Progress 07/15/20 to 07/14/23
Outputs
Target Audience:Research findings have been disseminated through invited seminars and peer-reviewed publications, reaching the broader scientific community, policymakers, and regulatory agencies. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Three graduate students, four Postdoctoral Scholars, and four undergraduate researchers worked closely with the project under the direct supervision of the PI and Co-PIs. As part of the training, one graduate student and three postdocs got proficient working in a BSL-3 facility. Undergraduate students were trained in developing and validating serological assays. Sequencing, protein prediction, and bioinformatics workflows were developed and standardized. How have the results been disseminated to communities of interest?We investigated the prevalence of SARS-CoV-2 in white-tailed deer (n=34) in Camp David, Maryland, during February 2022 and found ongoing infections in 44% of animals and antibodies to SARS-CoV-2 in 41%. The whole genome sequences (n=5) were identified to be Delta sub-lineage AY.3; however, there was no Delta AY.3, but a large number of Omicron variants was identified from humans in Maryland at this time.The deer (n=14) had a high titre of antibodies to B.1 lineage, Alpha and Delta, compared to Beta, Gamma, and Omicron variants in pseudovirus neutralization coupled antigen cartography. We have also analyzed the temporal distribution of SARS-CoV-2 variants available in GISAID from humans and deer. Deers were found to harbor some of the earlier variants of SARS-CoV-2 when these variants were no longer circulating in humans. The results were presented at the American Society of Virology 2023 conference. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
The association of the receptor binding domain (RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein with human angiotensin-converting enzyme 2 (hACE2) represents the first required step for cellular entry. SARS-CoV-2 has continued to evolve with the emergence of several novel variants, and amino acid changes in the RBD have been implicated with increased fitness and potential for immune evasion. Reliably predicting the effect of amino acid changes on the ability of the RBD to interact more strongly with the hACE2 can help assess the implications for public health and the potential for spillover and adaptation into other animals. Here, we developed a two-step framework that first relies on 48 independent 4-ns molecular dynamics (MD) trajectories of RBD−hACE2 variants to collect binding energy terms decomposed into Coulombic, covalent, van der Waals, lipophilic, generalized Born solvation, hydrogen bonding, π−π packing, and self-contact correction terms. The second step implements a neural network to classify and quantitatively predict binding affinity changes using the decomposed energy terms as descriptors. Citation: Chen C, Boorla VS, Banerjee D, Chowdhury R, Cavener VS, Nissly RH, Gontu A, Boyle NR, Vandegrift K, Nair MS, Kuchipudi SV, Maranas CD. Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2. Proc Natl Acad Sci U S A. 2021 Oct 19;118(42):e2106480118. doi: 10.1073/pnas.2106480118. Following a report from USDA observing 40% seroprevalence in white-tailed deer in US, we have tested 283 retropharyngeal lymph node samples collected from white-tailed deer in Iowa from April 2020 to January of 2021 and observed widespread SARS-CoV-2 infection (33.2% samples SARS-CoV-2 RNA positive) in deer. The whole-genome analysis indicated the evidence of multiple humans to deer spillover which is the first report of SARS-CoV-2 infections in wild white-tailed deer. Citation: Kuchipudi SV, Surendran-Nair M, Ruden RM, Yon M, Nissly RH, Vandegrift KJ, Nelli RK, Li L, Jayarao BM, Maranas CD, Levine N, Willgert K, Conlan AJK, Olsen RJ, Davis JJ, Musser JM, Hudson PJ, Kapur V. Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer. Proc Natl Acad Sci U S A. 2022 Feb 8;119(6):e2121644119. doi: 10.1073/pnas.2121644119. PMID: 35078920; PMCID: PMC8833191. We examined the hypothesis that the Omicron variant is actively and asymptomatically infecting the free-ranging deer of New York City. We collected 155 deer samples between December 2021 and February 2022 from Staten Island, New York. Of 135 serum samples, 19 (14.1%) indicated SARS-CoV-2 exposure, and 11 reacted most strongly to the wild-type B.1 lineage. Of the 71 swabs, 8 were positive for SARS-CoV-2 RNA (4 Omicron and 4 Delta). Two of the animals had active infections and robust neutralizing antibodies, revealing evidence of reinfection or early seroconversion in deer. It suggests that the Variants of concern continue to circulate among and may reinfect US deer populations. Citation: Vandegrift KJ, Yon M, Surendran Nair M, Gontu A, Ramasamy S, Amirthalingam S, Neerukonda S, Nissly RH, Chothe SK, Jakka P, LaBella L, Levine N, Rodriguez S, Chen C, Sheersh Boorla V, Stuber T, Boulanger JR, Kotschwar N, Aucoin SG, Simon R, Toal KL, Olsen RJ, Davis JJ, Bold D, Gaudreault NN, Dinali Perera K, Kim Y, Chang KO, Maranas CD, Richt JA, Musser JM, Hudson PJ, Kapur V, Kuchipudi SV. SARS-CoV-2 Omicron (B.1.1.529) Infection of Wild White-Tailed Deer in New York City. Viruses. 