1
|
Mecklenburg L, Ducore R, Boyle M, Newell A, Boone L, Luft J, Romeike A, Haverkamp AK, Mansfield K, Penraat KA, Baczenas JJ, Minor N, O'Connor SL, O'Connor DH. A new genotype of hepatitis A virus causing transient liver enzyme elevations in Mauritius-origin laboratory-housed Macaca fascicularis. Vet Pathol 2024; 61:488-496. [PMID: 37953600 DOI: 10.1177/03009858231209691] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Hepatitis A virus (HAV) infects humans and nonhuman primates, typically causing an acute self-limited illness. Three HAV genotypes have been described so far for humans, and three genotypes have been described for nonhuman primates. We observed transiently elevated liver enzymes in Mauritius-origin laboratory-housed macaques in Germany and were not able to demonstrate an etiology including HAV by serology and polymerase chain reaction (PCR). HAV is a rare pathogen in cynomolgus macaques, and since all employees were routinely vaccinated against HAV, it was not a part of the routine vaccination and screening program. A deep sequencing approach identified a new HAV genotype (referred to as Simian_HAV_Macaca/Germany/Mue-1/2022) in blood samples from affected animals. This HAV was demonstrated by reverse transcription PCR in blood and liver and by in situ hybridization in liver, gall bladder, and septal ducts. A commercial vaccine was used to protect animals from liver enzyme elevation. The newly identified simian HAV genotype demonstrates 80% nucleotide sequence identity to other simian and human HAV genotypes. There was deeper divergence between Simian_HAV_Macaca/Germany/Mue-1/2022 and other previously described HAVs, including both human and simian viruses. In situ hybridization indicated persistence in the biliary epithelium up to 3 months after liver enzymes were elevated. Vaccination using a commercial vaccine against human HAV prevented reoccurrence of liver enzyme elevations. Because available assays for HAV did not detect this new HAV genotype, knowledge of its existence may ameliorate potential significant epidemiological and research implications in laboratories globally.
Collapse
Affiliation(s)
| | - Rebecca Ducore
- Labcorp Early Development Laboratories Inc., Chantilly, VA
| | - Molly Boyle
- Labcorp Early Development Laboratories Inc., Somerset, NJ
| | - Andrew Newell
- Labcorp Early Development Laboratories Ltd., Harrogate, UK
| | - Laura Boone
- Labcorp Early Development Laboratories Inc., Greenfield, IN
| | - Joerg Luft
- Labcorp Early Development Services GmbH, Muenster, Germany
| | | | | | | | | | | | - Nick Minor
- University of Wisconsin-Madison, Madison, WI
| | | | | |
Collapse
|
2
|
Aguillon SM, Haase Cox SK, Langdon QK, Gunn TR, Baczenas JJ, Banerjee SM, Donny AE, Moran BM, Gutiérrez-Rodríguez C, Ríos-Cárdenas O, Morris MR, Powell DL, Schumer M. Pervasive gene flow despite strong and varied reproductive barriers in swordtails. bioRxiv 2024:2024.04.16.589374. [PMID: 38659793 PMCID: PMC11042374 DOI: 10.1101/2024.04.16.589374] [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] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
One of the mechanisms that can lead to the formation of new species occurs through the evolution of reproductive barriers. However, recent research has demonstrated that hybridization has been pervasive across the tree of life even in the presence of strong barriers. Swordtail fishes (genus Xiphophorus) are an emerging model system for studying the interface between these barriers and hybridization. We document overlapping mechanisms that act as barriers between closely related species, X. birchmanni and X. cortezi, by combining genomic sequencing from natural hybrid populations, artificial crosses, behavioral assays, sperm performance, and developmental studies. We show that strong assortative mating plays a key role in maintaining subpopulations with distinct ancestry in natural hybrid populations. Lab experiments demonstrate that artificial F1 crosses experience dysfunction: crosses with X. birchmanni females were largely inviable and crosses with X. cortezi females had a heavily skewed sex ratio. Using F2 hybrids we identify several genomic regions that strongly impact hybrid viability. Strikingly, two of these regions underlie genetic incompatibilities in hybrids between X. birchmanni and its sister species X. malinche. Our results demonstrate that ancient hybridization has played a role in the origin of this shared genetic incompatibility. Moreover, ancestry mismatch at these incompatible regions has remarkably similar consequences for phenotypes and hybrid survival in X. cortezi × X. birchmanni hybrids as in X. malinche × X. birchmanni hybrids. Our findings identify varied reproductive barriers that shape genetic exchange between naturally hybridizing species and highlight the complex evolutionary outcomes of hybridization.
