Genomic epidemiology reveals the dominance of Hennepin County in the transmission of SARS-CoV-2 in Minnesota from 2020 to 2022
ABSTRACTSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had an unprecedented impact on human health and highlights the need for genomic epidemiology studies to increase our understanding of virus evolution and spread and to inform policy decisions. We sequenced viral genomes from ov...
| Main Authors: | , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
American Society for Microbiology
2023-12-01
|
| Series: | mSphere |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/msphere.00232-23 |
| _version_ | 1797384683659460608 |
|---|---|
| author | Matthew Scotch Kimberly Lauer Eric D. Wieben Yesesri Cherukuri Julie M. Cunningham Eric W. Klee Jonathan J. Harrington Julie S. Lau Samantha J. McDonough Mark Mutawe John C. O'Horo Chad E. Rentmeester Nicole R. Schlicher Valerie T. White Susan K. Schneider Peter T. Vedell Xiong Wang Joseph D. Yao Bobbi S. Pritt Andrew P. Norgan |
| author_facet | Matthew Scotch Kimberly Lauer Eric D. Wieben Yesesri Cherukuri Julie M. Cunningham Eric W. Klee Jonathan J. Harrington Julie S. Lau Samantha J. McDonough Mark Mutawe John C. O'Horo Chad E. Rentmeester Nicole R. Schlicher Valerie T. White Susan K. Schneider Peter T. Vedell Xiong Wang Joseph D. Yao Bobbi S. Pritt Andrew P. Norgan |
| author_sort | Matthew Scotch |
| collection | DOAJ |
| description | ABSTRACTSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had an unprecedented impact on human health and highlights the need for genomic epidemiology studies to increase our understanding of virus evolution and spread and to inform policy decisions. We sequenced viral genomes from over 22,000 patient samples tested at Mayo Clinic Laboratories between 2020 and 2022 and used Bayesian phylodynamics to describe county and regional spread in Minnesota. The earliest calculated introduction into Minnesota was to Hennepin County from a domestic source around 22 January 2020; 6 weeks before the first confirmed case in the state. This led to the virus spreading to Northern Minnesota and, eventually, the rest of the state. International introductions were most abundant in Hennepin (home to the Minneapolis/St. Paul International Airport) totaling 45 (out of 107) over the 2-year period. Southern Minnesota counties were most common for domestic introductions, with 19 (out of 64), potentially driven by bordering states such as Iowa and Wisconsin as well as Illinois, which is nearby. Hennepin also was, by far, the most dominant source of in-state transmissions to other Minnesota locations (n = 772) over the 2-year period. We also analyzed the diversity of the location source of SARS-CoV-2 viruses in each county and noted the timing of state-wide policies as well as trends in clinical cases. Neither the number of clinical cases nor the major policy decisions, such as the end of the lockdown period in 2020 or the end of all restrictions in 2021, appeared to have an impact on virus diversity across each individual county.IMPORTANCEWe analyzed over 22,000 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes of patient samples tested at Mayo Clinic Laboratories during a 2-year period in the COVID-19 pandemic, which included Alpha, Delta, and Omicron variants of concern to examine the roles and relationships of Minnesota virus transmission. We found that Hennepin County, the most populous county, drove the transmission of SARS-CoV-2 viruses in the state after including the formation of earlier clades including 20A, 20C, and 20G, as well as variants of concern Alpha and Delta. We also found that Hennepin County was the source for most of the county-to-county introductions after an initial predicted introduction with the virus in early 2020 from an international source, while other counties acted as transmission “sinks.” In addition, major policies, such as the end of the lockdown period in 2020 or the end of all restrictions in 2021, did not appear to have an impact on virus diversity across individual counties. |
| first_indexed | 2024-03-08T21:40:13Z |
| format | Article |
| id | doaj.art-8777d24714df47e7ade07b71b5f5db3e |
| institution | Directory Open Access Journal |
| issn | 2379-5042 |
| language | English |
| last_indexed | 2024-03-08T21:40:13Z |
| publishDate | 2023-12-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSphere |
