1
|
Nissly RH, Lim L, Keller MR, Bird IM, Bhushan G, Misra S, Chothe SK, Sill MC, Kumar NV, Sivakumar AVN, Naik BR, Jayarao BM, Kuchipudi SV. The Susceptibility of Chickens to Zika Virus: A Comprehensive Study on Age-Dependent Infection Dynamics and Host Responses. Viruses 2024; 16:569. [PMID: 38675911 PMCID: PMC11054531 DOI: 10.3390/v16040569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 03/22/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
Zika virus (ZIKV) remains a public health concern, with epidemics in endemic regions and sporadic outbreaks in new areas posing significant threats. Several mosquito-borne flaviviruses that can cause human illness, including West Nile, Usutu, and St. Louis encephalitis, have associations with birds. However, the susceptibility of chickens to ZIKV and their role in viral epidemiology is not currently known. We investigated the susceptibility of chickens to experimental ZIKV infection using chickens ranging from 1-day-old chicks to 6-week-old birds. ZIKV caused no clinical signs in chickens of all age groups tested. Viral RNA was detected in the blood and tissues during the first 5 days post-inoculation in 1-day and 4-day-old chicks inoculated with a high viral dose, but ZIKV was undetectable in 6-week-old birds at all timepoints. Minimal antibody responses were observed in 6-week-old birds, and while present in younger chicks, they waned by 28 days post-infection. Innate immune responses varied significantly between age groups. Robust type I interferon and inflammasome responses were measured in older chickens, while limited innate immune activation was observed in younger chicks. Signal transducer and activator of transcription 2 (STAT2) is a major driver of host restriction to ZIKV, and chicken STAT2 is distinct from human STAT2, potentially contributing to the observed resistance to ZIKV infection. The rapid clearance of the virus in older chickens coincided with an effective innate immune response, highlighting age-dependent susceptibility. Our study indicates that chickens are not susceptible to productive ZIKV infection and are unlikely to play a role in the ZIKV epidemiology.
Collapse
Affiliation(s)
- Ruth H. Nissly
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA; (R.H.N.); (L.L.); (M.R.K.); (I.M.B.); (G.B.); (B.M.J.)
| | - Levina Lim
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA; (R.H.N.); (L.L.); (M.R.K.); (I.M.B.); (G.B.); (B.M.J.)
- DermBiont, Inc., 451 D Street, Suite 908, Boston, MA 02210, USA
| | - Margo R. Keller
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA; (R.H.N.); (L.L.); (M.R.K.); (I.M.B.); (G.B.); (B.M.J.)
| | - Ian M. Bird
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA; (R.H.N.); (L.L.); (M.R.K.); (I.M.B.); (G.B.); (B.M.J.)
- Applied Biological Sciences Group, The Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - Gitanjali Bhushan
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA; (R.H.N.); (L.L.); (M.R.K.); (I.M.B.); (G.B.); (B.M.J.)
- College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
| | - Sougat Misra
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, PA 15261, USA; (S.M.); (S.K.C.)
| | - Shubhada K. Chothe
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, PA 15261, USA; (S.M.); (S.K.C.)
| | - Miranda C. Sill
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA;
| | - Nagaram Vinod Kumar
- College of Veterinary Science, Sri Venkateswara Veterinary University, Tirupati 517 602, Andhra Pradesh, India; (N.V.K.); (A.V.N.S.); (B.R.N.)
| | - A. V. N. Sivakumar
- College of Veterinary Science, Sri Venkateswara Veterinary University, Tirupati 517 602, Andhra Pradesh, India; (N.V.K.); (A.V.N.S.); (B.R.N.)
| | - B. Rambabu Naik
- College of Veterinary Science, Sri Venkateswara Veterinary University, Tirupati 517 602, Andhra Pradesh, India; (N.V.K.); (A.V.N.S.); (B.R.N.)
| | - Bhushan M. Jayarao
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA; (R.H.N.); (L.L.); (M.R.K.); (I.M.B.); (G.B.); (B.M.J.)
| | - Suresh V. Kuchipudi
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, PA 15261, USA; (S.M.); (S.K.C.)
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15261, USA
| |
Collapse
|
2
|
Panner Selvam MK, Kanagaraj V, Kathaperumal K, Nissly RH, Daly JM, Kuchipudi SV. Comparative transcriptome analysis of spleen of Newcastle Disease Virus (NDV) infected chicken and Japanese quail: a potential role of NF-κβ pathway activation in NDV resistance. Virusdisease 2023; 34:402-409. [PMID: 37780899 PMCID: PMC10533468 DOI: 10.1007/s13337-023-00833-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/18/2023] [Indexed: 10/03/2023] Open
Abstract
Newcastle disease (ND) affects a few hundred avian species including chicken and several species of domestic and wild birds. The clinical outcome of Newcastle disease virus (NDV) infection ranges from mild to severe fatal disease depending on the NDV pathotype and the host species involved. Japanese quails serve as natural reservoirs of NDV and play important role in NDV epidemiology. While infection of chicken with velogenic NDV results in severe often fatal illness, the same infection in Japanese quails results in inapparent infection. The molecular basis of this contrasting clinical outcomes of NDV infection is not yet clearly known. We compared global gene expression in spleen of chicken and Japanese quails infected with lentogenic and velogenic NDVs. We found contrasting regulation of key genes associated with NF-κB pathway and T-cell activation between chicken and Japanese quails. Our data suggests association of NDV resistance in Japanese quails to activation of NF-κB pathway and T cell proliferation. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-023-00833-y.
Collapse
Affiliation(s)
- Manesh Kumar Panner Selvam
- Department of Animal Biotechnology, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Vijayrani Kanagaraj
- Department of Animal Biotechnology, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Kumanan Kathaperumal
- Department of Animal Biotechnology, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Ruth H. Nissly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, USA
| | - Janet M. Daly
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Nottingham, UK
| | - Suresh V. Kuchipudi
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, USA
| |
Collapse
|
3
|
Li LX, Nissly RH, Swaminathan A, Bird IM, Boyle NR, Nair MS, Greenawalt DI, Gontu A, Cavener VS, Sornberger T, Freihaut JD, Kuchipudi SV, Bahnfleth WP. Inactivation of HCoV-NL63 and SARS-CoV-2 in aqueous solution by 254 nm UV-C. J Photochem Photobiol B 2023; 245:112755. [PMID: 37423001 DOI: 10.1016/j.jphotobiol.2023.112755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 05/29/2023] [Accepted: 07/03/2023] [Indexed: 07/11/2023]
Abstract
Ultraviolet germicidal irradiation (UVGI) is a highly effective means of inactivating many bacteria, viruses, and fungi. UVGI is an attractive viral mitigation strategy against coronaviruses, including the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of the coronavirus disease-2019 (COVID-19) pandemic. This investigation measures the susceptibility of two human coronaviruses to inactivation by 254 nm UV-C radiation. Human coronavirus NL63 and SARS-CoV-2 were irradiated in a collimated, dual-beam, aqueous UV reactor. By measuring fluence and integrating it in real-time, this reactor accounts for the lamp output transients during UVGI exposures. The inactivation rate constants of a one-stage exponential decay model were determined to be 2.050 cm2/mJ and 2.098 cm2/mJ for the NL63 and SARS-CoV-2 viruses, respectively. The inactivation rate constant for SARS-CoV-2 is within 2% of that of NL63, indicating that in identical inactivation environments, very similar UV 254 nm deactivation susceptibilities for these two coronaviruses would be achieved. Given the inactivation rate constant obtained in this study, doses of 1.1 mJ/cm2, 2.2 mJ/cm2, and 3.3 mJ/cm2 would result in a 90%, 99%, and 99.9% inactivation of the SARS-CoV-2 virus, respectively. The inactivation rate constant obtained in this study is significantly higher than values reported from many 254 nm studies, which suggests greater UV susceptibility to the UV-C than what was believed. Overall, results from this study indicate that 254 nm UV-C is effective for inactivation of human coronaviruses, including SARS-CoV-2.
Collapse
Affiliation(s)
- Lily X Li
- Pennsylvania State University, Department of Architectural Engineering, 104 Engineering Unit A, University Park, PA, 16802, United States of America
| | - Ruth H Nissly
- Pennsylvania State University, Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, University Park, PA 16802, United States of America
| | - Anand Swaminathan
- Pennsylvania State University, Department of Architectural Engineering, 104 Engineering Unit A, University Park, PA, 16802, United States of America
| | - Ian M Bird
- Pennsylvania State University, Huck Institutes of the Life Sciences, University Park, PA 16802, United States of America
| | - Nina R Boyle
- Pennsylvania State University, Huck Institutes of the Life Sciences, University Park, PA 16802, United States of America
| | - Meera Surendran Nair
- Pennsylvania State University, Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, University Park, PA 16802, United States of America
| | - Denver I Greenawalt
- Pennsylvania State University, Huck Institutes of the Life Sciences, University Park, PA 16802, United States of America
| | - Abhinay Gontu
- Pennsylvania State University, Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, University Park, PA 16802, United States of America
| | - Victoria S Cavener
- Pennsylvania State University, Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, University Park, PA 16802, United States of America
| | - Ty Sornberger
- Pennsylvania State University, Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, University Park, PA 16802, United States of America
| | - James D Freihaut
- Pennsylvania State University, Department of Architectural Engineering, 104 Engineering Unit A, University Park, PA, 16802, United States of America.
| | - Suresh V Kuchipudi
- Pennsylvania State University, Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, University Park, PA 16802, United States of America; Pennsylvania State University, Huck Institutes of the Life Sciences, University Park, PA 16802, United States of America.
| | - William P Bahnfleth
- Pennsylvania State University, Department of Architectural Engineering, 104 Engineering Unit A, University Park, PA, 16802, United States of America.
| |
Collapse
|
4
|
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; 15:1493. [PMID: 37515180 PMCID: PMC10386599 DOI: 10.3390/v15071493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/23/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infects many mammals, and SARS-CoV-2 circulation in nonhuman animals may increase the risk of novel variant emergence. Cats are highly susceptible to SARS-CoV-2 infection, and there were cases of virus transmission between cats and humans. The objective of this study was to assess the prevalence of SARS-CoV-2 variant infection of cats in an urban setting. We investigated the prevalence of SARS-CoV-2 variant infections in domestic and community cats in the city of Pittsburgh (n = 272). While no cats tested positive for SARS-CoV-2 viral RNA, 35 cats (12.86%) tested SARS-CoV-2-antibody-positive. Further, we compared a cat-specific experimental lateral flow assay (eLFA) and species-agnostic surrogate virus neutralization assay (sVNT) for SARS-CoV-2 antibody detection in cats (n = 71). The eLFA demonstrated 100% specificity compared to sVNT. The eLFA also showed 100% sensitivity for sera with >90% inhibition and 63.63% sensitivity for sera with 40-89% inhibition in sVNT. Using a variant-specific pseudovirus neutralization assay (pVNT) and antigen cartography, we found the presence of antibodies to pre-Omicron and Omicron SARS-CoV-2 variants. Hence, this approach proves valuable in identifying cat exposure to different SARS-CoV-2 variants. Our results highlight the continued exposure of cats to SARS-CoV-2 and warrant coordinated surveillance efforts.
