Fig. 1: Phylogenetic, neutralizing, binding, and genetic properties of isolated nanobodies against SARS-CoV-2 and SARS-CoV-1.

Phylogenetic analysis of 124 neutralizing nanobodies out of 593 binding nanobodies to the spike trimer of prototype SARS-CoV-2, isolated from the VHH library of an immunized alpaca. All nanobodies were constructed in Fc format and their cross-neutralization against SARS-CoV-2 and SARS-CoV-1 can be clustered in four groups (a, b, c, and d) and highlighted by the red branches. Neutralizing activities of each nanobody to SARS-CoV-2 and SARS-CoV-1 pseudoviruses are shown by half-maximal inhibitory concentration IC50 (μg/mL). The thirty-eight representative nanobodies selected for further evaluation are indicated by red triangle in Nb ID column. Results were calculated from three independent experiments and each performed in technical duplicates. The binding activity of each nanobody to the spike trimer, RBD, NTD, and S2 regions of prototype SARS-CoV-2 are indicated by the variable color scheme, with red for high binding (OD450 > 2), blue for medium binding (2 > OD450 > 1), and grey for low binding (OD450 < 1). The genetic features such as germline variable gene segment (V), diversity gene segment (D), and junction gene (J) as well as CDR3 length of each nanobody are indicated with various colors. See also Fig. S1. Source data are provided as a Source Data file.