| spelling | doaj.art-8777d24714df47e7ade07b71b5f5db3e2023-12-20T14:01:03ZengAmerican Society for MicrobiologymSphere2379-50422023-12-018610.1128/msphere.00232-23Genomic epidemiology reveals the dominance of Hennepin County in the transmission of SARS-CoV-2 in Minnesota from 2020 to 2022Matthew Scotch0Kimberly Lauer1Eric D. Wieben2Yesesri Cherukuri3Julie M. Cunningham4Eric W. Klee5Jonathan J. Harrington6Julie S. Lau7Samantha J. McDonough8Mark Mutawe9John C. O'Horo10Chad E. Rentmeester11Nicole R. Schlicher12Valerie T. White13Susan K. Schneider14Peter T. Vedell15Xiong Wang16Joseph D. Yao17Bobbi S. Pritt18Andrew P. Norgan19Research Affiliate, Mayo Clinic, Phoenix, Arizona, USADepartment of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USADepartment of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USAResearch Services, Mayo Clinic, Jacksonville, Florida, USADepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USADepartment of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USACenter for Individualized Medicine, Rochester, Minnesota, USACenter for Individualized Medicine, Rochester, Minnesota, USACenter for Individualized Medicine, Rochester, Minnesota, USACenter for Individualized Medicine, Rochester, Minnesota, USADivision of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USADepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USADepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USADepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USADepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USADepartment of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USAMinnesota Department of Health, St. Paul, Minnesota, USADepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USADepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USADepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USAABSTRACTSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had an unprecedented impact on human health and highlights the need for genomic epidemiology studies to increase our understanding of virus evolution and spread and to inform policy decisions. We sequenced viral genomes from over 22,000 patient samples tested at Mayo Clinic Laboratories between 2020 and 2022 and used Bayesian phylodynamics to describe county and regional spread in Minnesota. The earliest calculated introduction into Minnesota was to Hennepin County from a domestic source around 22 January 2020; 6 weeks before the first confirmed case in the state. This led to the virus spreading to Northern Minnesota and, eventually, the rest of the state. International introductions were most abundant in Hennepin (home to the Minneapolis/St. Paul International Airport) totaling 45 (out of 107) over the 2-year period. Southern Minnesota counties were most common for domestic introductions, with 19 (out of 64), potentially driven by bordering states such as Iowa and Wisconsin as well as Illinois, which is nearby. Hennepin also was, by far, the most dominant source of in-state transmissions to other Minnesota locations (n = 772) over the 2-year period. We also analyzed the diversity of the location source of SARS-CoV-2 viruses in each county and noted the timing of state-wide policies as well as trends in clinical cases. Neither the number of clinical cases nor the major policy decisions, such as the end of the lockdown period in 2020 or the end of all restrictions in 2021, appeared to have an impact on virus diversity across each individual county.IMPORTANCEWe analyzed over 22,000 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes of patient samples tested at Mayo Clinic Laboratories during a 2-year period in the COVID-19 pandemic, which included Alpha, Delta, and Omicron variants of concern to examine the roles and relationships of Minnesota virus transmission. We found that Hennepin County, the most populous county, drove the transmission of SARS-CoV-2 viruses in the state after including the formation of earlier clades including 20A, 20C, and 20G, as well as variants of concern Alpha and Delta. We also found that Hennepin County was the source for most of the county-to-county introductions after an initial predicted introduction with the virus in early 2020 from an international source, while other counties acted as transmission “sinks.” In addition, major policies, such as the end of the lockdown period in 2020 or the end of all restrictions in 2021, did not appear to have an impact on virus diversity across individual counties.https://journals.asm.org/doi/10.1128/msphere.00232-23epidemiologycomputational biologySARS-CoV-2Minnesotahigh-throughput nucleotide sequencing |