Collapse
Affiliation(s)
- Stepfanie M. Aguillon
- Department of Biology, Stanford University, Stanford, CA, USA
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Hidalgo, México
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Quinn K. Langdon
- Department of Biology, Stanford University, Stanford, CA, USA
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Hidalgo, México
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, CA, USA
| | - Theresa R. Gunn
- Department of Biology, Stanford University, Stanford, CA, USA
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Hidalgo, México
| | | | - Shreya M. Banerjee
- Department of Biology, Stanford University, Stanford, CA, USA
- Center for Population Biology, University of California, Davis, Davis, CA, USA
| | | | - Benjamin M. Moran
- Department of Biology, Stanford University, Stanford, CA, USA
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Hidalgo, México
| | | | - Oscar Ríos-Cárdenas
- Red de Biología Evolutiva, Instituto de Ecología A.C., Xalapa, Veracruz, México
| | - Molly R. Morris
- Department of Biological Sciences, Ohio University, Athens, Ohio, USA
| | - Daniel L. Powell
- Department of Biology, Stanford University, Stanford, CA, USA
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Hidalgo, México
| | - Molly Schumer
- Department of Biology, Stanford University, Stanford, CA, USA
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C., Calnali, Hidalgo, México
- Freeman Hrabowski Fellow, Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| |
Collapse
|
3
|
Moran BM, Payne CY, Powell DL, Iverson ENK, Donny AE, Banerjee SM, Langdon QK, Gunn TR, Rodriguez-Soto RA, Madero A, Baczenas JJ, Kleczko KM, Liu F, Matney R, Singhal K, Leib RD, Hernandez-Perez O, Corbett-Detig R, Frydman J, Gifford C, Schartl M, Havird JC, Schumer M. A lethal mitonuclear incompatibility in complex I of natural hybrids. Nature 2024; 626:119-127. [PMID: 38200310 PMCID: PMC10830419 DOI: 10.1038/s41586-023-06895-8] [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: 07/30/2021] [Accepted: 11/23/2023] [Indexed: 01/12/2024]
Abstract
The evolution of reproductive barriers is the first step in the formation of new species and can help us understand the diversification of life on Earth. These reproductive barriers often take the form of hybrid incompatibilities, in which alleles derived from two different species no longer interact properly in hybrids1-3. Theory predicts that hybrid incompatibilities may be more likely to arise at rapidly evolving genes4-6 and that incompatibilities involving multiple genes should be common7,8, but there has been sparse empirical data to evaluate these predictions. Here we describe a mitonuclear incompatibility involving three genes whose protein products are in physical contact within respiratory complex I of naturally hybridizing swordtail fish species. Individuals homozygous for mismatched protein combinations do not complete embryonic development or die as juveniles, whereas those heterozygous for the incompatibility have reduced complex I function and unbalanced representation of parental alleles in the mitochondrial proteome. We find that the effects of different genetic interactions on survival are non-additive, highlighting subtle complexity in the genetic architecture of hybrid incompatibilities. Finally, we document the evolutionary history of the genes involved, showing signals of accelerated evolution and evidence that an incompatibility has been transferred between species via hybridization.
Collapse
Affiliation(s)
- Benjamin M Moran
- Department of Biology, Stanford University, Stanford, CA, USA.
- Centro de Investigaciones Científicas de las Huastecas 'Aguazarca', A.C., Calnali, Hidalgo, Mexico.
| | - Cheyenne Y Payne
- Department of Biology, Stanford University, Stanford, CA, USA
- Centro de Investigaciones Científicas de las Huastecas 'Aguazarca', A.C., Calnali, Hidalgo, Mexico
| | - Daniel L Powell
- Department of Biology, Stanford University, Stanford, CA, USA
- Centro de Investigaciones Científicas de las Huastecas 'Aguazarca', A.C., Calnali, Hidalgo, Mexico
| | - Erik N K Iverson
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | | | | | - Quinn K Langdon
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Theresa R Gunn
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Angel Madero
- Department of Biology, Stanford University, Stanford, CA, USA
| | - John J Baczenas
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Fang Liu
- Stanford University Mass Spectrometry Core, Stanford University, Stanford, CA, USA
| | - Rowan Matney
- Stanford University Mass Spectrometry Core, Stanford University, Stanford, CA, USA
| | - Kratika Singhal
- Stanford University Mass Spectrometry Core, Stanford University, Stanford, CA, USA
| | - Ryan D Leib
- Stanford University Mass Spectrometry Core, Stanford University, Stanford, CA, USA
| | - Osvaldo Hernandez-Perez
- Centro de Investigaciones Científicas de las Huastecas 'Aguazarca', A.C., Calnali, Hidalgo, Mexico
| | - Russell Corbett-Detig
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Casey Gifford
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA
- Developmental Biochemistry, Biozentrum, University of Würzburg, Würzburg, Germany
| | - Justin C Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Molly Schumer
- Department of Biology, Stanford University, Stanford, CA, USA.