Collapse
Affiliation(s)
- Santhamani Ramasamy
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Abhinay Gontu
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | | | - Diana Ruggiero
- S.R. Scientific LLC, 5854 Ellsworth Ave., Pittsburgh, PA 15232, USA
| | - Becky Morrow
- S.R. Scientific LLC, 5854 Ellsworth Ave., Pittsburgh, PA 15232, USA
- Frankie's Friends, 740 5th Ave, New Kensington, PA 15068, USA
| | - Sheweta Gupta
- S.R. Scientific LLC, 5854 Ellsworth Ave., Pittsburgh, PA 15232, USA
| | - Saranya Amirthalingam
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | | | | | - Michele Yon
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Ruth H Nissly
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Padmaja Jakka
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Shubhada K Chothe
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Lindsey C LaBella
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Deepanker Tewari
- Pennsylvania Department of Agriculture, Pennsylvania Veterinary Laboratory, Harrisburg, PA 17110, USA
| | - Meera Surendran Nair
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Suresh V Kuchipudi
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Huck Institute of Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| |
Collapse
|
5
|
Chothe SK, Byukusenge M, Sekhwal MK, Li L, LaBella LC, Jakka P, Palchak K, Barry R, Yon M, Nissly RH, Kelly KM, Jayarao BM, Surendran Nair M, Kuchipudi SV. Complete Genome Sequence of a Bovine Coronavirus Isolated from a Goat in Pennsylvania, USA. Microbiol Resour Announc 2023:e0012223. [PMID: 37133378 DOI: 10.1128/mra.00122-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
We report a complete genome sequence of bovine coronavirus (BCoV) isolated from a goat in the state of Pennsylvania in 2022. BCoV often causes calf scours and winter dysentery in cattle.
Collapse
Affiliation(s)
- Shubhada K Chothe
- Pennsylvania State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Maurice Byukusenge
- Pennsylvania State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Manoj K Sekhwal
- Pennsylvania State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Lingling Li
- Pennsylvania State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Lindsey Cecelia LaBella
- Pennsylvania State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Padmaja Jakka
- Pennsylvania State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Kay Palchak
- Pennsylvania State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Rhiannon Barry
- Pennsylvania State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Michele Yon
- Pennsylvania State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Ruth H Nissly
- Pennsylvania State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Kathleen M Kelly
- Pennsylvania State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Bhushan M Jayarao
- Pennsylvania State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Meera Surendran Nair
- Pennsylvania State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Suresh V Kuchipudi
- Pennsylvania State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| |
Collapse
|
6
|
Chothe SK, Jakka P, Boorla VS, Ramasamy S, Gontu A, Nissly RH, Brown J, Turner G, Sewall BJ, Reeder DM, Field KA, Engiles JB, Amirthalingam S, Ravichandran A, LaBella L, Nair MS, Maranas CD, Kuchipudi SV. Little Brown Bats ( Myotis lucifugus) Support the Binding of SARS-CoV-2 Spike and Are Likely Susceptible to SARS-CoV-2 Infection. Viruses 2023; 15:v15051103. [PMID: 37243189 DOI: 10.3390/v15051103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), believed to have originated from a bat species, can infect a wide range of non-human hosts. Bats are known to harbor hundreds of coronaviruses capable of spillover into human populations. Recent studies have shown a significant variation in the susceptibility among bat species to SARS-CoV-2 infection. We show that little brown bats (LBB) express angiotensin-converting enzyme 2 receptor and the transmembrane serine protease 2, which are accessible to and support SARS-CoV-2 binding. All-atom molecular dynamics (MD) simulations revealed that LBB ACE2 formed strong electrostatic interactions with the RBD similar to human and cat ACE2 proteins. In summary, LBBs, a widely distributed North American bat species, could be at risk of SARS-CoV-2 infection and potentially serve as a natural reservoir. Finally, our framework, combining in vitro and in silico methods, is a useful tool to assess the SARS-CoV-2 susceptibility of bats and other animal species.
Collapse
Affiliation(s)
- Shubhada K Chothe
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Padmaja Jakka
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Veda Sheersh Boorla
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Santhamani Ramasamy
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Abhinay Gontu
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Ruth H Nissly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Justin Brown
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Pennsylvania Game Commission, 2001 Elmerton Ave, Harrisburg, PA 17110, USA
| | - Gregory Turner
- Pennsylvania Game Commission, 2001 Elmerton Ave, Harrisburg, PA 17110, USA
| | - Brent J Sewall
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - DeeAnn M Reeder
- Department of Biology, Bucknell University, Lewisburg, PA 17837, USA
| | - Kenneth A Field
- Department of Biology, Bucknell University, Lewisburg, PA 17837, USA
| | - Julie B Engiles
- Departments of Pathobiology and Clinical Studies, New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, PA 19348, USA
| | - Saranya Amirthalingam
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Abirami Ravichandran
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lindsey LaBella
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Meera Surendran Nair
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Suresh V Kuchipudi
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| |
Collapse
|
7
|
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; 14:v14122770. [PMID: 36560774 PMCID: PMC9785669 DOI: 10.3390/v14122770] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/19/2022] [Accepted: 12/01/2022] [Indexed: 12/15/2022] Open
Abstract
There is mounting evidence of SARS-CoV-2 spillover from humans into many domestic, companion, and wild animal species. Research indicates that humans have infected white-tailed deer, and that deer-to-deer transmission has occurred, indicating that deer could be a wildlife reservoir and a source of novel SARS-CoV-2 variants. We examined the hypothesis that the Omicron variant is actively and asymptomatically infecting the free-ranging deer of New York City. Between December 2021 and February 2022, 155 deer on Staten Island, New York, were anesthetized and examined for gross abnormalities and illnesses. Paired nasopharyngeal swabs and blood samples were collected and analyzed for the presence of SARS-CoV-2 RNA and antibodies. 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. Variants of concern continue to circulate among and may reinfect US deer populations, and establish enzootic transmission cycles in the wild: this warrants a coordinated One Health response, to proactively surveil, identify, and curtail variants of concern before they can spill back into humans.
Collapse
Affiliation(s)
- Kurt J. Vandegrift
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- The Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Correspondence: (K.J.V.); (V.K.); (S.V.K.); Tel.: +1-814-574-9852 (K.J.V.); +1-814-865-9788 (V.K.); +1-814-863-4436 (S.V.K.)
| | - Michele Yon
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Meera Surendran Nair
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Abhinay Gontu
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Santhamani Ramasamy
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Saranya Amirthalingam
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | | | - Ruth H. Nissly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Shubhada K. Chothe
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Padmaja Jakka
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lindsey LaBella
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Nicole Levine
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - Sophie Rodriguez
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - Chen Chen
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Veda Sheersh Boorla
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Tod Stuber
- National Veterinary Services Laboratories, Veterinary Services, U.S. Department of Agriculture, Ames, IA 50010, USA
| | | | | | | | - Richard Simon
- City of New York Parks & Recreation, New York, NY 10029, USA
| | - Katrina L. Toal
- City of New York Parks & Recreation, New York, NY 10029, USA
| | - Randall J. Olsen
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX 77030, USA
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - James J. Davis
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA
- Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Dashzeveg Bold
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Natasha N. Gaudreault
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Krishani Dinali Perera
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Yunjeong Kim
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Costas D. Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Juergen A. Richt
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - James M. Musser
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX 77030, USA
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Peter J. Hudson
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- The Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Vivek Kapur
- The Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA
- Correspondence: (K.J.V.); (V.K.); (S.V.K.); Tel.: +1-814-574-9852 (K.J.V.); +1-814-865-9788 (V.K.); +1-814-863-4436 (S.V.K.)
| | - Suresh V. Kuchipudi
- The Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Correspondence: (K.J.V.); (V.K.); (S.V.K.); Tel.: +1-814-574-9852 (K.J.V.); +1-814-865-9788 (V.K.); +1-814-863-4436 (S.V.K.)
| |
Collapse
|
8
|
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; 12:12094. [PMID: 35840592 PMCID: PMC9284484 DOI: 10.1038/s41598-022-16071-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/04/2022] [Indexed: 11/30/2022] Open
Abstract
The emergence of a novel pathogen in a susceptible population can cause rapid spread of infection. 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 prioritisation 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.
Collapse
Affiliation(s)
- Katriina Willgert
- Disease Dynamics Unit (DDU), Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, UK
| | - Meera Surendran-Nair
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.,Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Suresh V Kuchipudi
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.,Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Rachel M Ruden
- Wildlife Bureau, Iowa Department of Natural Resources, Des Moines, IA, USA.,Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Michele Yon
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Ruth H Nissly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.,Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Kurt J Vandegrift
- The Center for Infectious Disease Dynamics, Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Rahul K Nelli
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Lingling Li
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Bhushan M Jayarao
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Nicole Levine
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Animal Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Randall J Olsen
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, 77030, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, 10021, USA.,Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10021, USA
| | - James J Davis
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, USA.,Division of Data Science and Learning, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - James M Musser
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, 77030, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, 10021, USA.,Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10021, USA
| | - Peter J Hudson
- The Center for Infectious Disease Dynamics, Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Vivek Kapur
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Animal Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Andrew J K Conlan
- Disease Dynamics Unit (DDU), Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| |
Collapse
|
9
|
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; 14:v14071358. [PMID: 35891340 PMCID: PMC9317974 DOI: 10.3390/v14071358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 02/04/2023] Open
Abstract
Multiple domestic and wild animal species are susceptible to SARS-CoV-2 infection. Cattle and swine are susceptible to experimental SARS-CoV-2 infection. The unchecked transmission of SARS-CoV-2 in animal hosts could lead to virus adaptation and the emergence of novel variants. In addition, the spillover and subsequent adaptation of SARS-CoV-2 in livestock could significantly impact food security as well as animal and public health. Therefore, it is essential to monitor livestock species for SARS-CoV-2 spillover. 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. Serum samples collected prior to the COVID-19 pandemic were used to determine the cut-off threshold. 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. The iELISAs for cattle, swine, and chicken were found to have 100% sensitivity and specificity. These tools facilitate the surveillance that is necessary to quickly identify spillovers into the three most important agricultural species worldwide.
