is added into the cell pore and mixed softly, then cultivated in an incubator at 37° C. and 5% CO2 for 72 hours. The supernatant is collected and detected activity by Elisa. First, an anti-human IgG(Fc) and a detection antigen are diluted with pH 9.6 carbonic acid coating solution to 10 μg/mL, 96-well microtiter plate coated with 100 μL at 4° C. for overnight; or at 37° C., 2 hours; then sealed off by 4% skim milk powder-PBS and 300 μL/well, treated for 1˜2 h at 37° C. The liquid in microtiter plate is discarded, the rest is washed with PBST for three times, then added transfection and cultivated for 48 hours, the supernatant of 100 μl/well is treated at 37° C. for 1 h. The culture medium and PBS control are set up. The liquid in the microtiter plate is discarded and the rest is washed with PBST for three times, and HRP goat anti-human IgG(Fc) 1: 2000 and HRP goat anti-human IgG 1: 5000 are added respectively. Then 100 μl/well is treated at 37° C. for 1 h. The liquid in the microtiter plate is discarded, the rest is washed with PBST for five times, and the OPD chromogenic solution is added, 100 μL/well, avoid light for coloration; The absorption value of OD490 wavelength is read by Microplate Reader.

(39) Four heavy chains are paired with five Kappa chains and four Lambda chains respectively. Elisa results (FIG. 4) show that there is no positive result in the pairing of kappa chains and heavy chains, and five positive clones are obtained from the pairing of lambda chains and heavy chains. The positive rate is 5/36.

Embodiment 3 an Optimized Antibody Gene Screening Method for Flu Virus Monoclonal Antibody

(40) Use the method of RACE antibody library construction described in embodiment 1, total RNAs are isolated from PBMC of volunteers before and 7 days after the injection of influenza vaccine, and construct the RACE libraries of heavy chain, Kappa chain and Lambda chain respectively according to the method described in embodiment 2. Use Illumina Miseq 2×250 system to sequence high-throughput. The methods of data processing, the determination of FR and CDR regions, and the selection of candidate CDR3 amino acid sequences are the same as those described in embodiment 1.

(41) TABLE-US-00017 TABLE 10  CDR3 frequency analysis of heavy chain before and after  immunization of influenza vaccine Frequency on 7.sup.th day Frequency Frequency  after before change of Heavy chain immunization immunization V V gene CDR3_Seq (%) (%) gene (%) MSWNDRVVAP 4.84 0.07 IGHV2-70*13 100% (SEQ ID NO. 59) SVVSFPPY 4.17 0.05 IGHV3-74*01  75% (SEQ ID NO. 60) EVGGERAY 2.88 0.06 IGHV3-7*01  25% (SEQ ID NO. 61) DRDASGDFDI 1.95 0.03 IGHV1-3*01   0% (SEQ ID NO. 62) APGGQWAY 1.21 0.01 IGHV3-7*01  25% (SEQ ID NO. 63) SSVVSFPPY 0.97 0.03 IGHV3-74*01  75% (SEQ ID NO. 64) DRVTGDNFYYYMGV 0.78 0.02 IGHV3-23*01   0% (SEQ ID NO. 65) GSTIMVTL 0.76 0.01 IGHV3-53*01 100% (SEQ ID NO. 66) LQFFEGRHMDV 0.67 0 IGHV2-70*13 100% (SEQ ID NO. 67) DRVASGDFDI 0.47 0.02 IGHV3-23*01   0% (SEQ ID NO. 68) LLSGGENPSYYYHMDV 0.4 0.01 IGHV2-70*01 100% (SEQ ID NO. 69) KTYGSGSFDYFDY 0.35 0.01 IGHV4-59*01  40% (SEQ ID NO. 70) GATVVNDLEY 0.33 0 IGHV3-53*01 100% (SEQ ID NO. 71) GGTIRVTL 0.33 0.01 IGHV3-53*01 100% (SEQ ID NO. 72) MNWNDRVVDP 0.33 0 IGHV2-70 (SEQ ID NO. 73) GGTIMVTL 0.32 0 IGHV3-53*01 100% (SEQ ID NO. 74) DYLSGTYTPPLY 0.32 0 IGHV1-24*01 100% (SEQ ID NO. 75) ERGEVGDSVDNFYYYMDV 0.28 0 IGHV4-59*01  40% (SEQ ID NO. 76) PMTYYYDISDAGAYYFDT 0.28 0.01 IGHV4-4*02   0  (SEQ ID NO. 77) PPTAHHFNAFYI 0.28 0.01 IGHV4-39*01  22% (SEQ ID NO. 78)