2022 Dec 12;14(12):2770. doi: 10.3390/v14122770. PMID: 36560774; PMCID: PMC9785669. To monitor SARS-CoV-2 infections in livestock, we developed and optimized species-specific indirect ELISAs (iELISAs) to detect anti-SARS-CoV-2 antibodies in cattle, swine, and chickens using the spike protein receptor-binding domain (RBD) antigen. For the assay optimization, we have used the serum samples collected prior to the COVID-19 pandemic as negative samples to determine the cut-off threshold. SARS-CoV-2 B.1 lineage RBD hyperimmunized sera from cattle (n= 3), swine (n= 6), and chicken (n= 3) were used as the positive controls. The iELISAs were evaluated compared to a live virus neutralization test using cattle (n= 150), swine (n= 150), and chicken (n= 150) serum samples collected during the COVID-19 pandemic. None of the cattle, swine and chicken serum samples collected during the COVID-19 pandemic were positive for SARS-CoV-2 antibodies. The iELISAs for cattle, swine, and chicken were found to have 100% sensitivity and specificity based on hyperimmune sera testing. Citation: Gontu A, Marlin EA, Ramasamy S, Neerukonda S, Anil G, Morgan J, Quraishi M, Chen C, Boorla VS, Nissly RH, Jakka P, Chothe SK, Ravichandran A, Kodali N, Amirthalingam S, LaBella L, Kelly K, Natesan P, Minns AM, Rossi RM, Werner JR, Hovingh E, Lindner SE, Tewari D, Kapur V, Vandegrift KJ, Maranas CD, Surendran Nair M, Kuchipudi SV. Development and Validation of Indirect Enzyme-Linked Immunosorbent Assays for Detecting Antibodies to SARS-CoV-2 in Cattle, Swine, and Chicken. Viruses. 2022 Jun 22;14(7):1358. doi: 10.3390/v14071358. PMID: 35891340; PMCID: PMC9317974. High prevalence of SARS-CoV-2 infection in white-tailed deer (Odocoileus virginianus) has been reported in multiple locations, likely resulting from several human-to-deer spillover events followed by deer-to-deer transmission. Knowledge of the risk and direction of SARS-CoV-2 transmission between humans and potential reservoir hosts is essential for effective disease control and prioritization of interventions. Using genomic data, we reconstruct the transmission history of SARS-CoV-2 in humans and deer, estimate the case finding rate and attempt to infer relative rates of transmission between species. We found no evidence of direct or indirect transmission from deer to human. However, with an estimated case finding rate of only 4.2%, spillback to humans cannot be ruled out. The extensive transmission of SARS-CoV-2 within deer populations and the large number of unsampled cases highlights the need for active surveillance at the human-animal interface. Citation: Willgert K, Didelot X, Surendran-Nair M, Kuchipudi SV, Ruden RM, Yon M, Nissly RH, Vandegrift KJ, Nelli RK, Li L, Jayarao BM, Levine N, Olsen RJ, Davis JJ, Musser JM, Hudson PJ, Kapur V, Conlan AJK. Transmission history of SARS-CoV-2 in humans and white-tailed deer. Sci Rep. 2022 Jul 15;12(1):12094. doi: 10.1038/s41598-022-16071-z. PMID: 35840592; To investigate whether SARS-CoV-2 spilled over into cattle in the United States, we tested 549 serum samples collected during early 2022-2023 for the presence of antibodies. We have tested the serum samples using mMultiple diagnostic assays were used to rule out the presence or absence of antibodies. In the pseudovirus neutralization assays, a proportion of serum samples (n=56 for Delta and n=48 for Omicron) showed percent inhibition of >60% and none of the samples showed >90% inhibition even at the 1:20 dilution of serum. On further rigorous testing with live virus neutralization assays, GenScript surrogate virus neutralization assays, and in-house indirect ELISA, we found 3 samples positive in sVNT (n=2 in Delta and n=1 in Omicron sVNT) and one sample positive in indirect ELISA. It indicates that there is no significant exposure or transmission of SARS-CoV-2 in cattle. Our results also warrant the rigorous testing of cattle serum samples before declaring them antibody positive (Manuscript under preparation). ?