Collapse
Affiliation(s)
- Abhinay Gontu
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (R.H.N.); (K.K.)
| | - Erika A. Marlin
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
- Clinical & Diagnostic Assay Development Group, Pfizer, Pearl River, NY 10965, USA
| | - Santhamani Ramasamy
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
| | | | - Gayatri Anil
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
| | - Jasmine Morgan
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
| | - Meysoon Quraishi
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
| | - Chen Chen
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA; (C.C.); (V.S.B.); (C.D.M.)
| | - Veda Sheersh Boorla
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA; (C.C.); (V.S.B.); (C.D.M.)
| | - Ruth H. Nissly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (R.H.N.); (K.K.)
| | - Padmaja Jakka
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (R.H.N.); (K.K.)
| | - Shubhada K. Chothe
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
| | - Abirami Ravichandran
- Department of Integrative and Biomedical Physiology, The Pennsylvania State University, University Park, PA 16802, USA;
| | - Nishitha Kodali
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
- Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.M.M.); (R.M.R.); (S.E.L.); (V.K.); (K.J.V.)
| | - Saranya Amirthalingam
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
- Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.M.M.); (R.M.R.); (S.E.L.); (V.K.); (K.J.V.)
| | - Lindsey LaBella
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
| | - Kathleen Kelly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (R.H.N.); (K.K.)
| | - Pazhanivel Natesan
- Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600007, India;
| | - Allen M. Minns
- Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.M.M.); (R.M.R.); (S.E.L.); (V.K.); (K.J.V.)
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Randall M. Rossi
- Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.M.M.); (R.M.R.); (S.E.L.); (V.K.); (K.J.V.)
| | - Jacob R. Werner
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA;
| | - Ernest Hovingh
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
| | - Scott E. Lindner
- Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.M.M.); (R.M.R.); (S.E.L.); (V.K.); (K.J.V.)
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Deepanker Tewari
- Pennsylvania Department of Agriculture, Pennsylvania Veterinary Laboratory, Harrisburg, PA 17110, USA;
| | - Vivek Kapur
- Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.M.M.); (R.M.R.); (S.E.L.); (V.K.); (K.J.V.)
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802, USA;
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kurt J. Vandegrift
- Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.M.M.); (R.M.R.); (S.E.L.); (V.K.); (K.J.V.)
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Costas D. Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA; (C.C.); (V.S.B.); (C.D.M.)
| | - Meera Surendran Nair
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (R.H.N.); (K.K.)
- Correspondence: (M.S.N.); (S.V.K.)
| | - Suresh V. Kuchipudi
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.G.); (E.A.M.); (S.R.); (G.A.); (J.M.); (M.Q.); (P.J.); (S.K.C.); (N.K.); (S.A.); (L.L.); (E.H.)
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (R.H.N.); (K.K.)
- Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA; (A.M.M.); (R.M.R.); (S.E.L.); (V.K.); (K.J.V.)
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802, USA
- Correspondence: (M.S.N.); (S.V.K.)
| |
Collapse
|
10
|
Ravichandran A, Nissly RH, Chothe S, Jakka P, Kuchipudi SV. Characterization of a Novel Oncolytic Virus for Cancer Therapy. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r3158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Abirami Ravichandran
- Integrative and Biomedical PhysiologyPennsylvania State UniversityUniversity ParkPA
- Veterinary and Biomedical Sciences and the Huck Institutes of Life SciencesPennsylvania State UniversityUniversity ParkPA
| | - Ruth H. Nissly
- Veterinary and Biomedical Sciences and the Huck Institutes of Life SciencesPennsylvania State UniversityUniversity ParkPA
| | - Shubhada Chothe
- Veterinary and Biomedical Sciences and the Huck Institutes of Life SciencesPennsylvania State UniversityUniversity ParkPA
| | - Padmaja Jakka
- Veterinary and Biomedical Sciences and the Huck Institutes of Life SciencesPennsylvania State UniversityUniversity ParkPA
| | - Suresh V. Kuchipudi
- Integrative and Biomedical PhysiologyPennsylvania State UniversityUniversity ParkPA
- Department of Veterinary and Biomedical SciencesHuck Institutes of Life SciencesPennsylvania State UniversityUniversity ParkPA
| |
Collapse
|
11
|
Chen C, Boorla VS, Chowdhury R, Nissly RH, Gontu A, Chothe SK, LaBella L, Jakka P, Ramasamy S, Vandegrift KJ, Nair MS, Kuchipudi SV, Maranas CD. A CNN model for predicting binding affinity changes between SARS-CoV-2 spike RBD variants and ACE2 homologues. bioRxiv 2022:2022.03.22.485413. [PMID: 35350198 PMCID: PMC8963690 DOI: 10.1101/2022.03.22.485413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The cellular entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) involves the association of its receptor binding domain (RBD) with human angiotensin converting enzyme 2 (hACE2) as the first crucial step. Efficient and reliable prediction of RBD-hACE2 binding affinity changes upon amino acid substitutions can be valuable for public health surveillance and monitoring potential spillover and adaptation into non-human species. Here, we introduce a convolutional neural network (CNN) model trained on protein sequence and structural features to predict experimental RBD-hACE2 binding affinities of 8,440 variants upon single and multiple amino acid substitutions in the RBD or ACE2. The model achieves a classification accuracy of 83.28% and a Pearson correlation coefficient of 0.85 between predicted and experimentally calculated binding affinities in five-fold cross-validation tests and predicts improved binding affinity for most circulating variants. We pro-actively used the CNN model to exhaustively screen for novel RBD variants with combinations of up to four single amino acid substitutions and suggested candidates with the highest improvements in RBD-ACE2 binding affinity for human and animal ACE2 receptors. We found that the binding affinity of RBD variants against animal ACE2s follows similar trends as those against human ACE2. White-tailed deer ACE2 binds to RBD almost as tightly as human ACE2 while cattle, pig, and chicken ACE2s bind weakly. The model allows testing whether adaptation of the virus for increased binding with other animals would cause concomitant increases in binding with hACE2 or decreased fitness due to adaptation to other hosts.
Collapse
Affiliation(s)
- Chen Chen
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Veda Sheersh Boorla
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Ratul Chowdhury
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Ruth H. Nissly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Abhinay Gontu
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Shubhada K. Chothe
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lindsey LaBella
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Padmaja Jakka
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Santhamani Ramasamy
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kurt J. Vandegrift
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Meera Surendran Nair
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Suresh V. Kuchipudi
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Costas D. Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| |
Collapse
|
12
|
Vandegrift KJ, Yon M, Surendran-Nair M, Gontu A, Amirthalingam S, Nissly RH, Levine N, Stuber T, DeNicola AJ, Boulanger JR, Kotschwar N, Aucoin SG, Simon R, Toal K, Olsen RJ, Davis JJ, Bold D, Gaudreault NN, Richt JA, Musser JM, Hudson PJ, Kapur V, Kuchipudi SV. Detection of SARS-CoV-2 Omicron variant (B.1.1.529) infection of white-tailed deer. bioRxiv 2022:2022.02.04.479189. [PMID: 35169802 PMCID: PMC8845426 DOI: 10.1101/2022.02.04.479189] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
White-tailed deer ( Odocoileus virginianus ) are highly susceptible to infection by SARS-CoV-2, with multiple reports of widespread spillover of virus from humans to free-living deer. While the recently emerged SARS-CoV-2 B.1.1.529 Omicron variant of concern (VoC) has been shown to be notably more transmissible amongst humans, its ability to cause infection and spillover to non-human animals remains a challenge of concern. We found that 19 of the 131 (14.5%; 95% CI: 0.10-0.22) white-tailed deer opportunistically sampled on Staten Island, New York, between December 12, 2021, and January 31, 2022, were positive for SARS-CoV-2 specific serum antibodies using a surrogate virus neutralization assay, indicating prior exposure. The results also revealed strong evidence of age-dependence in antibody prevalence. A significantly (χ 2 , p < 0.001) greater proportion of yearling deer possessed neutralizing antibodies as compared with fawns (OR=12.7; 95% CI 4-37.5). Importantly, SARS-CoV-2 nucleic acid was detected in nasal swabs from seven of 68 (10.29%; 95% CI: 0.0-0.20) of the sampled deer, and whole-genome sequencing identified the SARS-CoV-2 Omicron VoC (B.1.1.529) is circulating amongst the white-tailed deer on Staten Island. Phylogenetic analyses revealed the deer Omicron sequences clustered closely with other, recently reported Omicron sequences recovered from infected humans in New York City and elsewhere, consistent with human to deer spillover. Interestingly, one individual deer was positive for viral RNA and had a high level of neutralizing antibodies, suggesting either rapid serological conversion during an ongoing infection or a "breakthrough" infection in a previously exposed animal. Together, our findings show that the SARS-CoV-2 B.1.1.529 Omicron VoC can infect white-tailed deer and highlights an urgent need for comprehensive surveillance of susceptible animal species to identify ecological transmission networks and better assess the potential risks of spillback to humans. KEY FINDINGS These studies provide strong evidence of infection of free-living white-tailed deer with the SARS-CoV-2 B.1.1.529 Omicron variant of concern on Staten Island, New York, and highlight an urgent need for investigations on human-to-animal-to-human spillovers/spillbacks as well as on better defining the expanding host-range of SARS-CoV-2 in non-human animals and the environment.