- Centro de Investigaciones Científicas de las Huastecas 'Aguazarca', A.C., Calnali, Hidalgo, Mexico.
- Howard Hughes Medical Institute, Stanford, CA, USA.
| |
Collapse
|
4
|
Langdon QK, Groh JS, Aguillon SM, Powell DL, Gunn T, Payne C, Baczenas JJ, Donny A, Dodge TO, Du K, Schartl M, Ríos-Cárdenas O, Gutierrez-Rodríguez C, Morris M, Schumer M. Genome evolution is surprisingly predictable after initial hybridization. bioRxiv 2023:2023.12.21.572897. [PMID: 38187753 PMCID: PMC10769416 DOI: 10.1101/2023.12.21.572897] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Over the past two decades, evolutionary biologists have come to appreciate that hybridization, or genetic exchange between distinct lineages, is remarkably common - not just in particular lineages but in taxonomic groups across the tree of life. As a result, the genomes of many modern species harbor regions inherited from related species. This observation has raised fundamental questions about the degree to which the genomic outcomes of hybridization are repeatable and the degree to which natural selection drives such repeatability. However, a lack of appropriate systems to answer these questions has limited empirical progress in this area. Here, we leverage independently formed hybrid populations between the swordtail fish Xiphophorus birchmanni and X. cortezi to address this fundamental question. We find that local ancestry in one hybrid population is remarkably predictive of local ancestry in another, demographically independent hybrid population. Applying newly developed methods, we can attribute much of this repeatability to strong selection in the earliest generations after initial hybridization. We complement these analyses with time-series data that demonstrates that ancestry at regions under selection has remained stable over the past ~40 generations of evolution. Finally, we compare our results to the well-studied X. birchmanni×X. malinche hybrid populations and conclude that deeper evolutionary divergence has resulted in stronger selection and higher repeatability in patterns of local ancestry in hybrids between X. birchmanni and X. cortezi.
Collapse
Affiliation(s)
- Quinn K. Langdon
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
- Gladstone Institute of Virology, Gladstone Institutes, San Francisco, California
| | - Jeffrey S. Groh
- Center for Population Biology and Department of Evolution and Ecology, University of California, Davis
| | - Stepfanie M. Aguillon
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles
| | - Daniel L. Powell
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | - Theresa Gunn
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | - Cheyenne Payne
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | | | - Alex Donny
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | - Tristram O. Dodge
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
| | - Kang Du
- Xiphophorus Genetic Stock Center, Texas State University San Marcos
| | - Manfred Schartl
- Xiphophorus Genetic Stock Center, Texas State University San Marcos
- Developmental Biochemistry, Biocenter, University of Würzburg
| | | | | | | | - Molly Schumer
- Department of Biology, Stanford University
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”, A.C
- Freeman Hrabowski Fellow, Howard Hughes Medical Institute
| |
Collapse
|
5
|
Jaeger AS, Marano J, Riemersma KK, Castaneda D, Pritchard EM, Pritchard JC, Bohm EK, Baczenas JJ, O'Connor SL, Weger-Lucarelli J, Friedrich TC, Aliota MT. Gain without pain: adaptation and increased virulence of Zika virus in vertebrate host without fitness cost in mosquito vector. J Virol 2023; 97:e0116223. [PMID: 37800949 PMCID: PMC10653995 DOI: 10.1128/jvi.01162-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 08/21/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE Previously, we modeled direct transmission chains of Zika virus (ZIKV) by serially passaging ZIKV in mice and mosquitoes and found that direct mouse transmission chains selected for viruses with increased virulence in mice and the acquisition of non-synonymous amino acid substitutions. Here, we show that these same mouse-passaged viruses also maintain fitness and transmission capacity in mosquitoes. We used infectious clone-derived viruses to demonstrate that the substitution in nonstructural protein 4A contributes to increased virulence in mice.