(42) TABLE-US-00018 TABLE 11  CDR3 frequency analysis of Kappa chain before and after immunization of influenza vaccine Frequency on 7.sup.th day Frequency Frequency after before change Kappa chain immunization immunization V of V CDR3_Seq (%) (%) gene gene (%) QQRSDWPYT 2.993274 0.01 IGKV3-11*01  −9% (SEQ ID NO. 79) QQYDA 2.178924 0.01 IGKV1-33*01 100% (SEQ ID NO. 80) HQSSIRSWT 1.560191 0.01 IGKV1-39*01  21% (SEQ ID NO. 81) LQHNTYPQT 1.399475 0.01 IGKV1D-17*02 100% (SEQ ID NO. 82) QQSSTSSWT 1.274091 0 IGKV1-39*01  21% (SEQ ID NO. 83) QQYNNWPPYT 1.19955 0.48 IGKV3-15*01 −31% (SEQ ID NO. 84) MQGKYWPT 1.103035 0.01 IGKV2-30*01 100% (SEQ ID NO. 85) QQYRGSSCT 1.060809 0 IGKV3-20*01  50% (SEQ ID NO. 86) QQYGSSPPWT 1.020738 0.07 IGKV3-20*01    0.5 (SEQ ID NO. 87) QQYDYSSST 0.998763 0 IGKV3-20*01    0.5 (SEQ ID NO. 88)

(43) TABLE-US-00019 TABLE 12  CDR3 frequency analysis of Lambda chain before and  after immunization of influenza vaccine Frequency Frequency on 7.sup.th Frequency change day after before of V Lambda chain- immunization immunization V gene CDR3_Seq (%) (%) gene (%) AAWDDDLSGPV 16.83722 0.23 IGLV1-47*01 100% (SEQ ID NO. 89) AAWDDSQNGPL 2.558374 0.03 IGLV1-44*01  20% (SEQ ID NO. 90) QT 1.711464 3.48 IGLV4-69*01 −100%  (SEQ ID NO. 91) ATWDDNLSGPV 1.589042 0.02 IGLV1-47*01 100% (SEQ ID NO. 92) QV 1.483721 0 IGLV3-21*01 100% (SEQ ID NO. 93) AAWDDNFSGAEV 1.269279 0.01 IGLV1-47*01 100% (SEQ ID NO. 94) SSYTSSSTPWV 1.175902 0.05 IGLV2-14*01/03   0% (SEQ ID NO. 95) AVWDNSLNGFYV 1.161244 0.01 IGLV1-44*01  20% (SEQ ID NO. 96) AAWDDSLSPPEV 1.099626 0.01 IGLV1-47*01/02 100% (SEQ ID NO. 97) ATWDDDLSGPV 1.037193 0.01 IGLV1-47*01/02 100% (SEQ ID NO. 98)

(44) The expression frame is constructed by fusion of PCR; the frame includes promoter, variable region and antibody constant region. The selected antibody heavy chain gene and light chain gene are randomly paired and transfected 293FT cells for expression and the supernatant is obtained for Elisa assay, its affinity to antigens is tested.

(45) The concrete methods for expression in vitro can be referred to dengue virus cases. Elisa results show that one functional antibody per pair is obtained from the pairing of candidate Kappa chain and Lambda chain with heavy chain respectively. From FIG. 5, we can see that the success rate of pairing is 2/15.

Embodiment 4 Full-Length Sequences of Variable Region of Antibody Obtained by Combining the Sequencing Results of RACE and RT Libraries

(46) The optimized full-length sequence selection method of the variable region described in embodiment 2 may partially make up for the insufficient reading length of the sequence. But for partial antibody variable region, such as containing long length of CDR and FR regions or 5′ UTR may lead to low splicing rate. It is difficult to obtain the full length sequence of the high frequency variable region by the described selection in turn method with locking CDR3. For example, in four sequences of highest-frequency CDR3 in Table 9, the corresponding splicing rate of two CDR3 is about 40%.

(47) A method is developed to obtain the full-length sequence of variable region of antibody by combining the results of RACE and RT libraries sequencing. The RACE and RT methods are used to construct library and sequence for the same sample in parallel, and the consistency of high-frequency CDR3 in the two libraries is compared. The CDR3 homology cluster is locked and the maximum frequency variable region full length DNA sequence containing the CDR3 homology cluster is selected from the RT library.