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Ramasamy S, Gontu A, Neerukonda S, Ruggiero D, Morrow B, Gupta S, Amirthalingam S, Hardham JM, Lizer JT, Yon M, Nissly RH, Jakka P, Chothe SK, LaBella LC, Tewari D, Nair MS, Kuchipudi SV. SARS-CoV-2 Prevalence and Variant Surveillance among Cats in Pittsburgh, Pennsylvania, USA. Viruses. 2023 Jun 30;15(7):1493. doi: 10.3390/v15071493. PMID: 37515180; PMCID: PMC10386599
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Progress 07/15/21 to 07/14/22
Outputs
Target Audience:Virologists, animal health specilists, policy makers, disease ecologists, livestcok producers and indutry, wildlfie biologists, state and federal governmnet agencies and policy makers Changes/Problems:We had come challenegs initially in finidng suitable and qualifued technical perosnnel for this project due to the pandemic. What opportunities for training and professional development has the project provided?Three graduate students, four Postdoctoral Scholars, and four undergraduate researchers worked closely with the project under the direct supervision of the PI and Co-PIs. As part of the training, one graduate student and three postdocs got proficient working in a BSL-3 facility. Undergraduate students were trained on developing and validating serological assays. Sequencing, protein prediction and bioinformatics workflows were developed and standardized. How have the results been disseminated to communities of interest?The results from the antigen cartography study will be presented at the 2021 annual meeting of Conference of Research Workers in Animal Diseases (CRWAD): "Antigen cartography for the determination of historical SARS-CoV-2 variant exposure in animals using serology". CRWAD is one of the oldest and largest international research conferences featuring cutting-edge research on animal health and disease, population health, and translational medicine to veterinarians and animal health scientists. The sero-surveillance results were presented at the 2021 CRWAD annual meeting: "Development and validation of serological assays to detect the spillover of SARS-CoV-2 in livestock". Manuscripts published: Willgert, Katriina, et al. "Transmission history of SARS-CoV-2 in humans and white-tailed deer." Scientific reports 12.1 (2022): 1-9. Gontu, Abhinay, et al. "Development and Validation of Indirect Enzyme-Linked Immunosorbent Assays for Detecting Antibodies to SARS-CoV-2 in Cattle, Swine, and Chicken." Viruses 14.7 (2022): 1358. Kuchipudi, Suresh V., et al. "Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer." Proceedings of the National Academy of Sciences 119.6 (2022): e2121644119. Chen, Chen, et al. "Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2." Proceedings of the National Academy of Sciences 118.42 (2021). Results are shared with and extension veterinarians in the team who connects regularly with the livestock farmers in PA. What do you plan to do during the next reporting period to accomplish the goals?Four manuscripts are under preparation. They will be completed and submitted to peer-reviewed journals of high impact in the field of infectious diseases.
Impacts
What was accomplished under these goals?
