On March 11 a new epidemic of an unusual pneumonia appearing to originate in the Huanan Seafood Market in Wuhan (China) was eventually declared to be a pandemic. More than 150,000 cases of 2019-nCoV infected until March 10, 2020, and almost 6000 deaths in almost 140 countries in the world. Unfortunately there currently is no vaccine to fight this disease.

In January 2020, Chen et al obtained the sequence of the virus from a sample obtained from bronchoalveolar lavage fluids from an infected patient in December 2019 1. They concluded that it is a new human coronavirus, and called it 2019-nCoV (or Covid-19). Later, the team of Wrapp et al determined the three-dimensional structure by X-rays (resolution 3,46 Å) of one of the key proteins for the development of a vaccine against this disease, the spike (S) glycoprotein 2.

With these results, it is possible to determine the B-cell epitopes that could be the basis for developing a vaccine, it means, it is basically residues present on the surface of an antigen that stimulates humoral immune responses 34. In fact, the goal of epitope prediction is to design the minimal immune unit that invoke strong humal responses in human body 4, Therefore, the goal of this paper is determine in silico the consensus of linear and conformational B-cells epitopes obtained from the spike glycoprotein. Since these in silico methods obtain a large number of results, structural and energetic properties are considered from a function called <F> as will be explained in the next section.

We have obtained 373 B-cell epitopes according to results obtained from the sequence and the three-dimensional structure of the spike glycoprotein (PDB ID) 6VSB as detailed below: 24 linear B-cell epitopes (the threshold is 0,35) yields with the BePiPred 2.0 program. The ABCPred predicted 49 epitopes of the length of 10 amino acids whose score is equal to or greater than 0,66. The BCPred program based on the hydrophilicity, flexible, accessibility and exposed surface were predicted 15, 14, 30 and 8, respectively. The Emili procedure generated 22 epitopes with a threshold of 1 and a window size of 6; and Kolasar antigenic were 37 (threshold 1,044 and windows size = 7). Discotope 1.1 (threshold = -7,7) yields 19, and ElliPro was 14 (minimum score = 0,5 and maximum distance = 6 Å). CBTope (threshold = -0.3) predicted 31, COBEpro (threshold = 0 .69) was 59, SEPPA 3.0 was 41 and finally SVMTripP was 10 (windows size = 10 and threshold = 0.325).

The next step was to calculate the consensus of B cell epitopes and the function <F>. To visualize this calculation, we let us focus on the region between 276 to 287 amino acids as show in Table 1.

In the first and second columns of Table 1, the position (abbreviated Pos) and their corresponding amino acid sequence of spike glycoprotein are shown. The third column indicates the value of Q, that is, the Similitud Index calculated by Isea et al. The consensus B cell epitope will be one whose values of Q are greater than 4 (with a minimum extension of four amino acids). As seen in Table 1, the consensus B cell epitope will be KYNENGT (highlighted in bold for easy viewing). The value <Q> will be simply the average of these Q values, which is (6+5+5+6+6+6+6) / 7 = 5,71.

The value δΔG is the sum of the Gibbs energy contributions, it means, 0,04+2,51+0,63+0,51+0,81+2,24+0,88=7,62; while the average mobility value (<R>) is equal to (3.22+3.75+4.19+4.94+4.95+4.49+3.99)/7=4,22.

Therefore the value of the function <F> obtained from the glycoprotein and extrapolate to the consensus of B cell epitope KYNENGT is equal to 10,31 (ie., 5,71·7,62/4.22).

Table 2 shows the values obtained according to the procedure described above. However, it is important to verify that the regions are exposed to the solvent. For this reason, we calculated the average value that was obtained from two different programs from the data shown in Table 1. From the previous example, the degree of solvent exposure obtained with the PoPMusic program is simply (34,98+2,18+39,07+33,60+48,86+2,49+29,27)/7 =27,21 (see the values in Table 1); while the average value with the Polivew program is 2,29. To compare these values, they must be normalized it, taking into account that the maximum values are 100 and 9 for PoPMusIc and Polyview, respectively. The average value of the degree of exposure to the solvent is 0,26 (ie., 27,21/100+2,29/9). This last result indicates that this epitope (theoretically) is 26% exposed to the solvent. The rest of the results are shown directly in Table 2.

The results in Table 2 have been ordered according to the position of their amino acid sequence in the spike glycoprotein. It is interesting to comment that 12 of the 22 consensus epitopes obtained in this work have a value of <F> less than 6, which would imply that they could be possible candidates for the design of a vaccine. However of these 12, only 7 have an average value of exposure to the solvent greater than 40%. So the best candidates for the development of a vaccine appear to be: SSANNCT, PLQSYGFQPT, TESNKKFLP, NNSYEC, AENS, LPDPSK and YDPLQPE.

The present work calculated the consensus linear and conformational B-cell epitopes from a new coronavirus 2019-nCoV obtained from spike glycoprotein. With this information, it may be possible to design a vaccine for this disease. We employed a function called <F> that considers energy factors and the structure of the glycoprotein for selected the best candidates of B cell epitopes. Finally, the next step is to begin to validate these results with in vivo experiments.