Collapse
Affiliation(s)
- Anna S. Jaeger
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, Minnesota, USA
| | - Jeffrey Marano
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Kasen K. Riemersma
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David Castaneda
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, Minnesota, USA
| | - Elise M. Pritchard
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, Minnesota, USA
| | - Julia C. Pritchard
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, Minnesota, USA
| | - Ellie K. Bohm
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, Minnesota, USA
| | - John J. Baczenas
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Shelby L. O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Matthew T. Aliota
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, Minnesota, USA
| |
Collapse
|
6
|
Jaeger AS, Marano J, Riemersma K, Castañeda D, Pritchard E, Pritchard J, Bohm EK, Baczenas JJ, O’Connor SL, Weger-Lucarelli J, Friedrich TC, Aliota MT. Gain without pain: Adaptation and increased virulence of Zika virus in vertebrate host without fitness cost in mosquito vector. bioRxiv 2023:2023.03.20.533515. [PMID: 36993525 PMCID: PMC10055270 DOI: 10.1101/2023.03.20.533515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Zika virus (ZIKV) is now in a post-pandemic period, for which the potential for re-emergence and future spread is unknown. Adding to this uncertainty is the unique capacity of ZIKV to directly transmit between humans via sexual transmission. Recently, we demonstrated that direct transmission of ZIKV between vertebrate hosts leads to rapid adaptation resulting in enhanced virulence in mice and the emergence of three amino acid substitutions (NS2A-A117V, NS2A-A117T, and NS4A-E19G) shared among all vertebrate-passaged lineages. Here, we further characterized these host-adapted viruses and found that vertebrate-passaged viruses also have enhanced transmission potential in mosquitoes. To understand the contribution of genetic changes to the enhanced virulence and transmission phenotype, we engineered these amino acid substitutions, singly and in combination, into a ZIKV infectious clone. We found that NS4A-E19G contributed to the enhanced virulence and mortality phenotype in mice. Further analyses revealed that NS4A-E19G results in increased neurotropism and distinct innate immune signaling patterns in the brain. None of the substitutions contributed to changes in transmission potential in mosquitoes. Together, these findings suggest that direct transmission chains could enable the emergence of more virulent ZIKV strains without compromising mosquito transmission capacity, although the underlying genetics of these adaptations are complex.
Collapse
Affiliation(s)
- Anna S. Jaeger
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities
| | - Jeffrey Marano
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University
| | - Kasen Riemersma
- Department of Pathobiological Sciences, University of Wisconsin-Madison
| | - David Castañeda
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities
| | - Elise Pritchard
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities
| | - Julia Pritchard
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities
| | - Ellie K. Bohm
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities
| | - John J. Baczenas
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, United States
- Wisconsin National Primate Research Center, University of Wisconsin-Madison
| | - Shelby L. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, United States
- Wisconsin National Primate Research Center, University of Wisconsin-Madison
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison
- Wisconsin National Primate Research Center, University of Wisconsin-Madison
| | - Matthew T. Aliota
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities
| |
Collapse
|
7
|
Curlin JZ, Schmitt K, Remling‐Mulder L, Morrison J, Baczenas JJ, Tibbits CV, Goff K, O'Connor S, Stenglein M, Marx P, Akkina R. Evolution of SIVmac239 following serial passaging in humanized mice. J Med Primatol 2022; 51:284-287. [PMID: 36030392 PMCID: PMC9536747 DOI: 10.1111/jmp.12614] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/05/2022] [Accepted: 08/13/2022] [Indexed: 11/28/2022]
Abstract
Serial passage of SIVmac239 allows for greater understanding of the genetic changes necessary for cross-species transmission of primate lentiviruses into humans. Using humanized mice, we show that adaptive mutations continue to accumulate in SIVmac239 during four serial passages, with persistent CD4+ T cell decline and increases in plasma viral loads.