Collapse
Affiliation(s)
- Kurt J. Vandegrift
- The Center for Infectious Disease Dynamics, Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Michele Yon
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences and Huck Institutes of the Life Sciences, The Pennsylvania State University, PA,16802, USA
| | - Meera Surendran-Nair
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences and Huck Institutes of the Life Sciences, The Pennsylvania State University, PA,16802, USA
| | - Abhinay Gontu
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences and Huck Institutes of the Life Sciences, The Pennsylvania State University, PA,16802, USA
| | - Saranya Amirthalingam
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences and Huck Institutes of the Life Sciences, The Pennsylvania State University, PA,16802, USA
| | - Ruth H. Nissly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences and Huck Institutes of the Life Sciences, The Pennsylvania State University, PA,16802, USA
| | - Nicole Levine
- Department of Animal Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Tod Stuber
- National Veterinary Services Laboratories, Veterinary Services, U.S. Department of Agriculture, Ames, Iowa, USA
| | | | | | | | - Sarah Grimké Aucoin
- City of New York Parks & Recreation, 1234 5 Avenue, 5 Floor, New York, NY 10029, USA
| | - Richard Simon
- City of New York Parks & Recreation, 1234 5 Avenue, 5 Floor, New York, NY 10029, USA
| | - Katrina Toal
- City of New York Parks & Recreation, 1234 5 Avenue, 5 Floor, New York, NY 10029, USA
| | - Randall J. Olsen
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX 77030, USA
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, NY 10021, USA
| | - James J. Davis
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago and Division of Data Science and Learning, Argonne National Laboratory, Argonne, Illinois, USA
| | - Dashzeveg Bold
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Natasha N. Gaudreault
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - Juergen A. Richt
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS, USA
| | - James M. Musser
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX 77030, USA
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, NY 10021, USA
| | - Peter J. Hudson
- The Center for Infectious Disease Dynamics, Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Vivek Kapur
- Department of Animal Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Suresh V. Kuchipudi
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences and Huck Institutes of the Life Sciences, The Pennsylvania State University, PA,16802, USA
| |
Collapse
|
13
|
Mabrouk MT, Chiem K, Rujas E, Huang WC, Jahagirdar D, Quinn B, Surendran Nair M, Nissly RH, Cavener VS, Boyle NR, Sornberger TA, Kuchipudi SV, Ortega J, Julien JP, Martinez-Sobrido L, Lovell J. Lyophilized, thermostable Spike or RBD immunogenic liposomes induce protective immunity against SARS-CoV-2 in mice. Sci Adv 2021; 7:eabj1476. [PMID: 34851667 PMCID: PMC8635435 DOI: 10.1126/sciadv.abj1476] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 10/12/2021] [Indexed: 05/22/2023]
Abstract
The COVID-19 pandemic has spurred interest in potent and thermostable SARS-CoV-2 vaccines. Here, we assess low-dose immunization with lyophilized nanoparticles decorated with recombinant SARS-CoV-2 antigens. The SARS-CoV-2 Spike glycoprotein or its receptor-binding domain (RBD; mouse vaccine dose, 0.1 μg) was displayed on liposomes incorporating a particle-inducing lipid, cobalt porphyrin-phospholipid (dose, 0.4 μg), along with monophosphoryl lipid A (dose, 0.16 μg) and QS-21 (dose, 0.16 μg). Following optimization of lyophilization conditions, Spike or RBD-decorated liposomes were effectively reconstituted and maintained conformational capacity for binding human angiotensin-converting enzyme 2 (hACE2) for at least a week when stored at 60°C in lyophilized but not liquid format. Prime-boost intramuscular vaccination of hACE2-transgenic mice with the reconstituted vaccine formulations induced effective antibody responses that inhibited RBD binding to hACE2 and neutralized pseudotyped and live SARS-CoV-2. Two days following viral challenge, immunized transgenic mice cleared the virus and were fully protected from lethal disease.
Collapse
Affiliation(s)
- Moustafa T. Mabrouk
- Department of Biomedical Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Kevin Chiem
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Edurne Rujas
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Wei-Chiao Huang
- Department of Biomedical Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Dushyant Jahagirdar
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
| | - Breandan Quinn
- Department of Biomedical Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Meera Surendran Nair
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Ruth H. Nissly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Victoria S. Cavener
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Nina R. Boyle
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Ty A. Sornberger
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Suresh V. Kuchipudi
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Joaquin Ortega
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
| | - Jean-Philippe Julien
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
- Departments of Biochemistry and Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | - Jonathan Lovell
- Department of Biomedical Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
- Corresponding author.
| |
Collapse
|
14
|
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; 118:e2106480118. [PMID: 34588290 PMCID: PMC8594574 DOI: 10.1073/pnas.2106480118] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 01/22/2023] Open
Abstract
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 introduce 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. The computational base achieves a validation accuracy of 82.8% for classifying single-amino acid substitution variants of the RBD as worsening or improving binding affinity for hACE2 and a correlation coefficient of 0.73 between predicted and experimentally calculated changes in binding affinities. Both metrics are calculated using a fivefold cross-validation test. Our method thus sets up a framework for screening binding affinity changes caused by unknown single- and multiple-amino acid changes offering a valuable tool to predict host adaptation of SARS-CoV-2 variants toward tighter hACE2 binding.
Collapse
Affiliation(s)
- Chen Chen
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802
| | - Veda Sheersh Boorla
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802
| | - Deepro Banerjee
- The Bioinformatics and Genomics Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Ratul Chowdhury
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802
| | - Victoria S Cavener
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Ruth H Nissly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Abhinay Gontu
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Nina R Boyle
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Kurt Vandegrift
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802
| | - Meera Surendran Nair
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Suresh V Kuchipudi
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802;
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802;
| |
Collapse
|
15
|
Kumar R, Christensen ND, Kaddis Maldonado RJ, Bewley MC, Ostman A, Sudol M, Chen EC, Buchkovich NW, Gontu A, Surendran Nair M, Nissly RH, Minns AM, Kapur V, Rossi R, Kuchipudi SV, Lindner SE, Parent LJ, Flanagan JM, Buchkovich NJ. Monoclonal Antibodies to S and N SARS-CoV-2 Proteins as Probes to Assess Structural and Antigenic Properties of Coronaviruses. Viruses 2021; 13:v13101899. [PMID: 34696329 PMCID: PMC8537396 DOI: 10.3390/v13101899] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/08/2021] [Accepted: 09/17/2021] [Indexed: 01/18/2023] Open
Abstract
Antibodies targeting the spike (S) and nucleocapsid (N) proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are essential tools. In addition to important roles in the treatment and diagnosis of infection, the availability of high-quality specific antibodies for the S and N proteins is essential to facilitate basic research of virus replication and in the characterization of mutations responsible for variants of concern. We have developed panels of mouse and rabbit monoclonal antibodies (mAbs) to the SARS-CoV-2 spike receptor-binding domain (S-RBD) and N protein for functional and antigenic analyses. The mAbs to the S-RBD were tested for neutralization of native SARS-CoV-2, with several exhibiting neutralizing activity. The panels of mAbs to the N protein were assessed for cross-reactivity with the SARS-CoV and Middle East respiratory syndrome (MERS)-CoV N proteins and could be subdivided into sets that showed unique specificity for SARS-CoV-2 N protein, cross-reactivity between SARS-CoV-2 and SARS-CoV N proteins only, or cross-reactivity to all three coronavirus N proteins tested. Partial mapping of N-reactive mAbs were conducted using truncated fragments of the SARS-CoV-2 N protein and revealed near complete coverage of the N protein. Collectively, these sets of mouse and rabbit monoclonal antibodies can be used to examine structure/function studies for N proteins and to define the surface location of virus neutralizing epitopes on the RBD of the S protein.
Collapse
Affiliation(s)
- Rinki Kumar
- Department of Microbiology & Immunology, Penn State College of Medicine, Hershey, PA 17033, USA; (R.K.); (A.O.); (N.W.B.); (L.J.P.)
| | - Neil D. Christensen
- Department of Pathology, Penn State College of Medicine, Hershey, PA 17033, USA
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; (R.H.N.); (A.M.M.); (V.K.); (R.R.); (S.V.K.); (S.E.L.); (J.M.F.)
- Correspondence: (N.D.C.); (N.J.B.)
| | - Rebecca J. Kaddis Maldonado
- Department of Medicine, Penn State College of Medicine, Hershey, PA 17033, USA; (R.J.K.M.); (M.S.); (E.C.C.)
| | - Maria C. Bewley
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA;
| | - Alexandria Ostman
- Department of Microbiology & Immunology, Penn State College of Medicine, Hershey, PA 17033, USA; (R.K.); (A.O.); (N.W.B.); (L.J.P.)
| | - Malgorzata Sudol
- Department of Medicine, Penn State College of Medicine, Hershey, PA 17033, USA; (R.J.K.M.); (M.S.); (E.C.C.)
| | - Eunice C. Chen
- Department of Medicine, Penn State College of Medicine, Hershey, PA 17033, USA; (R.J.K.M.); (M.S.); (E.C.C.)
| | - Natalie W. Buchkovich
- Department of Microbiology & Immunology, Penn State College of Medicine, Hershey, PA 17033, USA; (R.K.); (A.O.); (N.W.B.); (L.J.P.)
| | - Abhinay Gontu
- Department of Veterinary and Biomedical Sciences, Penn State University, University Park, PA 16802, USA; (A.G.); (M.S.N.)
| | - Meera Surendran Nair
- Department of Veterinary and Biomedical Sciences, Penn State University, University Park, PA 16802, USA; (A.G.); (M.S.N.)
| | - Ruth H. Nissly
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; (R.H.N.); (A.M.M.); (V.K.); (R.R.); (S.V.K.); (S.E.L.); (J.M.F.)
- Department of Veterinary and Biomedical Sciences, Penn State University, University Park, PA 16802, USA; (A.G.); (M.S.N.)
| | - Allen M. Minns
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; (R.H.N.); (A.M.M.); (V.K.); (R.R.); (S.V.K.); (S.E.L.); (J.M.F.)
- Department of Animal Science, Penn State University, University Park, PA 16802, USA
| | - Vivek Kapur
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; (R.H.N.); (A.M.M.); (V.K.); (R.R.); (S.V.K.); (S.E.L.); (J.M.F.)
