Selection and characterization of human scFvs targeting the SARS-CoV-2 nucleocapsid protein isolated from antibody libraries of COVID-19 patients

The Data Set is a collection of the Fasta of sequencing of 6 human library of scFvs (VH-linker VL) obtain from the IgM repertoire and of 6 human libraries of scFvs (VH-linker VL) obtain from the IgG_IgA repertoire of 6 patients that recover from COVID19.

Each of the 12 libraries (6 for the IgM and 6 for the IaG/IgA repertoire) were sequenced by ION TORRENT technology by Genomnia. For each scFv library an independently VH and a VL Ion Torrent library was constructed as follows. VH and VL were amplified using primers (VH_fus_F- VH_fus_R and VL_fus_F - VL_fus_R_BXX) having, at the 3’end, the region presents in the pLinker220 plasmid flanking the VH or VL and, at the 5’ end, the Ion Torrent adaptors. In this step, Unique Molecular Identifiers (UMI) consisting of 13 degenerate bases are also introduced in the reverse primer used to amplify the VH and VH regions.  The amplified VH and VL were then subjected to a second PCR using the primers A_fus – trP1_fus to build the fusion library. Sequencing was performed on an Ion Torrent platform (IonS5) with 400bp chemistry on a 530 chip. Both types of sequencing libraries were constructed by Genomnia. Each VH library was individually sequenced to a 400bp read on a 530 chip, yielding approximately 20-25 million reads per sample. The VL libraries, on the other hand, were barcoded and sequenced in a pool of three libraries from different patients, aiming to obtain 6-10 million reads per library. All sequencing runs were of good quality, with an average of 73% of the reads mapping to immunoglobulin genes used for clonotype identification (i.e. less than 30% polyclonal reads) and less than 20% low-quality sequences

 The correspondence between the library number (#) and the # of the patient in the sequencing  files name is as follows:

Library #

Patient # in the file name

lib 1

pz24

lib 2

pz26

lib 3

pz27

lib 4

pz39

lib 5

pz42

lib 6

pz44

The correspondence between the library number (#) and the file name for each of the VH and  sequencing is as follows:

Library #

File name VH Sequences

lib 1 IgM VH

PANANTICOVID_I_Auto_user_S5-00513-163-30pM_24_IgM_VH_414__REANALYSIS_488_rawtf.fa

lib 1 IgG_IgA VH

PANANTICOVID_I_Auto_user_S5-00513-162-30pM_24_IgG_IgA_VH_407_469_rawtf.fa

lib 2 IgM VH

PANANTICOVID_I_Auto_user_S5-00513-157-30pM_pz26_VH_IgM_404_REANALYSIS_460_rawtf.fa

lib 2 IgG_IgA VH

PANANTICOVID_I_Auto_user_S5-00513-158-30pM_pz26_VH_IgG_IgA_403_458_rawtf.fa

lib 3 IgM VH

PANANTICOVID_I_Auto_user_S5-00513-161-30pM_27_IgM_VH_408_465_rawtf.fa

lib 3 IgG_IgA VH

PANANTICOVID_I_Auto_user_S5-00513-164-30pM_27_IgG_IgA_VH_413_482_rawtf.fa

lib 4 IgM VH

PANANTICOVID_II_Auto_user_S5-00513-159-30pM_pz39_IgM_VH_406_461_rawtf.fa

PANANTICOVID_I_Auto_user_S5-00513-159-30pM_pz39_IgM_VH_406_REANALYSIS_477_rawtf.fa

lib 4 IgG_IgA VH

PANANTICOVID_I_Auto_user_S5-00513-160-30pM_pz39_IgG_IgA_VH_405_463_rawtf.fa

lib 5 IgM VH

PANANTICOVID_II_Auto_user_S5-00513-166-30pM_pz42_VH_IgM_415_486_rawtf.fa

lib 5 IgG_IgA VH

PANANTICOVID_I_Auto_user_S5-00513-167-30pM_42_IgG_IgA_VH_418_489_rawtf.fa

lib 6 IgM VH

PANANTICOVID_I_Auto_user_S5-00513-168-30pM_44_IgM_VH_417_491_rawtf.fa

lib 6 IgG_IgA  VH

PANANTICOVID_I_Auto_user_S5-00513-169-30pM_pz44_IgG_IgA_VH_420_493_rawtf.fa