Collapse
Affiliation(s)
- James Z. Curlin
- Department of Microbiology, Immunology and PathologyColorado State UniversityFort CollinsColoradoUSA
- ADEAR Training Program, Department of MedicineUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Kimberly Schmitt
- Department of Microbiology, Immunology and PathologyColorado State UniversityFort CollinsColoradoUSA
| | - Leila Remling‐Mulder
- Department of Microbiology, Immunology and PathologyColorado State UniversityFort CollinsColoradoUSA
| | - Jared Morrison
- Department of Microbiology, Immunology and PathologyColorado State UniversityFort CollinsColoradoUSA
| | - John J. Baczenas
- Department of Pathology and Laboratory MedicineUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Corina Valencia Tibbits
- Department of Pathology and Laboratory MedicineUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Kelly Goff
- Department of Tropical MedicineSchool of Public Health and Tropical MedicineNew OrleansLouisianaUSA
| | - Shelby O'Connor
- Department of Pathology and Laboratory MedicineUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Mark Stenglein
- Department of Microbiology, Immunology and PathologyColorado State UniversityFort CollinsColoradoUSA
| | - Preston Marx
- Department of Tropical MedicineSchool of Public Health and Tropical MedicineNew OrleansLouisianaUSA
- Tulane National Primate Research CenterCovingtonLouisianaUSA
| | - Ramesh Akkina
- Department of Microbiology, Immunology and PathologyColorado State UniversityFort CollinsColoradoUSA
| |
Collapse
|
8
|
Halfmann PJ, Kuroda M, Armbrust T, Theiler J, Balaram A, Moreno GK, Accola MA, Iwatsuki-Horimoto K, Valdez R, Stoneman E, Braun K, Yamayoshi S, Somsen E, Baczenas JJ, Mitamura K, Hagihara M, Adachi E, Koga M, McLaughlin M, Rehrauer W, Imai M, Yamamoto S, Tsutsumi T, Saito M, Friedrich TC, O’Connor SL, O’Connor DH, Gordon A, Korber B, Kawaoka Y. Characterization of the SARS-CoV-2 B.1.621 (Mu) variant. Sci Transl Med 2022; 14:eabm4908. [PMID: 35579540 PMCID: PMC9392899 DOI: 10.1126/scitranslmed.abm4908] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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] [Indexed: 12/13/2022]
Abstract
The SARS-CoV-2 B.1.621 (Mu) variant emerged in January 2021 and was categorized as a variant of interest by the World Health Organization in August 2021. This designation prompted us to study the sensitivity of this variant to antibody neutralization. In a live virus neutralization assay with serum samples from individuals vaccinated with the Pfizer/BioNTech or Moderna mRNA vaccines, we measured neutralization antibody titers against B.1.621, an early isolate (spike 614D), and a variant of concern (B.1.351, Beta variant). We observed reduced neutralizing antibody titers against the B.1.621 variant (3.4- to 7-fold reduction, depending on the serum sample and time after the second vaccination) compared to the early isolate and a similar reduction when compared to B.1.351. Likewise, convalescent serum from hamsters previously infected with an early isolate neutralized B.1.621 to a lower degree. Despite this antibody titer reduction, hamsters could not be efficiently rechallenged with the B.1.621 variant, suggesting that the immune response to the first infection is adequate to provide protection against a subsequent infection with the B.1.621 variant.
Collapse
Affiliation(s)
- Peter J. Halfmann
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53711.,Corresponding authors: (Y.K.); (P.H.)
| | - Makoto Kuroda
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53711
| | - Tammy Armbrust
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53711
| | - James Theiler
- Los Alamos National Laboratory, Space Data Science and Systems, Los Alamos, NM 87545
| | - Ariane Balaram
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53711
| | - Gage K. Moreno
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53705
| | - Molly A. Accola
- UW Health Clinical Laboratories, University of Wisconsin Hospital and Clinics, Madison, WI 53792
| | - Kiyoko Iwatsuki-Horimoto
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, 108-8639 Tokyo, Japan
| | - Riccardo Valdez
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
| | - Emily Stoneman
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI 48109
| | - Katarina Braun
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53711
| | - Seiya Yamayoshi
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, 108-8639 Tokyo, Japan
| | - Elizabeth Somsen
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53705
| | - John J. Baczenas
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53705.,Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715
| | - Keiko Mitamura
- Division of Infection Control, Eiju General Hospital, 110-8645, Tokyo, Japan
| | - Masao Hagihara
- Department of Hematology, Eiju General Hospital, 110-8645, Tokyo, Japan
| | - Eisuke Adachi
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, 108-8639, Tokyo, Japan
| | - Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, 108-8639, Tokyo, Japan
| | - Matthew McLaughlin
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53705
| | - William Rehrauer
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53705.,UW Health Clinical Laboratories, University of Wisconsin Hospital and Clinics, Madison, WI 53792
| | - Masaki Imai
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, 108-8639 Tokyo, Japan
| | - Shinya Yamamoto
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, 108-8639, Tokyo, Japan
| | - Takeya Tsutsumi
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, 108-8639, Tokyo, Japan
| | - Makoto Saito
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, 108-8639, Tokyo, Japan
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53711.,Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715
| | - Shelby L. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53705.,Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715
| | - David H. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53705.,Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715
| | - Aubree Gordon
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109
| | - Bette Korber
- Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, NM 87545.,The New Mexico Consortium, Los Alamos, NM 87545
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53711.,Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, 108-8639 Tokyo, Japan.,The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan.,Corresponding authors: (Y.K.); (P.H.)