- Department of Animal Science, Penn State University, University Park, PA 16802, USA
| | - Randall Rossi
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; (R.H.N.); (A.M.M.); (V.K.); (R.R.); (S.V.K.); (S.E.L.); (J.M.F.)
| | - Suresh V. Kuchipudi
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; (R.H.N.); (A.M.M.); (V.K.); (R.R.); (S.V.K.); (S.E.L.); (J.M.F.)
- Department of Veterinary and Biomedical Sciences, Penn State University, University Park, PA 16802, USA; (A.G.); (M.S.N.)
| | - Scott E. Lindner
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; (R.H.N.); (A.M.M.); (V.K.); (R.R.); (S.V.K.); (S.E.L.); (J.M.F.)
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA
| | - Leslie J. Parent
- Department of Microbiology & Immunology, Penn State College of Medicine, Hershey, PA 17033, USA; (R.K.); (A.O.); (N.W.B.); (L.J.P.)
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; (R.H.N.); (A.M.M.); (V.K.); (R.R.); (S.V.K.); (S.E.L.); (J.M.F.)
- Department of Medicine, Penn State College of Medicine, Hershey, PA 17033, USA; (R.J.K.M.); (M.S.); (E.C.C.)
| | - John M. Flanagan
- Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA; (R.H.N.); (A.M.M.); (V.K.); (R.R.); (S.V.K.); (S.E.L.); (J.M.F.)
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA;
| | - Nicholas J. Buchkovich
- Department of Microbiology & Immunology, Penn State College of Medicine, Hershey, PA 17033, USA; (R.K.); (A.O.); (N.W.B.); (L.J.P.)
- Correspondence: (N.D.C.); (N.J.B.)
| |
Collapse
|
16
|
Kuchipudi SV, Yon M, Surendran Nair M, Byukusenge M, Barry RM, Nissly RH, Williams J, Pierre T, Mathews T, Walner-Pendleton E, Dunn P, Barnhart D, Loughrey S, Davison S, Kelly DJ, Tewari D, Jayarao BM. A Highly Sensitive and Specific Probe-Based Real-Time PCR for the Detection of Avibacterium paragallinarum in Clinical Samples From Poultry. Front Vet Sci 2021; 8:609126. [PMID: 33912603 PMCID: PMC8071849 DOI: 10.3389/fvets.2021.609126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/10/2021] [Indexed: 11/30/2022] Open
Abstract
Avibacterium paragallinarum (historically called Hemophilus paragallinarum) causes infectious coryza (IC), which is an acute respiratory disease of chickens. Recently, outbreaks of IC have been reported in Pennsylvania (PA) in broilers, layer pullets, and laying hens, causing significant respiratory disease and production losses. A tentative diagnosis of IC can be made based on history, clinical signs, and characteristic gross lesions. However, isolation and identification of the organism are required for a definitive diagnosis. Major challenges with the bacteriological diagnosis of A. paragallinarum include that the organism is difficult to isolate, slow-growing, and can only be successfully isolated during the acute stage of infection and secondary bacterial infections are also common. As there were very limited whole genomes of A. paragallinarum in the public databases, we carried out whole-genome sequencing (WGS) of PA isolates and based on the WGS data analysis; we designed a novel probe-based PCR assay targeting a highly conserved sequence in the recN, the DNA repair protein gene of A. paragallinarum. The assay includes an internal control, with a limit of detection (LOD) of 3.93 genomic copies. The PCR efficiency ranged between 90 and 97%, and diagnostic sensitivity of 98.5% compared with conventional gel-based PCR. The test was highly specific, and no cross-reactivity was observed with other species of Avibacterium and a range of other common poultry respiratory viral and bacterial pathogens. Real-time PCR testing on 419 clinical samples from suspected flocks yielded 94 positives and 365 negatives in agreement with diagnostic bacterial culture-based detection. We also compared the recN PCR assay with a previous HPG-2 based real-time PCR assay which showed a PCR efficiency of 79%.
Collapse
Affiliation(s)
- Suresh V Kuchipudi
- Animal Diagnostic Laboratory, Pennsylvania State University, University Park, PA, United States.,Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, United States
| | - Michele Yon
- Animal Diagnostic Laboratory, Pennsylvania State University, University Park, PA, United States
| | - Meera Surendran Nair
- Animal Diagnostic Laboratory, Pennsylvania State University, University Park, PA, United States
| | - Maurice Byukusenge
- Animal Diagnostic Laboratory, Pennsylvania State University, University Park, PA, United States
| | - Rhiannon M Barry
- Animal Diagnostic Laboratory, Pennsylvania State University, University Park, PA, United States
| | - Ruth H Nissly
- Animal Diagnostic Laboratory, Pennsylvania State University, University Park, PA, United States
| | - Jen Williams
- Animal Diagnostic Laboratory, Pennsylvania State University, University Park, PA, United States
| | - Traci Pierre
- Animal Diagnostic Laboratory, Pennsylvania State University, University Park, PA, United States
| | - Tammy Mathews
- Animal Diagnostic Laboratory, Pennsylvania State University, University Park, PA, United States
| | - Eva Walner-Pendleton
- Animal Diagnostic Laboratory, Pennsylvania State University, University Park, PA, United States
| | - Patricia Dunn
- Animal Diagnostic Laboratory, Pennsylvania State University, University Park, PA, United States
| | - Denise Barnhart
- Pennsylvania Animal Diagnostic Laboratory, New Bolton Center, University of Pennsylvania, Philadelphia, PA, United States
| | - Sean Loughrey
- Pennsylvania Animal Diagnostic Laboratory, New Bolton Center, University of Pennsylvania, Philadelphia, PA, United States
| | - Sherrill Davison
- Pennsylvania Animal Diagnostic Laboratory, New Bolton Center, University of Pennsylvania, Philadelphia, PA, United States
| | - Dona J Kelly
- Pennsylvania Animal Diagnostic Laboratory, New Bolton Center, University of Pennsylvania, Philadelphia, PA, United States
| | - Deepanker Tewari
- Pennsylvania Veterinary Laboratory, Harrisburg, PA, United States
| | - Bhushan M Jayarao
- Animal Diagnostic Laboratory, Pennsylvania State University, University Park, PA, United States
| |
Collapse
|
17
|
Goike J, Hsieh CL, Horton A, Gardner EC, Bartzoka F, Wang N, Javanmardi K, Herbert A, Abbassi S, Renberg R, Johanson MJ, Cardona JA, Segall-Shapiro T, Zhou L, Nissly RH, Gontu A, Byrom M, Maranhao AC, Battenhouse AM, Gejji V, Soto-Sierra L, Foster ER, Woodard SL, Nikolov ZL, Lavinder J, Voss WN, Annapareddy A, Ippolito GC, Ellington AD, Marcotte EM, Finkelstein IJ, Hughes RA, Musser JM, Kuchipudi SV, Kapur V, Georgiou G, Dye JM, Boutz DR, McLellan JS, Gollihar JD. Synthetic repertoires derived from convalescent COVID-19 patients enable discovery of SARS-CoV-2 neutralizing antibodies and a novel quaternary binding modality. bioRxiv 2021:2021.04.07.438849. [PMID: 33851158 PMCID: PMC8043448 DOI: 10.1101/2021.04.07.438849] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The ongoing evolution of SARS-CoV-2 into more easily transmissible and infectious variants has sparked concern over the continued effectiveness of existing therapeutic antibodies and vaccines. Hence, together with increased genomic surveillance, methods to rapidly develop and assess effective interventions are critically needed. Here we report the discovery of SARS-CoV-2 neutralizing antibodies isolated from COVID-19 patients using a high-throughput platform. Antibodies were identified from unpaired donor B-cell and serum repertoires using yeast surface display, proteomics, and public light chain screening. Cryo-EM and functional characterization of the antibodies identified N3-1, an antibody that binds avidly (Kd,app = 68 pM) to the receptor binding domain (RBD) of the spike protein and robustly neutralizes the virus in vitro. This antibody likely binds all three RBDs of the trimeric spike protein with a single IgG. Importantly, N3-1 equivalently binds spike proteins from emerging SARS-CoV-2 variants of concern, neutralizes UK variant B.1.1.7, and binds SARS-CoV spike with nanomolar affinity. Taken together, the strategies described herein will prove broadly applicable in interrogating adaptive immunity and developing rapid response biological countermeasures to emerging pathogens.
