Immunogenic fusion proteins induce neutralizing SARS-CoV-2 antibodies in the serum and milk of sheep

Antigen-specific polyclonal immunoglobulins derived from the serum, colostrum, or milk of immunized ruminant animals have potential as scalable therapeutics for the control of viral diseases including COVID-19. Here we show that the immunization of sheep with fusions of the SARS-CoV-2 receptor binding domain (RBD) to ovine IgG2a Fc domains promotes significantly higher levels of antigen-specific antibodies compared to native RBD or full-length spike antigens. This antibody population contained elevated levels of neutralizing antibodies that suppressed binding between the RBD and hACE2 receptors in vitro. A second immune-stimulating fusion candidate, Granulocyte-macrophage colony-stimulating factor (GM-CSF), induced high neutralizing responses in select animals but narrowly missed achieving significance. We further demonstrated that the antibodies induced by these fusion antigens were transferred into colostrum/milk and possessed cross-neutralizing activity against diverse SARS-CoV-2 variants. Our findings highlight a new pathway for recombinant antigen design in ruminant animals with applications in immune milk production and animal health.

Immunogenic fusion proteins induce neutralizing SARS-CoV-2 antibodies in the serum and milk of sheep.

Antigen-specific polyclonal immunoglobulins derived from the serum, colostrum, or milk of immunized ruminant animals have potential as scalable therapeutics for the control of viral diseases including COVID-19. Here we show that the immunization of sheep with fusions of the SARS-CoV-2 receptor binding domain (RBD) to ovine IgG2a Fc domains promotes significantly higher levels of antigen-specific antibodies compared to native RBD or full-length spike antigens. This antibody population contained elevated levels of neutralizing antibodies that suppressed binding between the RBD and hACE2 receptors in vitro. A second immune-stimulating fusion candidate, Granulocyte-macrophage colony-stimulating factor (GM-CSF), induced high neutralizing responses in select animals but narrowly missed achieving significance. We further demonstrated that the antibodies induced by these fusion antigens were transferred into colostrum/milk and possessed cross-neutralizing activity against diverse SARS-CoV-2 variants. Our findings highlight a new pathway for recombinant antigen design in ruminant animals with applications in immune milk production and animal health.

Deep mutational learning predicts ACE2 binding and antibody escape to combinatorial mutations in the SARS-CoV-2 receptor-binding domain.

The continual evolution of SARS-CoV-2 and the emergence of variants that show resistance to vaccines and neutralizing antibodies threaten to prolong the COVID-19 pandemic. Selection and emergence of SARS-CoV-2 variants are driven in part by mutations within the viral spike protein and in particular the ACE2 receptor-binding domain (RBD), a primary target site for neutralizing antibodies. Here, we develop deep mutational learning (DML), a machine-learning-guided protein engineering technology, which is used to investigate a massive sequence space of combinatorial mutations, representing billions of RBD variants, by accurately predicting their impact on ACE2 binding and antibody escape. A highly diverse landscape of possible SARS-CoV-2 variants is identified that could emerge from a multitude of evolutionary trajectories. DML may be used for predictive profiling on current and prospective variants, including highly mutated variants such as Omicron, thus guiding the development of therapeutic antibody treatments and vaccines for COVID-19.

Impact of prepartum administration of a vaccine against infectious calf diarrhea on nonspecific colostral immunoglobulin concentrations of dairy cows.

Passive transfer of colostral immunoglobulins from the cow to the calf is essential for calf health. The objective of this study was to determine if prepartum administration of a vaccine stimulates increased concentrations of colostral immunoglobulins of dairy cows beyond what is explained by vaccine-specific immunoglobulins. A prospective cohort study was conducted on a spring-calving commercial dairy farm that had a policy of only vaccinating cows with even ear tag numbers with a calf diarrhea vaccine, whereas cows with odd ear tag numbers were left unvaccinated. Cows in the vaccinated group (even ear tag numbers, n = 204) received a sensitizer and booster vaccination with a vaccine against bovine rotavirus (serotypes G6 and G10), bovine coronavirus, and E. coli having the K99 pili adherence factor. A sensitizer was given because the study vaccine was different from the vaccine previously used. Cows in the control group (odd ear tag numbers, n = 194) received a 2-mL subcutaneous sterile saline solution. Both groups received two treatments at a 3-wk interval, completing the treatments approximately 2 wk prior to the planned start of calving. During the calving period, technicians separated calves from cows immediately after parturition and prior to suckling, and cows were completely milked out within 6 h of parturition. Vaccine-specific, total, and nonvaccine-specific (total minus vaccine-specific) concentrations of immunoglobulin classes A, G1, G2a, and M (IgA, IgG1, IgG2a, and IgM, respectively) were quantified by mass spectrometry for 20 colostrum samples from each treatment group. Predicted mean non-vaccine-specific colostral IgM concentrations were 8.76 (95% CI = 7.18-10.67) and 5.78 (95% CI = 4.74-7.05) mg/mL for vaccinated and control cows, respectively (P = 0.005). Predicted mean non-vaccine-specific colostral IgG1 concentrations were 106.08 (95% CI = 92.07-120.08) and 95.30 (95% CI = 81.30-109.31) mg/mL among vaccinated and control cows, respectively; however, these means were not significantly different (P = 0.278). It is thus possible that the vaccine, in addition to specifically managing infectious calf diarrhea, may also have non-specific benefits by improving colostrum quality through increased non-vaccine-specific colostrum IgM concentrations. Further research is necessary to determine the mechanism for these preliminary findings, whether the effect may occur in other immunoglobulin classes, and what impacts it may have on calf health outcomes.

Unlike human babies, calves do not receive protective immune proteins (immunoglobulins) from the mother before birth, so a sufficient volume of immunoglobulin-rich colostrum of adequate quality must be consumed within hours of birth. It can be a challenge to meet this requirement for all dairy calves. Prior to calving, cows can be vaccinated with a vaccine against specific infectious causes of calf diarrhea to stimulate elevated concentrations of specific immunoglobulins in their colostrum, which is consumed by their calves to protect them until their own immune systems develop. We enrolled cows that were either vaccinated or not with a calf diarrhea vaccine and, using novel laboratory techniques, measured concentrations of immunoglobulin classes A, G, and M in their colostrum. As expected, vaccinated cows had elevated concentrations of vaccine-specific immunoglobulins in their colostrum. However, they also had elevated non-vaccine-specific concentrations of immunoglobulin M. The vaccine may therefore have stimulated a nonspecific increase in colostral immunoglobulin M concentrations. Further research is necessary to confirm the preliminary findings of the present study and determine the mechanism for this apparent nonspecific increase in colostral immunoglobulin M concentrations, whether it may occur in other immunoglobulin classes, and whether it may benefit calf health and growth.

Deep mutational scanning for therapeutic antibody engineering.

The biophysical and functional properties of monoclonal antibody (mAb) drug candidates are often improved by protein engineering methods to increase the probability of clinical efficacy. One emerging method is deep mutational scanning (DMS) which combines the power of exhaustive protein mutagenesis and functional screening with deep sequencing and bioinformatics. The application of DMS has yielded significant improvements to the affinity, specificity, and stability of several preclinical antibodies alongside novel applications such as introducing multi-specific binding properties. DMS has also been applied directly on target antigens to precisely map antibody-binding epitopes and notably to profile the mutational escape potential of viral targets (e.g., SARS-CoV-2 variants). Finally, DMS combined with machine learning is enabling advances in the computational screening and engineering of therapeutic antibodies.