1. Determine the susceptibility of livestock to SARS-CoV-2 1a: Investigate the comparative replication of SARS-CoV-2 isolates in livestock primary respiratory cells A remarkable feature reported with SARS-CoV-2 is the ability to infect many animal species, and multiple natural spillover events of captive and free-living animals have been documented. In particular, we others4 showed widespread natural SARS-CoV-2 infection of white tailed-deer, the most abundant large mammal species in the USA. Through computational SARS-CoV-2 Spike protein was predicted to bind strongly to deer ACE2, unlike ACE2 of cattle and pigs, and deer are highly susceptible to experimental SARS-CoV-2 infection. Whole genome sequencing of viral RNA recovered from retropharyngeal lymph node (RPLN) tissue revealed multiple spillover events into deer followed by onward transmission among deer. Additional investigations of RPLN and nasal swab specimens have since confirmed SARS-CoV-2 in multiple regions throughout the United States with viruses from ancestral B.1 lineage and Alpha, Gamma, Delta, and Omicron variants described. We have further explored relative fitness of SARS-CoV-2 variants in deer in vitro using primary deer cell culture. Fibroblasts isolated from fresh deer RPLN were established and confirmed to express high levels of ACE2. B.1, Alpha, Beta, Gamma, Delta, and Omicron variant human isolates were all found to infect deer RPLN fibroblasts (RPLNf) but differ in replication kinetics and with varying levels of infectious virus production. Beta and Alpha variants showed higher fitness in RPLNf cells and replicated to higher titers than ancestral B.1 and other variants tested. Consistent with the higher infectious titers, we found a significant (p<0.01) increase in the intracellular viral RNA in RPLNf cells infected with Alpha and Beta variants compared to wildtype. Using a negative strand PCR79 we characterized the differences in the replication efficiency of the SARS-CoV-2 variants. Alpha variant replicated faster, as evidenced by the higher total and negative strand viral RNA at 24 hours, whereas the beta variant showed a more significant temporal increase in replication as evidenced by a greater increase in total and negative strand viral RNA from 24 to 72 hours. 2.a. Seroprevalence of SARS-CoV-2 antibodies in domestic livestock and wildlife Antigen cartography is a major tool in understanding antigenic drift in influenza A virus, and its application to SARS-CoV-2 has recently been verified in large-scale studies. To implement antigen cartography for deer, we established a pseudovirus system to express the Spike protein of SARS-CoV-2 variants to test the ability of deer sera to neutralize each variant in a pseudovirus neutralization test (pVNT). Using the neutralization titers from this assay, an antigenic map representing distances between variant Spike proteins (antigens) was created with antigen positioning on par with published human antigenic maps.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Willgert, Katriina, et al. "Transmission history of SARS-CoV-2 in humans and white-tailed deer." Scientific reports 12.1 (2022): 1-9.
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Gontu, Abhinay, et al. "Development and Validation of Indirect Enzyme-Linked Immunosorbent Assays for Detecting Antibodies to SARS-CoV-2 in Cattle, Swine, and Chicken." Viruses 14.7 (2022): 1358.
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Kuchipudi, Suresh V., et al. "Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer." Proceedings of the National Academy of Sciences 119.6 (2022): e2121644119.
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Chen, Chen, et al. "Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2." Proceedings of the National Academy of Sciences 118.42 (2021).
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Progress 07/15/20 to 07/14/21
Outputs
Target Audience:Computation model for prediction of the impact of amino acid changes in SARS-CoV-2 spike protein on the infectivity of the virus has been published in the Proceedings of the National Academy of Sciences (PNS) journal to disseminate the results tothe wider scientific community. A new article was also published through Penn State News to disseminate the information to the broader general public. https://www.pnas.org/content/118/42/e2106480118 https://news.psu.edu/story/670936/2021/09/29/research/new-tool-predicts-changes-may-make-covid-variants-more-infectious Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Three graduate students, two Postdoctoral Scholars a research associate, and four undergraduate researchers worked closely with the project under the direct supervision of the PI and Co-PIs. As part of the training, all the graduate students and a postdoc got proficient working in a BSL-3 facility. Undergraduate students were trained on developing and validating serological assays. Sequencing, protein prediction, and bioinformatics workflows were developed and standardized. How have the results been disseminated to communities of interest?The sero-surveillnace results will be presented at the 2021 annual meeting of the Conference of Research Workers in Animal Diseases (CRWAD): "Development and validation of serological assays to detect