Collapse
Affiliation(s)
- Jule Goike
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ching-Lin Hsieh
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andrew Horton
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Elizabeth C. Gardner
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Foteini Bartzoka
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Nianshuang Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Kamyab Javanmardi
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andrew Herbert
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Shawn Abbassi
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Rebecca Renberg
- CCDC Army Research Laboratory, Biotechnology Branch, Adelphi, MD, USA
| | - Michael J. Johanson
- National Center for Therapeutics Manufacturing, Texas A&M University, College Station, TX, USA
| | - Jose A. Cardona
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | | | - Ling Zhou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ruth H. Nissly
- Department of Veterinary and Biomedical Science and Animal Diagnostic Laboratory, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Abhinay Gontu
- Department of Veterinary and Biomedical Science and Animal Diagnostic Laboratory, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Michelle Byrom
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andre C. Maranhao
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Anna M. Battenhouse
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Varun Gejji
- National Center for Therapeutics Manufacturing, Texas A&M University, College Station, TX, USA
| | - Laura Soto-Sierra
- National Center for Therapeutics Manufacturing, Texas A&M University, College Station, TX, USA
- Department of Agricultural and Biological Engineering, Texas A&M University, College Station, TX, USA
| | - Emma R. Foster
- National Center for Therapeutics Manufacturing, Texas A&M University, College Station, TX, USA
- Department of Agricultural and Biological Engineering, Texas A&M University, College Station, TX, USA
| | - Susan L. Woodard
- National Center for Therapeutics Manufacturing, Texas A&M University, College Station, TX, USA
| | - Zivko L. Nikolov
- National Center for Therapeutics Manufacturing, Texas A&M University, College Station, TX, USA
- Department of Agricultural and Biological Engineering, Texas A&M University, College Station, TX, USA
| | - Jason Lavinder
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Will N. Voss
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ankur Annapareddy
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- CCDC Army Research Laboratory-South, Austin, TX, USA
| | - Gregory C. Ippolito
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Andrew D. Ellington
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Edward M. Marcotte
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ilya J. Finkelstein
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Randall A. Hughes
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- CCDC Army Research Laboratory-South, Austin, TX, USA
| | - James M. Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| | - Suresh V. Kuchipudi
- Department of Veterinary and Biomedical Science and Animal Diagnostic Laboratory, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Vivek Kapur
- Department of Animal Science and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - George Georgiou
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - John M. Dye
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Daniel R. Boutz
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- CCDC Army Research Laboratory-South, Austin, TX, USA
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jimmy D. Gollihar
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- CCDC Army Research Laboratory-South, Austin, TX, USA
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| |
Collapse
|
18
|
Kuchipudi SV, Surendran Nair M, Yon M, Gontu A, Nissly RH, Barry R, Greenawalt D, Pierre T, Li L, Thirumalapura N, Tewari D, Jayarao B. A Novel Real-Time PCR Assay for the Rapid Detection of Virulent Streptococcus equi Subspecies zooepidemicus-An Emerging Pathogen of Swine. Front Vet Sci 2021; 8:604675. [PMID: 33644143 PMCID: PMC7907462 DOI: 10.3389/fvets.2021.604675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/20/2021] [Indexed: 12/03/2022] Open
Abstract
Streptococcus equi subspecies zooepidemicus, a zoonotic bacterial pathogen caused a series of outbreaks with high mortality affecting swine herds in multiple locations of the USA and Canada in 2019. Further genetic analysis revealed that this agent clustered with ATCC 35246, a S. zooepidemicus strain associated with high mortality outbreaks in swine herds of China originally reported in 1977. Rapid and accurate diagnosis is absolutely critical for controlling and limiting further spread of this emerging disease of swine. Currently available diagnostic methods including bacteriological examination and PCR assays do not distinguish between the virulent strains and avirulent commensal strains of S. zooepidemicus, which is critical given that this pathogen is a normal inhabitant of the swine respiratory tract. Based on comparative analyses of whole genome sequences of the virulent isolates and avirulent sequences, we identified a region in the SzM gene that is highly conserved and restricted to virulent S. zooepidemicus strains. We developed and validated a novel probe-based real-time PCR targeting the conserved region of SzM. The assay was highly sensitive and specific to the virulent swine isolates of Streptococcus equi subspecies zooepidemicus. No cross reactivity was observed with avirulent S. zooepidemicus isolates as well as other streptococcal species and a panel of porcine respiratory bacterial and viral pathogens. The PCR efficiency of the assay was 96.64 % and was able to detect as little as 20 fg of the bacterial DNA. We then validated the diagnostic sensitivity and specificity of the new PCR assay using a panel of clinical samples (n = 57) and found that the assay has 100% sensitivity and specificity as compared to bacteriological culture method. In summary, the PCR assay will be an extremely valuable tool for the rapid accurate detection of virulent swine S. zooepidemicus isolates and directly from clinical samples.
Collapse
Affiliation(s)
- Suresh V Kuchipudi
- Animal Diagnostic Laboratory, Pennsylvania State University, Wiley Lane, University Park, PA, United States.,Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, United States
| | - Meera Surendran Nair
- Animal Diagnostic Laboratory, Pennsylvania State University, Wiley Lane, University Park, PA, United States
| | - Michele Yon
- Animal Diagnostic Laboratory, Pennsylvania State University, Wiley Lane, University Park, PA, United States
| | - Abhinay Gontu
- Animal Diagnostic Laboratory, Pennsylvania State University, Wiley Lane, University Park, PA, United States
| | - Ruth H Nissly
- Animal Diagnostic Laboratory, Pennsylvania State University, Wiley Lane, University Park, PA, United States
| | - Rhiannon Barry
- Animal Diagnostic Laboratory, Pennsylvania State University, Wiley Lane, University Park, PA, United States
| | - Denver Greenawalt
- Animal Diagnostic Laboratory, Pennsylvania State University, Wiley Lane, University Park, PA, United States
| | - Traci Pierre
- Animal Diagnostic Laboratory, Pennsylvania State University, Wiley Lane, University Park, PA, United States
| | - Lingling Li
- Animal Diagnostic Laboratory, Pennsylvania State University, Wiley Lane, University Park, PA, United States
| | | | - Deepanker Tewari
- Pennsylvania Veterinary Laboratory, Harrisburg, PA, United States
| | - Bhushan Jayarao
- Animal Diagnostic Laboratory, Pennsylvania State University, Wiley Lane, University Park, PA, United States
| |
Collapse
|
19
|
Huang WC, Zhou S, He X, Chiem K, Mabrouk MT, Nissly RH, Bird IM, Strauss M, Sambhara S, Ortega J, Wohlfert EA, Martinez-Sobrido L, Kuchipudi SV, Davidson BA, Lovell JF. SARS-CoV-2 RBD Neutralizing Antibody Induction is Enhanced by Particulate Vaccination. Adv Mater 2020. [PMID: 33111375 DOI: 10.1002/adma.v32.5010.1002/adma.202005637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein is a candidate vaccine antigen that binds angiotensin-converting enzyme 2 (ACE2), leading to virus entry. Here, it is shown that rapid conversion of recombinant RBD into particulate form via admixing with liposomes containing cobalt-porphyrin-phospholipid (CoPoP) potently enhances the functional antibody response. Antigen binding via His-tag insertion into the CoPoP bilayer results in a serum-stable and conformationally intact display of the RBD on the liposome surface. Compared to other vaccine formulations, immunization using CoPoP liposomes admixed with recombinant RBD induces multiple orders of magnitude higher levels of antibody titers in mice that neutralize pseudovirus cell entry, block RBD interaction with ACE2, and inhibit live virus replication. Enhanced immunogenicity can be accounted for by greater RBD uptake into antigen-presenting cells in particulate form and improved immune cell infiltration in draining lymph nodes. QS-21 inclusion in the liposomes results in an enhanced antigen-specific polyfunctional T cell response. In mice, high dose immunization results in minimal local reactogenicity, is well-tolerated, and does not elevate serum cobalt levels. Taken together, these results confirm that particulate presentation strategies for the RBD immunogen should be considered for inducing strongly neutralizing antibody responses against SARS-CoV-2.
Collapse
Affiliation(s)
- Wei-Chiao Huang
- Department of Biomedical Engineering, University at Buffalo, State University of New York, Buffalo, NY, 14260, USA
| | - Shiqi Zhou
- Department of Biomedical Engineering, University at Buffalo, State University of New York, Buffalo, NY, 14260, USA
| | - Xuedan He
- Department of Biomedical Engineering, University at Buffalo, State University of New York, Buffalo, NY, 14260, USA
| | - Kevin Chiem
- Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Moustafa T Mabrouk
- Department of Biomedical Engineering, University at Buffalo, State University of New York, Buffalo, NY, 14260, USA
| | - Ruth H Nissly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Ian M Bird
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Mike Strauss
- Department of Anatomy and Cell Biology, McGill University Montreal, Quebec, H3A 0C7, Canada
| | - Suryaprakash Sambhara
- Immunology and Pathogenesis Branch, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329-4027, USA
| | - Joaquin Ortega
- Department of Anatomy and Cell Biology, McGill University Montreal, Quebec, H3A 0C7, Canada
| | - Elizabeth A Wohlfert
- Department of Microbiology and Immunology, University at Buffalo, State University of New York, Buffalo, NY, 14203, USA
| | | | - Suresh V Kuchipudi
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, 16802, USA
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Bruce A Davidson
- Department of Anesthesiology, Department of Pathology and Anatomical Sciences, University at Buffalo, State University of New York, Buffalo, NY, 14203, USA
| | - Jonathan F Lovell
- Department of Biomedical Engineering, University at Buffalo, State University of New York, Buffalo, NY, 14260, USA
| |
Collapse
|
20
|
Nissly RH, Zaman N, Ibrahim PAS, McDaniel K, Lim L, Kiser JN, Bird I, Chothe SK, Bhushan GL, Vandegrift K, Neibergs HL, Kuchipudi SV. Influenza C and D viral load in cattle correlates with bovine respiratory disease (BRD): Emerging role of orthomyxoviruses in the pathogenesis of BRD. Virology 2020; 551:10-15. [PMID: 33010670 PMCID: PMC7519714 DOI: 10.1016/j.virol.2020.08.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/18/2020] [Accepted: 08/25/2020] [Indexed: 11/29/2022]
Abstract
Bovine respiratory disease (BRD) is the costliest disease affecting the cattle industry globally. Orthomyxoviruses, influenza C virus (ICV) and influenza D virus (IDV) have recently been implicated to play a role in BRD. However, there are contradicting reports about the association of IDV and ICV to BRD. Using the largest cohort study (cattle, n = 599) to date we investigated the association of influenza viruses in cattle with BRD. Cattle were scored for respiratory symptoms and pooled nasal and pharyngeal swabs were tested for bovine viral diarrhea virus, bovine herpesvirus 1, bovine respiratory syncytial virus, bovine coronavirus, ICV and IDV by real-time PCR. Cattle that have higher viral loads of IDV and ICV also have greater numbers of co-infecting viruses than controls. More strikingly, 2 logs higher IDV viral RNA in BRD-symptomatic cattle that are co-infected animals than those infected with IDV alone. Our results strongly suggest that ICV and IDV may be significant contributors to BRD.