(48) The method of concrete implementation is as follows: The RT method and the RACE method described in embodiment 1 are used to separate RNA from PBMC of blood sample of dengue patient at acute stage; construct heavy chain and light chain libraries by RT method at the same time.

(49) The steps of RT library construction are as follows: According to the method described in the embodiment 1, the first chain of cDNA is obtained, and the specific primers are used to amplify variable regions of heavy chain (VH), Kappa chain (VK) and Lambda chain (VL). The forward primer is designed in the conserved region of the variable region, and the reverse primer is designed in the constant region. The primer sequences are shown in Table 13, in which heavy chain primers are quoted from REF. 1.

(50) Adopt the 25 μL PCR amplification system consisting of 2.2 μM VH or 3.6 μM VK or 2.2 μM VL forward primers, 1 μM reverse primers, 2.5 μL AccuPrime Buffer I(Invitrogen), 2 μL cDNA and 0.75 μL AccuPrime Taq Polymerase.

(51) PCR program: 95° C. 2 min; 25 cycles (95° C. 30 sec, 56° C. 30 sec, 72° C. lmin); 72° C. 7 min; 4° C. The operation steps of gel cutting and purification of PCR products can be referred to the manual of QIAquick Gel Extraction Kit (Qiagen).

(52) The construction of high-throughput sequencing library can be referred to the manual of NEBNext® Ultra™ DNA Library Prep Kit for Illumina (NEB). After the library construction is finished, Bioanalyzer High Sensitivity DNA chip (Agilent) is used for QC and the sequencing platform is Illumina Miseq 2×300.

(53) TABLE-US-00020 TABLE 13  List of primers used in RT Library Construction VH chain IGHV_LR1 CGCAGACCCTCTCACTCAC forward (SEQ ID NO. 99) primers IGHV_LR2 TGGAGCTGAGGTGAAGAAGC (SEQ ID NO. 100) IGHV_LR3 TGCAATCTGGGTCTGAGTTG (SEQ ID NO. 101) IGHV_LR4 GGCTCAGGACTGGTGAAGC (SEQ ID NO. 102)  IGHV_LR5 TGGAGCAGAGGTGAAAAAGC (SEQ ID NO. 103) IGHV_LR6 GGTGCAGCTGTTGGAGTCT (SEQ ID NO. 104) IGHV_LR7 ACTGTTGAAGCCTTCGGAGA (SEQ ID NO. 105) IGHV_LR8 AAACCCACACAGACCCTCAC (SEQ ID NO. 106) IGHV_LR9 AGTCTGGGGCTGAGGTGAAG (SEQ ID NO. 107) IGHV_LR10 GGCCCAGGACTGGTGAAG (SEQ ID NO. 108) IGHV_LR11 GGTGCAGCTGGTGGAGTC (SEQ ID NO. 109) VH chain HGR AAGACCGATGGGCCCTTG reverse primers (SEQ ID NO. 110) VK chain kvf1 TGACCCAGTCTCCATCCTCC forward (SEQ ID NO. 111) primers kvf2 TGACCCAGTCTCCATCCTCA (SEQ ID NO. 112) kvf3 TGACCCAGTCTCCATCCTTCC (SEQ ID NO. 113) kvf4 TGACCCAGTCTCCATCCTTACT (SEQ ID NO. 114) kvf5 TGACCCAGTCTCCATCTGCC (SEQ ID NO. 115) kvf6 TGACCCAGTCTCCATCTTCC (SEQ ID NO. 116)  kvf7 TGACACAGTCTCCAGCCACC (SEQ ID NO. 117) kvf8 TGACACAGTCTCCAGGCACC (SEQ ID NO. 118) kvf9 TGACGCAGTCTCCAGGCAC (SEQ ID NO. 119) kvf10 TGACCCAGTCTCCAGACTCC (SEQ ID NO. 120) kvf11 TGACTCAGTCTCCACTCTCCC (SEQ ID NO. 121) kvf12 TGACCCAGTCTCCATTCTCCC (SEQ ID NO. 122) kvf13 TGACCCAGACTCCACTCTCTC (SEQ ID NO. 123) kvf14 TGACCCAGACTCCACTCTCC (SEQ ID NO. 124) kvf15 TGACCCAGTCTCCTTCCACC (SEQ ID NO. 125) kvf16 TCACGCAGTCTCCAGCATTC (SEQ ID NO. 126) kvf17 TGACGCAGTCTCCAGCCAC (SEQ ID NO. 127) kvf18 TGACCCAGTCTCCATCTTCTG (SEQ ID NO. 128) VK chain KCR ACACAACAGAGGCAGTTCCAG reverse  (SEQ ID NO. 129) primers VL chain lvf1 GGTCCTGGGCCCAGTCTGTCG forward (SEQ ID NO. 130) primers lvf2 GGTCCTGGGCCCAGTCTGCC (SEQ ID NO. 131) lvf3 GTCCTGGGCCCAGTCTGTGCT (SEQ ID NO. 132) lvf4 TGTCAGTGGTCCAGGCAGGGC (SEQ ID NO. 133) lvf5 GATCCTGGGCTCAGTCTGCCCTG (SEQ ID NO. 134) lvf6 GCTCTGAGGCCTCCTATGAGCTG (SEQ ID NO. 135) lvf7 GATCCGTGGCCTCCTATGAGCTG (SEQ ID NO. 136) lvf8 TCTCTGAGGCCTCCTATGAGCTG (SEQ ID NO. 137) lvf9 GCTCTGCGACCTCCTATGAGCTG (SEQ ID NO. 138) lvf10 GTTCTGTGGTTTCTTCTGAGCTG AC (SEQ ID NO. 139) lvf11 GCTCTGTGACCTCCTATGTGCTG (SEQ ID NO. 140) lvf12 TCTCTGTGGCCTCCTATGAGCTG (SEQ ID NO. 141) lvf13 GTTCTGTGGCCTCCTATGAGCTG (SEQ ID NO. 142) lvf14 GTCTCTGTGCTCTGCCTGTGCTG (SEQ ID NO. 143) lvf15 GGTCTCTCTCCCAGCCTGTGCTG (SEQ ID NO. 144) lvf16 GGTCTCTCTCCCAGCTTGTGCTG (SEQ ID NO. 145) lvf17 GTTCCCTCTCGCAGCCTGTGCT (SEQ ID NO. 146) lvf18 GTTCCCTCTCGCAGGCTGTGCT (SEQ ID NO. 147) lvf19 GGTCCAATTCTCAGACTGTGGTG AC (SEQ ID NO. 148) lvf20 GGTCCAATTCCCAGGCTGTGGTG (SEQ ID NO. 149) lvf21 GAGTGGATTCTCAGACTGTGGTG AC (SEQ ID NO. 150) lvf22 GGTCCCTCTCCCAGCCTGTGC (SEQ ID NO. 151) VL chain LCR AGTGTGGCCTTGTTGGCTTG reverse primers (SEQ ID NO. 152)