| |
Collapse
|
9
|
Curlin JZ, Schmitt K, Remling-Mulder L, Moriarty RV, Baczenas JJ, Goff K, O'Connor S, Stenglein M, Marx PA, Akkina R. In vivo Infection Dynamics and Human Adaptive Changes of SIVsm-Derived Viral Siblings SIVmac239, SIVB670, and SIVhu in Humanized Mice as a Paralog of HIV-2 Genesis. Front Virol 2021; 1. [PMID: 37168442 PMCID: PMC10168645 DOI: 10.3389/fviro.2021.813606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Simian immunodeficiency virus native to sooty mangabeys (SIVsm) is believed to have given rise to HIV-2 through cross-species transmission and evolution in the human. SIVmac239 and SIVB670, pathogenic to macaques, and SIVhu, isolated from an accidental human infection, also have origins in SIVsm. With their common ancestral lineage as that of HIV-2 from the progenitor SIVsm, but with different passage history in different hosts, they provide a unique opportunity to evaluate cross-species transmission to a new host and their adaptation/evolution both in terms of potential genetic and phenotypic changes. Using humanized mice with a transplanted human system, we evaluated in vivo replication kinetics, CD4+ T cell dynamics and genetic adaptive changes during serial passage with a goal to understand their evolution under human selective immune pressure. All the three viruses readily infected hu-mice causing chronic viremia. While SIVmac and SIVB670 caused CD4+ T cell depletion during sequential passaging, SIVhu with a deletion in nef gene was found to be less pathogenic. Deep sequencing of the genomes of these viruses isolated at different times revealed numerous adaptive mutations of significance that increased in frequency during sequential passages. The ability of these viruses to infect and replicate in humanized mice provides a new small animal model to study SIVs in vivo in addition to more expensive macaques. Since SIVmac and related viruses have been indispensable in many areas of HIV pathogenesis, therapeutics and cure research, availability of this small animal hu-mouse model that is susceptible to both SIV and HIV viruses is likely to open novel avenues of investigation for comparative studies using the same host.
Collapse
|
10
|
Chandrashekar A, Liu J, Yu J, McMahan K, Tostanoski LH, Jacob-Dolan C, Mercado NB, Anioke T, Chang A, Gardner S, Giffin VM, Hope DL, Nampanya F, Patel S, Sanborn O, Sellers D, Wan H, Martinot AJ, Baczenas JJ, O’Connor SL, Pessaint L, Valentin D, Espina B, Wattay L, Ferrari MG, Brown R, Cook A, Bueno-Wilkerson D, Teow E, Andersen H, Lewis MG, Barouch DH. Prior infection with SARS-CoV-2 WA1/2020 partially protects rhesus macaques against reinfection with B.1.1.7 and B.1.351 variants. Sci Transl Med 2021; 13:eabj2641. [PMID: 34546094 PMCID: PMC8829873 DOI: 10.1126/scitranslmed.abj2641] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 04/30/2021] [Accepted: 09/13/2021] [Indexed: 12/26/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that result in increased transmissibility and partial evasion of neutralizing antibodies have recently emerged. Whether natural immunity induced by the original SARS-CoV-2 WA1/2020 strain protects against rechallenge with these SARS-CoV-2 variants remains a critical unresolved question. In this study, we show that natural immunity induced by the WA1/2020 strain leads to partial but incomplete protection against the SARS-CoV-2 variants B.1.1.7 (alpha) and B.1.351 (beta) in rhesus macaques. We challenged rhesus macaques with B.1.1.7 and B.1.351 and showed that infection with these variants resulted in high viral replication in the upper and lower respiratory tract. We then infected rhesus macaques with the WA1/2020 strain and rechallenged them on day 35 with the WA1/2020, B.1.1.7, or B.1.351 variants. Natural immunity to WA1/2020 led to robust protection against rechallenge with WA1/2020 but only partial protection against rechallenge with B.1.351. An intermediate degree of protection was observed in rhesus macaques against rechallenge with B.1.1.7. These data demonstrate partial but incomplete protective efficacy of natural immunity induced by WA1/2020 against SARS-CoV-2 variants of concern. Our findings have important implications for both vaccination and public health strategies in the context of emerging SARS-CoV-2 variants of concern.