Collapse
Affiliation(s)
- Ruth H Nissly
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Noriza Zaman
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Puteri Ainaa S Ibrahim
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Kaitlin McDaniel
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Levina Lim
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Jennifer N Kiser
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Ian Bird
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Shubhada K Chothe
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Gitanjali L Bhushan
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Kurt Vandegrift
- The Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Holly L Neibergs
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Suresh V Kuchipudi
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA; The Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA, 16802, USA.
| |
Collapse
|
21
|
Huang W, Zhou S, He X, Chiem K, Mabrouk MT, Nissly RH, Bird IM, Strauss M, Sambhara S, Ortega J, Wohlfert EA, Martinez‐Sobrido L, Kuchipudi SV, Davidson BA, Lovell JF. SARS-CoV-2 RBD Neutralizing Antibody Induction is Enhanced by Particulate Vaccination. Adv Mater 2020; 32:e2005637. [PMID: 33111375 PMCID: PMC7645956 DOI: 10.1002/adma.202005637] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/25/2020] [Indexed: 05/21/2023]
Abstract
The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein is a candidate vaccine antigen that binds angiotensin-converting enzyme 2 (ACE2), leading to virus entry. Here, it is shown that rapid conversion of recombinant RBD into particulate form via admixing with liposomes containing cobalt-porphyrin-phospholipid (CoPoP) potently enhances the functional antibody response. Antigen binding via His-tag insertion into the CoPoP bilayer results in a serum-stable and conformationally intact display of the RBD on the liposome surface. Compared to other vaccine formulations, immunization using CoPoP liposomes admixed with recombinant RBD induces multiple orders of magnitude higher levels of antibody titers in mice that neutralize pseudovirus cell entry, block RBD interaction with ACE2, and inhibit live virus replication. Enhanced immunogenicity can be accounted for by greater RBD uptake into antigen-presenting cells in particulate form and improved immune cell infiltration in draining lymph nodes. QS-21 inclusion in the liposomes results in an enhanced antigen-specific polyfunctional T cell response. In mice, high dose immunization results in minimal local reactogenicity, is well-tolerated, and does not elevate serum cobalt levels. Taken together, these results confirm that particulate presentation strategies for the RBD immunogen should be considered for inducing strongly neutralizing antibody responses against SARS-CoV-2.
Collapse
Affiliation(s)
- Wei‐Chiao Huang
- Department of Biomedical EngineeringUniversity at BuffaloState University of New YorkBuffaloNY14260USA
| | - Shiqi Zhou
- Department of Biomedical EngineeringUniversity at BuffaloState University of New YorkBuffaloNY14260USA
| | - Xuedan He
- Department of Biomedical EngineeringUniversity at BuffaloState University of New YorkBuffaloNY14260USA
| | - Kevin Chiem
- Texas Biomedical Research InstituteSan AntonioTX78227USA
| | - Moustafa T. Mabrouk
- Department of Biomedical EngineeringUniversity at BuffaloState University of New YorkBuffaloNY14260USA
| | - Ruth H. Nissly
- Animal Diagnostic LaboratoryDepartment of Veterinary and Biomedical SciencesPennsylvania State UniversityUniversity ParkPA16802USA
| | - Ian M. Bird
- Animal Diagnostic LaboratoryDepartment of Veterinary and Biomedical SciencesPennsylvania State UniversityUniversity ParkPA16802USA
| | - Mike Strauss
- Department of Anatomy and Cell BiologyMcGill University MontrealQuebecH3A 0C7Canada
| | - Suryaprakash Sambhara
- Immunology and Pathogenesis BranchCenters for Disease Control and Prevention1600 Clifton RoadAtlantaGA30329‐4027USA
| | - Joaquin Ortega
- Department of Anatomy and Cell BiologyMcGill University MontrealQuebecH3A 0C7Canada
| | - Elizabeth A. Wohlfert
- Department of Microbiology and ImmunologyUniversity at BuffaloState University of New YorkBuffaloNY14203USA
| | | | - Suresh V. Kuchipudi
- Animal Diagnostic LaboratoryDepartment of Veterinary and Biomedical SciencesPennsylvania State UniversityUniversity ParkPA16802USA
- Animal Diagnostic LaboratoryDepartment of Veterinary and Biomedical SciencesThe Center for Infectious Disease DynamicsThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Bruce A. Davidson
- Department of AnesthesiologyDepartment of Pathology and Anatomical SciencesUniversity at BuffaloState University of New YorkBuffaloNY14203USA
| | - Jonathan F. Lovell
- Department of Biomedical EngineeringUniversity at BuffaloState University of New YorkBuffaloNY14260USA
| |
Collapse
|
22
|
Salazar E, Kuchipudi SV, Christensen PA, Eagar TN, Yi X, Zhao P, Jin Z, Long SW, Olsen RJ, Chen J, Castillo B, Leveque C, Towers DM, Lavinder J, Gollihar JD, Cardona J, Ippolito GC, Nissly RH, Bird IM, Greenawalt D, Rossi RM, Gontu A, Srinivasan S, Poojary IB, Cattadori IM, Hudson PJ, Joselyn N, Prugar L, Huie K, Herbert A, Bernard DW, Dye J, Kapur V, Musser JM. Relationship between Anti-Spike Protein Antibody Titers and SARS-CoV-2 In Vitro Virus Neutralization in Convalescent Plasma. bioRxiv 2020:2020.06.08.138990. [PMID: 32577662 PMCID: PMC7302218 DOI: 10.1101/2020.06.08.138990] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Newly emerged pathogens such as SARS-CoV-2 highlight the urgent need for assays that detect levels of neutralizing antibodies that may be protective. We studied the relationship between anti-spike ectodomain (ECD) and anti-receptor binding domain (RBD) IgG titers, and SARS-CoV-2 virus neutralization (VN) titers generated by two different in vitro assays using convalescent plasma samples obtained from 68 COVID-19 patients, including 13 who donated plasma multiple times. Only 23% (16/68) of donors had been hospitalized. We also studied 16 samples from subjects found to have anti-spike protein IgG during surveillance screening of asymptomatic individuals. We report a strong positive correlation between both plasma anti-RBD and anti-ECD IgG titers, and in vitro VN titer. Anti-RBD plasma IgG correlated slightly better than anti-ECD IgG titer with VN titer. The probability of a VN titer ≥160 was 80% or greater with anti-RBD or anti-ECD titers of ≥1:1350. Thirty-seven percent (25/68) of convalescent plasma donors lacked VN titers ≥160, the FDA-recommended level for convalescent plasma used for COVID-19 treatment. Dyspnea, hospitalization, and disease severity were significantly associated with higher VN titer. Frequent donation of convalescent plasma did not significantly decrease either VN or IgG titers. Analysis of 2,814 asymptomatic adults found 27 individuals with anti-RBD or anti-ECD IgG titers of ≥1:1350, and evidence of VN ≥1:160. Taken together, we conclude that anti-RBD or anti-ECD IgG titers can serve as a surrogate for VN titers to identify suitable plasma donors. Plasma anti-RBD or anti-ECD titer of ≥1:1350 may provide critical information about protection against COVID-19 disease.
Collapse
Affiliation(s)
- Eric Salazar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Suresh V. Kuchipudi
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania
| | - Paul A. Christensen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Todd N. Eagar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Xin Yi
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Picheng Zhao
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Zhicheng Jin
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - S. Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - Randall J. Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - Jian Chen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Brian Castillo
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Christopher Leveque
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Dalton M. Towers
- Department of Molecular Biosciences, University of Texas at Austin
| | - Jason Lavinder
- Department of Molecular Biosciences, University of Texas at Austin
| | - Jimmy D. Gollihar
- CCDC Army Research Laboratory-South, University of Texas, Austin, Texas
| | - Jose Cardona
- CCDC Army Research Laboratory-South, University of Texas, Austin, Texas
| | - Gregory C. Ippolito
- Department of Molecular Biosciences, University of Texas at Austin
- Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, Texas
| | - Ruth H. Nissly
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Ian M. Bird
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Denver Greenawalt
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Randall M. Rossi
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Abinhay Gontu
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Sreenidhi Srinivasan
- Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania
| | - Indira B. Poojary
- Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania
| | - Isabella M. Cattadori
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania
| | - Peter J. Hudson
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania
| | - Nicole Joselyn
- USAMRIID (United States Army Medical Research Institute of Infectious Diseases), Frederick, Maryland
| | - Laura Prugar
- USAMRIID (United States Army Medical Research Institute of Infectious Diseases), Frederick, Maryland
| | - Kathleen Huie
- USAMRIID (United States Army Medical Research Institute of Infectious Diseases), Frederick, Maryland
| | - Andrew Herbert
- USAMRIID (United States Army Medical Research Institute of Infectious Diseases), Frederick, Maryland
| | - David W. Bernard
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - John Dye
- USAMRIID (United States Army Medical Research Institute of Infectious Diseases), Frederick, Maryland
| | - Vivek Kapur
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania
- Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania
| | - James M. Musser
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| |
Collapse
|
23
|
Chothe SK, Nissly RH, Lim L, Bhushan G, Bird I, Radzio-Basu J, Jayarao BM, Kuchipudi SV. NLRC5 Serves as a Pro-viral Factor During Influenza Virus Infection in Chicken Macrophages. Front Cell Infect Microbiol 2020; 10:230. [PMID: 32509599 PMCID: PMC7248199 DOI: 10.3389/fcimb.2020.00230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/23/2020] [Indexed: 01/09/2023] Open
Abstract
Avian influenza viruses (AIVs) cause major economic losses to the global poultry industry. Many host factors have been identified that act as regulators of the inflammatory response and virus replication in influenza A virus (IAV) infected cells including nucleotide-binding oligomerization domain (NOD) like receptor (NLR) family proteins. Evidence is emerging that NLRC5, the largest NLR member, is a regulator of host immune responses against invading pathogens including viruses; however, its role in the avian immune system and AIV pathogenesis has not been fully explored. In this study, we found that NLRC5 is activated by a range of low and highly pathogenic AIVs in primary chicken lung cells and a chicken macrophage cell line. Further, siRNA mediated NLRC5 knockdown in chicken macrophages resulted in a significant reduction in AIV replication which was associated with the upregulation of genes associated with activated NFκB signaling pathway. The knockdown of NLRC5 enhanced the expression of genes known to be associated with viral defense and decreased innate cytokine gene expression following AIV infection. Overall, our investigation strongly suggests that NLRC5 is a pro-viral factor during IAV infection in chicken and may contribute to pathogenesis through innate cytokine regulation. Further studies are warranted to investigate the IAV protein(s) that may regulate activation of NLRC5.