(54) The library sequencing and analysis are carried out according to the method described in embodiment 1, the correlation of high frequency CDR3 region between RACE library and RT library is compared, see FIGS. 6(a) and 6(b) for the analysis of CDR3 frequency correlation between RACE library and RT library.

(55) The results show that the correlation R.sup.2 value of heavy chain and Lambda chain CDR3 in the two libraries is about 0.7; as shown in FIG. 6(a), the consistency of the highest frequency heavy chain and light chain CDR3 is very good, the high frequency heavy chain and light chain CDR3 in the top 10 of antibody spectrum also show some consistency, indicating that there is no significant deviation in most of the high frequency CDR3 rankings in the two libraries. For example, the highest frequency CDR3 (ARETDGMDV) (SEQ ID NO.153) of heavy chain of the sample 11-2 in FIG. 6(b) is the highest frequency CDR3 in both RACE and RT libraries. The amino acid sequences of the most abundant FR and CDR regions of the CDR3-ARETDGMDV (SEQ ID NO.153) homology cluster selected by using the RACE R12 file are FR1:QVQLVQSGAEVKRPGASVKVSCKAS (SEQ ID NO.154), FR2:MHWVRQAPGQRLEWMGW (SEQ ID NO.155), FR3:KYSQKFQGRVTITRDTSASTAYMELSSLRSEDTAVYYC (SEQ ID NO.156), CDR1:GYTFTTYA (SEQ ID NO.157), FR4:WGQG (SEQ ID NO.50), CDR2:INAGNGNT (SEQ ID NO.158). The amino acid sequences of the most abundant FR region and CDR region of CDR3-ARETDGMDV (SEQ ID NO.153) homology cluster selected by RT file are also consistent, which indicates that this method can be used to splice the variable region of high frequency CDR3 gene.