| spellingShingle | Matthew Scotch Kimberly Lauer Eric D. Wieben Yesesri Cherukuri Julie M. Cunningham Eric W. Klee Jonathan J. Harrington Julie S. Lau Samantha J. McDonough Mark Mutawe John C. O'Horo Chad E. Rentmeester Nicole R. Schlicher Valerie T. White Susan K. Schneider Peter T. Vedell Xiong Wang Joseph D. Yao Bobbi S. Pritt Andrew P. Norgan Genomic epidemiology reveals the dominance of Hennepin County in the transmission of SARS-CoV-2 in Minnesota from 2020 to 2022 mSphere epidemiology computational biology SARS-CoV-2 Minnesota high-throughput nucleotide sequencing |
| title | Genomic epidemiology reveals the dominance of Hennepin County in the transmission of SARS-CoV-2 in Minnesota from 2020 to 2022 |
| title_full | Genomic epidemiology reveals the dominance of Hennepin County in the transmission of SARS-CoV-2 in Minnesota from 2020 to 2022 |
| title_fullStr | Genomic epidemiology reveals the dominance of Hennepin County in the transmission of SARS-CoV-2 in Minnesota from 2020 to 2022 |
| title_full_unstemmed | Genomic epidemiology reveals the dominance of Hennepin County in the transmission of SARS-CoV-2 in Minnesota from 2020 to 2022 |
| title_short | Genomic epidemiology reveals the dominance of Hennepin County in the transmission of SARS-CoV-2 in Minnesota from 2020 to 2022 |
| title_sort | genomic epidemiology reveals the dominance of hennepin county in the transmission of sars cov 2 in minnesota from 2020 to 2022 |
| topic | epidemiology computational biology SARS-CoV-2 Minnesota high-throughput nucleotide sequencing |
| url | https://journals.asm.org/doi/10.1128/msphere.00232-23 |
| work_keys_str_mv | AT matthewscotch genomicepidemiologyrevealsthedominanceofhennepincountyinthetransmissionofsarscov2inminnesotafrom2020to2022 AT kimberlylauer genomicepidemiologyrevealsthedominanceofhennepincountyinthetransmissionofsarscov2inminnesotafrom2020to2022 AT ericdwieben genomicepidemiologyrevealsthedominanceofhennepincountyinthetransmissionofsarscov2inminnesotafrom2020to2022 AT yesesricherukuri genomicepidemiologyrevealsthedominanceofhennepincountyinthetransmissionofsarscov2inminnesotafrom2020to2022 AT juliemcunningham genomicepidemiologyrevealsthedominanceofhennepincountyinthetransmissionofsarscov2inminnesotafrom2020to2022 AT ericwklee genomicepidemiologyrevealsthedominanceofhennepincountyinthetransmissionofsarscov2inminnesotafrom2020to2022 AT jonathanjharrington genomicepidemiologyrevealsthedominanceofhennepincountyinthetransmissionofsarscov2inminnesotafrom2020to2022 AT julieslau genomicepidemiologyrevealsthedominanceofhennepincountyinthetransmissionofsarscov2inminnesotafrom2020to2022 AT samanthajmcdonough genomicepidemiologyrevealsthedominanceofhennepincountyinthetransmissionofsarscov2inminnesotafrom2020to2022 AT markmutawe genomicepidemiologyrevealsthedominanceofhennepincountyinthetransmissionofsarscov2inminnesotafrom2020to2022 AT johncohoro genomicepidemiologyrevealsthedominanceofhennepincountyinthetransmissionofsarscov2inminnesotafrom2020to2022 AT chaderentmeester genomicepidemiologyrevealsthedominanceofhennepincountyinthetransmissionofsarscov2inminnesotafrom2020to2022 AT nicolerschlicher genomicepidemiologyrevealsthedominanceofhennepincountyinthetransmissionofsarscov2inminnesotafrom2020to2022 AT valerietwhite genomicepidemiologyrevealsthedominanceofhennepincountyinthetransmissionofsarscov2inminnesotafrom2020to2022 AT susankschneider genomicepidemiologyrevealsthedominanceofhennepincountyinthetransmissionofsarscov2inminnesotafrom2020to2022 AT petertvedell genomicepidemiologyrevealsthedominanceofhennepincountyinthetransmissionofsarscov2inminnesotafrom2020to2022 AT xiongwang genomicepidemiologyrevealsthedominanceofhennepincountyinthetransmissionofsarscov2inminnesotafrom2020to2022 AT josephdyao genomicepidemiologyrevealsthedominanceofhennepincountyinthetransmissionofsarscov2inminnesotafrom2020to2022 AT bobbispritt genomicepidemiologyrevealsthedominanceofhennepincountyinthetransmissionofsarscov2inminnesotafrom2020to2022 AT andrewpnorgan genomicepidemiologyrevealsthedominanceofhennepincountyinthetransmissionofsarscov2inminnesotafrom2020to2022 |