the spillover of SARS-CoV-2 in livestock". CRWAD is one of the oldest and largest international research conferences featuring cutting-edge research on animal health and disease, population health, and translational medicine to veterinarians and animal health scientists. Manuscript published in PNAS:Chen, Chen, et al. "Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2." Proceedings of the National Academy of Sciences 118.42 (2021). Results are shared with extension veterinarians in the team who connects regularly with the livestock farmers in Pennsylvania. What do you plan to do during the next reporting period to accomplish the goals? Currently, we are working on developing a computational model that can predict potential SARS-CoV-2 variants that increase the infection susceptibility of livestock animals like pigs, cattle, chickens, and deer. The novel computational tool (CNN_seq) is based on a convolutional neural network and takes only the sequence of the complex formed by ACE2 and RBD as the input, which considerably accelerates training and prediction processes. This enhancement in efficiency allows the use of a much-expanded dataset covering 8440 variants with single and multiple AA changes on either ACE2 or RBD proteins, leading to an accuracy of 83.28% and a correlation coefficient r of 0.85 for the obtained model. The CNN_seq model can be transferred to the animal case by combining the sequence of animal ACE2 with RBD and scanning on possible combinations of up to 4 AA changes on RBD to identify the variants that would potentially increase the ACE2-RBD binding affinity for these livestock animals. We plan to investigate the reason for replication inhibition of SARS-CoV-2 virus in cattle, pig and chicken primary epithelial cells through strand-specific RT-PCR of cellular contents of infected cells and transcriptomics (RNASeq) to identify host and/or viral factors that limit virus multiplication in these cells. We will further explore our predicted binding activities of SARS-CoV-2 variants in experimental settings by expressing bovine, porcine, or chicken ACE2 in BHK-21 cells. Infection studies in chickens with SARS-CoV2 will be attempted as we gain a deeper understanding of the molecular basics of transmission dynamics of SARS-CoV-2 isolates in chicken primary epithelial cells. Development and validation of serological assays for understanding the spillover events in several wildlife and livestock species are currently underway. A computational model that can predict potential SARS-CoV-2 variants that increase the infection susceptibility of livestock animals like pigs, cattle, chickens and deer will be developed. Two manuscripts are under preparation. They will be completed and submitted to peer-reviewed journals of high impact in the field of infectious diseases.
Impacts
What was accomplished under these goals?
1. Determine the susceptibility of livestock to SARS-CoV-2 1a: Investigate the comparative replication of SARS-CoV-2 isolates in livestock primary respiratory cells Culture conditions for successfully growing primary cattle, pig, and chicken cells were established. Multiple attempts were made to culture SARS-CoV-2 isolates on human primary tracheal/bronchial epithelial cells. While all isolates could be cultured, the growth of all isolates in this cell type was low. To obtain high titers of human-adapted SARS-CoV-2 for subsequent experiments, a human lung epithelial cell line overexpressing human cell receptor Angiotensin-converting enzyme 2 (A549-hACE2) was used instead of the primary human cells. Each isolate was passaged three times on A549-hACE2 cells. Samples from each passage were sequenced to monitor changes to the virus as it adapted to the human cells. Bovine and porcine primary tracheal epithelial cells and chicken primary lung cells were inoculated at a multiplicity of infection (MOI) 0.1 with the indicated human-cell-adapted isolates of SARS-CoV-2 and grown for up to 144 hours. A negligible increase in viral RNA was observed in the supernatant, and human A549-hACE2 cells infected simultaneously produced a minimum of 20-fold RNA increase over the same period. In addition, all samples collected from the bovine, porcine, and chicken cells demonstrated no competent viral production, with Tissue Culture Infectious Dose 50 (TCID50) results indicating viral levels ≤ 10 TCID50/mL. Overall, none of the animal cells were susceptible to the human-adapted SARS-CoV-2. In addition, embryonated chicken eggs also failed to produce any viable SARS-CoV-2 or increased viral RNA. The three SARS-CoV-2 isolates (Hong Kong/VM20001061/2020, Italy-INMI1, and USA-WA1/2020) used in these experiments were wild-type (Wuhan) lineage. Since 2020, several distinct genetic lineages have been described, with each variant type possessing unique mutations in spike protein and other viral proteins. Our computational predictions suggested that some of these spike variants may improve or reduce the binding affinity of SARS-CoV-2 to bovine, porcine, and chicken ACE2. We decided to explore if altered binding affinity might change the ability of SARS-CoV-2 to grow in these animal cells, starting with primary bovine tracheal epithelial cells. Representative isolates of wild-type, alpha, beta, and gamma lineages were