Embodiment 5 an Optimized Antibody Gene Screening Method for HA Monoclonal Antibody

(56) Use the method of RACE antibody library construction described in embodiment 1, total RNAs are isolated from spleen cells of mice immunized with HA antigen, and construct the RACE libraries of heavy chain and light chain respectively. Use Illumina Miseq 2×250 system for high-throughput sequencing. The methods of data processing, the determination of FR and CDR regions, and the selection of candidate CDR3 amino acid sequences are the same as those described in embodiment 1.

(57) The expression frame is constructed by fusion of PCR; the frame includes promoter, variable region and antibody constant region. The selected antibody heavy chain gene and light chain gene are randomly paired and transfected 293FT cells for expression and the supernatant is obtained for Elisa assay, its affinity to antigens is tested.

(58) The concrete methods for expression in vitro can be referred to dengue virus cases. Elisa results show that one affinity antibody is obtained from the pairing of candidate heavy chain and light chain.

(59) TABLE-US-00021 TABLE 14  Analysis of heavy chain CDR3 frequency after HA immunization in mice Frequency after Heavy chain CDR3_Seq immunization (%) TRGDY (SEQ ID NO. 159) 5.94 ARHTIPPYVMDY (SEQ ID NO. 160)  1.56 ARDEGIYGY (SEQ ID NO. 161) 1.48 ARGVYNYGRVWYFDV (SEQ ID NO. 162) 1.36 ARRDYDNYVPFAY (SEQ ID NO. 163) 1.25 TGDYEFGLFDY (SEQ ID NO. 164) 1.24 ARLSGTFAY (SEQ ID NO. 165) 1.01 ASLKGSAY (SEQ ID NO. 166) 0.92 AREGGYYFDY (SEQ ID NO. 167) 0.91 ARDNGHDWFAY (SEQ ID NO. 168) 0.87 ARRDYGNYVPFAY (SEQ ID NO. 169) 0.76 VLDYYGYAPFAY (SEQ ID NO. 170) 0.75 ARDLYYSHGGFAY (SEQ ID NO. 171) 0.70 ARVDGYLQGYYFGY (SEQ ID NO. 172) 0.69 ARGREGNGAMDY (SEQ ID NO. 173) 0.65 ARQEFYYGNYDAMDY (SEQ ID NO. 174) 0.61 ASGILNVMDY (SEQ ID NO. 175) 0.58 ARATVPAEIAY (SEQ ID NO. 176) 0.57 ARWTGTGDYAMDY (SEQ ID NO. 177) 0.56 ARSGLIYDGYYAWFAY (SEQ ID NO. 178) 0.53

(60) TABLE-US-00022 TABLE 15  Analysis of Kappa chain CDR3 frequency after HA immunization in mice Frequency after Kappa chain immunization (%) WQGTHFPWT (SEQ ID NO. 179)  4.62 QNGHSFPYT (SEQ ID NO. 180)  4.11 QQYYSYPRT (SEQ ID NO. 181) 3.86 QQYYRYPWT (SEQ ID NO. 182) 1.97 QQYYNYRT (SEQ ID NO. 183) 1.92 MQHLEYPFT (SEQ ID NO. 184) 1.83 QQYYSYPWT (SEQ ID NO. 185) 1.49 KQSYNLLT (SEQ ID NO. 186) 1.31 LHYDNLWT (SEQ ID NO. 187) 1.22 QQYYSYRT (SEQ ID NO. 188) 1.11 LQYDNLLT (SEQ ID NO. 189) 1.10 MQHLEYPYT (SEQ ID NO. 190) 1.04 QNDHSFPLT (SEQ ID NO. 191) 0.96 SQSTHVPPT (SEQ ID NO. 192) 0.89 FQGSHVPWT (SEQ ID NO. 193) 0.85 WQGTHFPQT (SEQ ID NO. 194) 0.84 QQWSSNPFT (SEQ ID NO. 195) 0.79 QQWSSNPPT (SEQ ID NO. 196) 0.79 HQWSSYRT (SEQ ID NO. 197) 0.78 KQSYNLWT (SEQ ID NO. 198) 0.76

(61) The applicant declares that the detailed method of the invention is explained by the above embodiments, but the invention is not limited to the above detailed methods, that is, it does not mean that the invention should rely on the above detailed methods for implementation. Technicians in the technical field should understand that any improvement in the invention, the equivalent replacement of the raw materials of the products of the invention and the addition of auxiliary components, and the selection of concrete ways, etc., fall within the protection scope and the public scope of the invention.