Collapse
Affiliation(s)
- Abishek Chandrashekar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jinyan Liu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Katherine McMahan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Lisa H. Tostanoski
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Catherine Jacob-Dolan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Noe B. Mercado
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Tochi Anioke
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Aiquan Chang
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Sarah Gardner
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Victoria M. Giffin
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - David L. Hope
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Felix Nampanya
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Shivani Patel
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Owen Sanborn
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Daniel Sellers
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Huahua Wan
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Amanda J. Martinot
- Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA
| | - John J. Baczenas
- Wisconsin National Primate Research Center and University of Wisconsin, Madison, WI 53711, USA
| | - Shelby L. O’Connor
- Wisconsin National Primate Research Center and University of Wisconsin, Madison, WI 53711, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
- Harvard Medical School, Boston, MA 02115, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| |
Collapse
|
11
|
Bohm EK, Vangorder-Braid JT, Jaeger AS, Moriarty RV, Baczenas JJ, Bennett NC, O’Connor SL, Fritsch MK, Fuhler NA, Noguchi KK, Aliota MT. Zika Virus Infection of Pregnant Ifnar1-/- Mice Triggers Strain-Specific Differences in Fetal Outcomes. J Virol 2021; 95:e0081821. [PMID: 34379510 PMCID: PMC8513483 DOI: 10.1128/jvi.00818-21] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/03/2021] [Indexed: 01/22/2023] Open
Abstract
Zika virus (ZIKV) is a flavivirus that causes a constellation of adverse fetal outcomes collectively termed congenital Zika syndrome (CZS). However, not all pregnancies exposed to ZIKV result in an infant with apparent defects. During the 2015 to 2016 American outbreak of ZIKV, CZS rates varied by geographic location. The underlying mechanisms responsible for this heterogeneity in outcomes have not been well defined. Therefore, we sought to characterize and compare the pathogenic potential of multiple Asian-/American-lineage ZIKV strains in an established Ifnar1-/- pregnant mouse model. Here, we show significant differences in the rate of fetal demise following maternal inoculation with ZIKV strains from Puerto Rico, Panama, Mexico, Brazil, and Cambodia. Rates of fetal demise broadly correlated with maternal viremia but were independent of fetus and placenta virus titer, indicating that additional underlying factors contribute to fetal outcome. Our results, in concert with those from other studies, suggest that subtle differences in ZIKV strains may have important phenotypic impacts. With ZIKV now endemic in the Americas, greater emphasis needs to be placed on elucidating and understanding the underlying mechanisms that contribute to fetal outcome. IMPORTANCE Zika virus (ZIKV) transmission has been reported in 87 countries and territories around the globe. ZIKV infection during pregnancy is associated with adverse fetal outcomes, including birth defects, microcephaly, neurological complications, and even spontaneous abortion. Rates of adverse fetal outcomes vary between regions, and not every pregnancy exposed to ZIKV results in birth defects. Not much is known about how or if the infecting ZIKV strain is linked to fetal outcomes. Our research provides evidence of phenotypic heterogeneity between Asian-/American-lineage ZIKV strains and provides insight into the underlying causes of adverse fetal outcomes. Understanding ZIKV strain-dependent pathogenic potential during pregnancy and elucidating underlying causes of diverse clinical sequelae observed during human infections is critical to understanding ZIKV on a global scale.
Collapse
Affiliation(s)
- Ellie K. Bohm
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, Minnesota, USA
| | - Jennifer T. Vangorder-Braid
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, Minnesota, USA
| | - Anna S. Jaeger
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, Minnesota, USA
| | - Ryan V. Moriarty
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - John J. Baczenas
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Natalie C. Bennett
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, Minnesota, USA
| | - Shelby L. O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Michael K. Fritsch
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nicole A. Fuhler
- Department of Psychiatry, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Kevin K. Noguchi
- Department of Psychiatry, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Matthew T. Aliota
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, Minnesota, USA
| |
Collapse
|
12
|
Moreno GK, Braun KM, Riemersma KK, Martin MA, Halfmann PJ, Crooks CM, Prall T, Baker D, Baczenas JJ, Heffron AS, Ramuta M, Khubbar M, Weiler AM, Accola MA, Rehrauer WM, O'Connor SL, Safdar N, Pepperell CS, Dasu T, Bhattacharyya S, Kawaoka Y, Koelle K, O'Connor DH, Friedrich TC. Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread. Nat Commun 2020; 11:5558. [PMID: 33144575 PMCID: PMC7609670 DOI: 10.1038/s41467-020-19346-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/06/2020] [Indexed: 12/25/2022] Open
Abstract
Evidence-based public health approaches that minimize the introduction and spread of new SARS-CoV-2 transmission clusters are urgently needed in the United States and other countries struggling with expanding epidemics. Here we analyze 247 full-genome SARS-CoV-2 sequences from two nearby communities in Wisconsin, USA, and find surprisingly distinct patterns of viral spread. Dane County had the 12th known introduction of SARS-CoV-2 in the United States, but this did not lead to descendant community spread. Instead, the Dane County outbreak was seeded by multiple later introductions, followed by limited community spread. In contrast, relatively few introductions in Milwaukee County led to extensive community spread. We present evidence for reduced viral spread in both counties following the statewide "Safer at Home" order, which went into effect 25 March 2020. Our results suggest patterns of SARS-CoV-2 transmission may vary substantially even in nearby communities. Understanding these local patterns will enable better targeting of public health interventions.
