Resistance to neutralization is an important characteristic of primary isolates of human immunodeficiency virus type 1 (HIV-1) that relates to the potential for successful vaccination to prevent infection and use of immunotherapeutics for treatment of established infection. In order to further elucidate mechanisms responsible for neutralization resistance, we studied the molecular mechanisms that determine the resistance of the primary virus isolate of the strain HIV-1 MN to neutralization by soluble CD4 (sCD4). As is the case for the global neutralization resistance phenotype, sCD4 resistance depended upon sequences in the amino-terminal heptad repeat region of gp41 (HR1), as well as on multiple functional interactions within the envelope complex. The functional interactions that determined the resistance included interactions between the variable loop 1 and 2 (V1/V2) region and sequences in or near the CD4 binding site (CD4bs) and with the V3 loop. Additionally, the V3 loop region was found to interact functionally with sequences in the outer domain of gp120, distant from the CD4bs and coreceptor-binding site, as well as with a residue thought to be located centrally in the coreceptor-binding site. These and previous results provide the basis for a model by which functional signals that determine the neutralization resistance, high-infectivity phenotype depend upon interactions occurring across the surface of the gp120 core structure and involving variable loop structures and gp41. This model should be useful in efforts to define epitopes that may be important for primary virus neutralization.Resistance to antibody-mediated neutralization of infectivity is characteristic of naturally occurring strains of human immunodeficiency virus type 1 (HIV-1) that have not been manipulated in the laboratory (15, 18). Such strains are commonly referred to as primary isolates. This property is a limiting factor with respect to efforts to develop a vaccine that may protect by induction of potent neutralizing antibodies. Induction of potent neutralizing antibodies is a common property of successful viral vaccines (26). Insights into the mechanisms of neutralization resistance of primary isolates of HIV-1 may indicate possible approaches to neutralization of such viruses and facilitate vaccine development.Our laboratory has previously reported studies of the MN strain of HIV-1 that have begun to address this issue (14,(21)(22)(23). The original isolate of the MN virus was propagated in a continuous T-cell line and is considered T-cell line adapted (TCLA) (12, 30). It is unusual among both primary and TCLA strains of HIV-1 in its high sensitivity to neutralization by antibodies in sera of infected patients and monoclonal antibodies (MAbs) against multiple linear and conformation-sensitive epitopes on the envelope glycoproteins (4,7,40,48). In an early study a neutralization-resistant variant of this strain was studied that was produced by growth of the MN strain virus in the presence of a highly neutralizing human serum (22). T...