used to infect cells at MOI 1. In this case, viruses were not the first human-cell-adapted. As observed before with the human-adapted viruses, little to no viral RNA was released into the supernatant of infected cells. Concurrently, no, or negligible increase in live virus as measured by TCID50 was observed following infection with any of the variants, and the live virus was near or below the limit of detection by 72 hours post-infection. Taken together, it has been observed that bovine - possibly chicken and porcine - primary respiratory cells are not susceptible to SARS-CoV-2. We plan to investigate the reason for this finding through strand-specific RT-PCR of cellular contents of infected cells and transcriptomics (RNASeq) to identify host and/or viral factors that limit SARS-CoV-2 in these cells. We will further explore our predicted binding activities of SARS-CoV-2 variants in experimental settings by expressing bovine, porcine or chicken ACE2 in BHK-21 cells. 1b: Susceptibility of chicken to experimental SARS-CoV-2 infection. The infection studies in chickens with a SARS-CoV2 described under objective 2a is currently underway as we are attempting to understand the colonization and transmission dynamics of SARS-CoV-2 isolates in chicken primary epithelial cells. 2.a. Seroprevalence of SARS-CoV-2 antibodies in domestic livestock In this aim, we developed and validated serological assays, including an indirect ELISA and Luciferase Immunoprecipitation System (LIPS) Assay for screening cattle, pigs, and chickens. Serum samples collected before December 2019 (pre-pandemic) and from 01/2020 through 10/2021(post-pandemic) from the PADLS and our network of animal diagnostic laboratories across the US were screened for the presence of anti-SARS-CoV-2 antibodies. These specimens included samples from unhealthy animals that are being investigated for disease and samples from healthy animals as part of regulatory or other surveillance efforts by state and local entities. Hyperimmune serum comprising polyclonal anti- SARS-CoV-2 antibodies were generated in chicken, pigs, and cattle as reference controls for validation and implementation of ELISA and LIPS assays. 2b. Establishing the mutational landscape in SARS-CoV-2 quasispecies from chicken, pig, andbovine cells. We passaged three different isolates of SARS-CoV-2 from Asia, Europe, and North America (strains Hong Kong/VM20001061/2020, Italy-INMI1, and USA-WA1/2020) in pig three times, and cell culture supernatants collected from the three passages will be used to analyze the viral genome mutations by Next Generation Sequencing (NGS). Although we observed several single nucleotide polymorphisms (SNPs) throughout the genomes, significant ones favoring or worsening binding of the spike protein to the host cell surface receptor or the downstream colonization was not observed using the computational prediction models. 2c. Investigate the potential for SARS-CoV-2 adaptation in livestock Using Monte Carlo simulations and biophysical energetic analyses of the SARS-CoV-1 spike protein and SARS-CoV-2 spike protein with human ACE2 proteins, we deciphered the interactions that govern the higher infectivity of SARS-CoV-2 compared to SARS-CoV-1.1 We further used molecular dynamics simulations to delineate the plausible interaction mechanism of human ACE2 protein with its membrane-bound partner protein ATR1. The association of the receptor-binding domain (RBD) of SARS-CoV-2 viral spike with a human angiotensin-converting enzyme (hACE2) represents the first required step for viral entry. Amino acid changes in the RBD have been implicated with increased infectivity and the potential for immune evasion. Hence, reliably predicting the effect of amino acid changes in the ability of the RBD to interact more strongly with the hACE2 receptor can help assess the public health implications and the potential for spillover and adaptation into other animals. We developed a two-step framework that first relies on 48 independent 4-ns molecular dynamics (MD) trajectories of RBD-hACE2 variants to collect binding energy terms.2 The second step implements a neural network to classify and quantitatively predict binding affinity using the decomposed energy terms as descriptors. We achieved an accuracy of 82.2% in terms of correctly classifying single amino-acid substitution variants of the RBD as worsening or improving binding affinity for hACE2 and a correlation coefficient r of 0.69 between predicted and experimentally calculated binding affinities. Both metrics are calculated using a 5-fold cross-validation test. Our method thus sets up a framework for effectively screening binding affinity change with unknown single and multiple amino-acid changes. This can be a valuable tool for predicting host adaptation and zoonotic spillover of current and future SARS-CoV-2 variants.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2
Chen Chen, Veda Sheersh Boorla, Deepro Banerjee, Ratul Chowdhury, Victoria S. Cavener, Ruth H. Nissly, Abhinay Gontu, Nina R. Boyle, Kurt Vandegrift, Meera Surendran Nair, Suresh V. Kuchipudi, Costas D. Maranas
Proceedings of the National Academy of Sciences Oct 2021, 118 (42) e2106480118; DOI: 10.1073/pnas.2106480118
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