Collapse
Affiliation(s)
- Gage K Moreno
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Katarina M Braun
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Kasen K Riemersma
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael A Martin
- Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University, Atlanta, GA, USA
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Peter J Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Chelsea M Crooks
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Trent Prall
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - David Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - John J Baczenas
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Anna S Heffron
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Mitchell Ramuta
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Manjeet Khubbar
- City of Milwaukee Health Department Laboratory, Milwaukee, WI, USA
| | - Andrea M Weiler
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Molly A Accola
- University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- The William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | - William M Rehrauer
- University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- The William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | - Shelby L O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Nasia Safdar
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Caitlin S Pepperell
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Trivikram Dasu
- City of Milwaukee Health Department Laboratory, Milwaukee, WI, USA
| | | | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Katia Koelle
- Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University, Atlanta, GA, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA.
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
13
|
Moreno GK, Braun KM, Riemersma KK, Martin MA, Halfmann PJ, Crooks CM, Prall T, Baker D, Baczenas JJ, Heffron AS, Ramuta M, Khubbar M, Weiler AM, Accola MA, Rehrauer WM, O'Connor SL, Safdar N, Pepperell CS, Dasu T, Bhattacharyya S, Kawaoka Y, Koelle K, O'Connor DH, Friedrich TC. Distinct patterns of SARS-CoV-2 transmission in two nearby communities in Wisconsin, USA. medRxiv 2020:2020.07.09.20149104. [PMID: 32676620 PMCID: PMC7359545 DOI: 10.1101/2020.07.09.20149104] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 01/12/2023]
Abstract
Evidence-based public health approaches that minimize the introduction and spread of new SARS-CoV-2 transmission clusters are urgently needed in the United States and other countries struggling with expanding epidemics. Here we analyze 247 full-genome SARS-CoV-2 sequences from two nearby communities in Wisconsin, USA, and find surprisingly distinct patterns of viral spread. Dane County had the 12th known introduction of SARS-CoV-2 in the United States, but this did not lead to descendant community spread. Instead, the Dane County outbreak was seeded by multiple later introductions, followed by limited community spread. In contrast, relatively few introductions in Milwaukee County led to extensive community spread. We present evidence for reduced viral spread in both counties, and limited viral transmission between counties, following the statewide Safer-at-Home public health order, which went into effect 25 March 2020. Our results suggest that early containment efforts suppressed the spread of SARS-CoV-2 within Wisconsin.
Collapse
Affiliation(s)
- Gage K Moreno
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Katarina M Braun
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Kasen K Riemersma
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Michael A Martin
- Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University, Atlanta, GA, United States of America
- Department of Biology, Emory University, Atlanta, GA, United States of America
| | - Peter J Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Chelsea M Crooks
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Trent Prall
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - David Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - John J Baczenas
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Anna S Heffron
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Mitchell Ramuta
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Manjeet Khubbar
- City of Milwaukee Health Department Laboratory, Milwaukee, WI, United States of America
| | - Andrea M Weiler
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Molly A Accola
- University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of 26 America and the William S. Middleton Memorial Veterans Hospital
| | - William M Rehrauer
- University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of 26 America and the William S. Middleton Memorial Veterans Hospital
| | - Shelby L O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Nasia Safdar
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin School of 28 Medicine and Public Health, Madison, WI
| | - Caitlin S Pepperell
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin School of 28 Medicine and Public Health, Madison, WI
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, 30 Madison, WI, United States of America
| | - Trivikram Dasu
- City of Milwaukee Health Department Laboratory, Milwaukee, WI, United States of America
| | - Sanjib Bhattacharyya
- City of Milwaukee Health Department Laboratory, Milwaukee, WI, United States of America
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Katia Koelle
- Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University, Atlanta, GA, United States of America
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America
| |
Collapse
|