Collapse
Affiliation(s)
- Shubhada K Chothe
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, United States
| | - Ruth H Nissly
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, United States
| | - Levina Lim
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, United States
| | - Gitanjali Bhushan
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, United States
| | - Ian Bird
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, United States
| | - Jessica Radzio-Basu
- Applied Biological and Biosecurity Research Laboratory, Pennsylvania State University, University Park, PA, United States
| | - Bhushan M Jayarao
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, United States
| | - Suresh V Kuchipudi
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, United States
| |
Collapse
|
24
|
Bhushan G, Lim L, Bird I, Chothe SK, Nissly RH, Kuchipudi SV. Iminosugars With Endoplasmic Reticulum α-Glucosidase Inhibitor Activity Inhibit ZIKV Replication and Reverse Cytopathogenicity in vitro. Front Microbiol 2020; 11:531. [PMID: 32373079 PMCID: PMC7179685 DOI: 10.3389/fmicb.2020.00531] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/12/2020] [Indexed: 11/26/2022] Open
Abstract
Zika virus (ZIKV), a vector-borne virus of the family Flaviviridae, continues to spread and remains a significant global public health threat. Currently, there are no approved vaccines or antivirals against ZIKV. We investigated the anti-ZIKV ability of three iminosugars with endoplasmic reticulum α-glucosidase inhibitor (ER-AGI) activity, namely deoxynojirimycin (DNJ), castanospermine, and celgosivir. None of the three iminosugars showed any significant cytotoxicity in Vero or human microglia CHME3 cells when applied for 72 h at concentrations up to 100 μM. Iminosugar treatment of Vero or CHME3 cells prior to ZIKV infection resulted in significant inhibition of ZIKV replication over 48 h. Reduction in ZIKV replication in iminosugar-treated cells was not associated with any significant change in the expression levels of key antiviral genes. Following infection with three different strains of ZIKV, iminosugar-treated Vero or CHME3 cells showed no cell death, whereas vehicle-treated control cells exhibited 50–60% cell death at 72 h post-infection (hpi). While there was no significant difference in apoptosis between iminosugar-treated and control cells, iminosugar-treated cells exhibited a substantial reduction of necrosis at 72 hpi following ZIKV infection. In summary, iminosugars with ER-AGI activity inhibit ZIKV replication and significantly reduce necrosis without altering the antiviral gene expression and apoptosis of infected human cells. The results of this study strongly suggest that iminosugars are promising anti-ZIKV antiviral agents and such warrant further in vivo studies.
Collapse
Affiliation(s)
- Gitanjali Bhushan
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, United States
| | - Levina Lim
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, United States
| | - Ian Bird
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, United States
| | - Shubhada K Chothe
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, United States
| | - Ruth H Nissly
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, United States
| | - Suresh V Kuchipudi
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, United States
| |
Collapse
|
25
|
Pujhari S, Brustolin M, Macias VM, Nissly RH, Nomura M, Kuchipudi SV, Rasgon JL. Heat shock protein 70 (Hsp70) mediates Zika virus entry, replication, and egress from host cells. Emerg Microbes Infect 2019; 8:8-16. [PMID: 30866755 PMCID: PMC6455116 DOI: 10.1080/22221751.2018.1557988] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Zika virus (ZIKV) is a historically neglected mosquito-borne flavivirus that has caused recent epidemics in the western hemisphere. ZIKV has been associated with severe symptoms including infant microcephaly and Guillain-Barré syndrome, stimulating interest in understanding factors governing ZIKV infection. Heat shock protein 70 (Hsp70) has been shown to be an infection factor for multiple viruses, leading us to investigate the role of Hsp70 in the ZIKV infection process. ZIKV infection induced Hsp70 expression in host cells 48-h post-infection. Inducing Hsp70 expression in mammalian cells increased ZIKV production, whereas inhibiting Hsp70 activity reduced ZIKV viral RNA production and virion release from the cell. Hsp70 was localized both on the cell surface where it could interact with ZIKV during the initial stages of the infection process, and intracellularly where it localized with viral RNA. Blocking cell surface-localized Hsp70 using antibodies decreased ZIKV cell infection rates and production of infectious virus particles, as did competition with recombinant Hsp70 protein. Overall, Hsp70 was found to play a functional role in both the pre- and post-ZIKV infection processes affecting viral entry, replication, and egress. Understanding the interactions between Hsp70 and ZIKV may lead to novel therapeutics for ZIKV infection.
Collapse
Affiliation(s)
- Sujit Pujhari
- a Department of Entomology , Center for Infectious Disease Dynamics and the Huck Institutes of the Life Sciences, The Pennsylvania State University , University Park , PA , USA
| | - Marco Brustolin
- a Department of Entomology , Center for Infectious Disease Dynamics and the Huck Institutes of the Life Sciences, The Pennsylvania State University , University Park , PA , USA
| | - Vanessa M Macias
- a Department of Entomology , Center for Infectious Disease Dynamics and the Huck Institutes of the Life Sciences, The Pennsylvania State University , University Park , PA , USA
| | - Ruth H Nissly
- b Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences , The Pennsylvania State University , University Park , PA , USA
| | - Masashi Nomura
- a Department of Entomology , Center for Infectious Disease Dynamics and the Huck Institutes of the Life Sciences, The Pennsylvania State University , University Park , PA , USA.,c Graduate School of Horticulture , Chiba University , Japan
| | - Suresh V Kuchipudi
- b Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences , The Pennsylvania State University , University Park , PA , USA
| | - Jason L Rasgon
- a Department of Entomology , Center for Infectious Disease Dynamics and the Huck Institutes of the Life Sciences, The Pennsylvania State University , University Park , PA , USA
| |
Collapse
|
26
|
Chothe SK, Sebastian A, Thomas A, Nissly RH, Wolfgang D, Byukusenge M, Mor SK, Goyal SM, Albert I, Tewari D, Jayarao BM, Kuchipudi SV. Whole-genome sequence analysis reveals unique SNP profiles to distinguish vaccine and wild-type strains of bovine herpesvirus-1 (BoHV-1). Virology 2018; 522:27-36. [PMID: 30014855 DOI: 10.1016/j.virol.2018.06.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/03/2018] [Accepted: 06/26/2018] [Indexed: 01/02/2023]
Abstract
Bovine herpesvirus-1 (BoHV-1) is a major pathogen affecting cattle worldwide causing primarily respiratory illness referred to as infectious bovine rhinotracheitis (IBR), along with reproductive disorders including abortion and infertility in cattle. While modified live vaccines (MLVs) effectively induce immune response against BoHV-1, they are implicated in disease outbreaks in cattle. Current diagnostic methods cannot distinguish between MLVs and field strains of BoHV-1. We performed whole genome sequencing of 18 BoHV-1 isolates from Pennsylvania and Minnesota along with five BoHV-1 vaccine strains using the Illumina Miseq platform. Based on nucleotide polymorphisms (SNPs) the sequences were clustered into three groups with two different vaccine groups and one distinct cluster of field isolates. Using this information, we developed a novel SNP-based PCR assay that can allow differentiation of vaccine and clinical strains and help accurately determine the incidence of BoHV-1 and the association of MLVs with clinical disease in cattle.
Collapse
Affiliation(s)
- Shubhada K Chothe
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, United States
| | - Aswathy Sebastian
- Dept of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, United States
| | - Asha Thomas
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, United States
| | - Ruth H Nissly
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, United States
| | - David Wolfgang
- Pennsylvania Department of Agriculture, Bureau of Animal Health and Diagnostic Services, Harrisburg, PA, United States
| | - Maurice Byukusenge
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, United States
| | - Sunil Kumar Mor
- Veterinary Population Medicine, University of Minnesota, St. Paul, MN, United States
| | - Sagar M Goyal
- Veterinary Population Medicine, University of Minnesota, St. Paul, MN, United States
| | - Istvan Albert
- Dept of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, United States
| | - Deepanker Tewari
- Pennsylvania Department of Agriculture, Bureau of Animal Health and Diagnostic Services, Harrisburg, PA, United States
| | - Bhushan M Jayarao
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, United States
| | - Suresh V Kuchipudi
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA, United States.
| |
Collapse
|
27
|
Vasudevan G, Vanamayya PR, Nagarajan S, Rajukumar K, Suba S, Venketash G, Tosh C, Sood R, Nissly RH, Kuchipudi SV. Infectious dose-dependent accumulation of live highly pathogenic avian influenza H5N1 virus in chicken skeletal muscle-implications for public health. Zoonoses Public Health 2017; 65:e243-e247. [PMID: 28941132 DOI: 10.1111/zph.12406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Indexed: 11/27/2022]
Abstract
Highly pathogenic avian influenza viruses (HPAIV) of H5N1 subtype are a major global threat to poultry and public health. Export of poultry products, such as chicken and duck meat, is a known source for the cross-boundary spread of HPAI H5N1 viruses. Humans get infected with HPAI H5N1 viruses either by close contact with infected poultry or through consumption of fresh/undercooked poultry meat. Skeletal muscle is the largest soft tissue in chicken that has been shown to contain virus during systemic HPAIV infection and supports productive virus infection. However, the time between infection of a chicken with H5N1 virus and presence of virus in muscle tissue is not yet known. Further, it is also not clear whether chicken infected with low doses of H5N1 virus that cause non-fatal subclinical infections continue to accumulate virus in skeletal muscle. We investigated the amount and duration of virus detection in skeletal muscle of chicken experimentally infected with different doses (102 , 103 and 104 EID50 ) of a HPAI H5N1 virus. Influenza viral antigen could be detected as early as 6 hr after infection and live virus was recovered from 48 hr after infection. Notably, chicken infected with lower levels of HPAI H5N1 virus (i.e., 102 EID50 ) did not die acutely, but continued to accumulate high levels of H5N1 virus in skeletal muscle until 6 days post-infection. Our data suggest that there is a potential risk of human exposure to H5N1 virus through meat from clinically healthy chicken infected with a low dose of virus. Our results highlight the need to implement rigorous monitoring systems to screen poultry meat from H5N1 endemic countries to limit the global spread of H5N1 viruses.
Collapse
Affiliation(s)
- G Vasudevan
- National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh, India.,Poultry Disease Diagnosis and Surveillance Laboratory, Veterinary College and Research Institute Campus, Tamil Nadu Veterinary and Animal Sciences University, Namakkal, Tamil Nadu, India
| | - P R Vanamayya
- National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh, India
| | - S Nagarajan
- National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh, India
| | - K Rajukumar
- National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh, India
| | - S Suba
- National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh, India
| | - G Venketash
- National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh, India
| | - C Tosh
- National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh, India
| | - R Sood
- National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh, India
| | - R H Nissly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - S V Kuchipudi
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| |
Collapse
|