Multimodal surveillance of SARS-CoV-2 at a university enables development of a robust outbreak response framework

[1]  Jared R. Auclair,et al.  Early Introduction and Rise of the Omicron Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variant in Highly Vaccinated University Populations , 2022, medRxiv.

[2]  Lance Hartung,et al.  Network-Side Digital Contact Tracing on a Large University Campus , 2022 .

[3]  Pardis C Sabeti,et al.  Containing the spread of mumps on college campuses , 2022, Royal Society Open Science.

[4]  P. Frazier,et al.  Modeling for COVID-19 college reopening decisions: Cornell, a case study , 2021, Proceedings of the National Academy of Sciences.

[5]  Christine M. Aceves,et al.  Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission , 2021, medRxiv.

[6]  D. O’Connor,et al.  SARS-CoV-2 Genomic Surveillance Reveals Little Spread From a Large University Campus to the Surrounding Community , 2021, Open forum infectious diseases.

[7]  Kenneth E Curewitz,et al.  Wastewater and surface monitoring to detect COVID-19 in elementary school settings: The Safer at School Early Alert project , 2021, medRxiv.

[8]  Amanda M Jovaag,et al.  Interventions to Disrupt Coronavirus Disease Transmission at a University, Wisconsin, USA, August–October 2020 , 2021, Emerging infectious diseases.

[9]  P. Remington,et al.  Risk Factors for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection and Presence of Anti–SARS-CoV-2 Antibodies Among University Student Dormitory Residents, September–November 2020 , 2021, Open forum infectious diseases.

[10]  O. Pybus,et al.  Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool , 2021, Virus evolution.

[11]  J. Ren,et al.  Rapid, Large-Scale Wastewater Surveillance and Automated Reporting System Enable Early Detection of Nearly 85% of COVID-19 Cases on a University Campus , 2021, medRxiv.

[12]  Mi-Kyung Lee,et al.  Impact of social distancing on the spread of common respiratory viruses during the coronavirus disease outbreak , 2021, PloS one.

[13]  Jessica L. Darby,et al.  High-resolution within-sewer SARS-CoV-2 surveillance facilitates informed intervention , 2021, Water Research.

[14]  C. McMahan,et al.  Risk of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Reinfection in a University Student Population , 2021, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[15]  Katherine Meierdiercks,et al.  Wastewater Surveillance for SARS-CoV-2 on College Campuses: Initial Efforts, Lessons Learned, and Research Needs , 2021, International journal of environmental research and public health.

[16]  R. Andino,et al.  Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant , 2021, Cell.

[17]  M. J. Broadhurst,et al.  Pilot program for test-based SARS-CoV-2 screening and environmental monitoring in an urban public school district , 2021, medRxiv.

[18]  Pardis C Sabeti,et al.  The case for altruism in institutional diagnostic testing , 2021, Scientific Reports.

[19]  D. Dinwiddie,et al.  Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677 , 2021, medRxiv.

[20]  Katherine Meierdiercks,et al.  Wastewater surveillance for SARS-CoV-2 on college campuses: Initial efforts, lessons learned and research needs , 2021, medRxiv.

[21]  K. Linka,et al.  Are college campuses superspreaders? A data-driven modeling study , 2021, Computer methods in biomechanics and biomedical engineering.

[22]  Ellsworth M. Campbell,et al.  Participation in Fraternity and Sorority Activities and the Spread of COVID-19 Among Residential University Communities — Arkansas, August 21–September 5, 2020 , 2021, MMWR. Morbidity and mortality weekly report.

[23]  G. Abowd,et al.  Empirical networks for localized COVID-19 interventions using WiFi infrastructure at university campuses , 2023, Frontiers in Digital Health.

[24]  K. Linka,et al.  Are college campuses superspreaders? A data-driven modeling study , 2020, medRxiv.

[25]  M. Springer,et al.  The Impacts of Testing Cadence, Mode of Instruction, and Student Density on Fall 2020 COVID-19 Rates On Campus , 2020, medRxiv.

[26]  Andrew D Smith,et al.  Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore , 2020, bioRxiv.

[27]  Xifeng Wu,et al.  Household transmission of COVID-19-a systematic review and meta-analysis , 2020, Journal of Infection.

[28]  Edward C. Holmes,et al.  A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology , 2020, Nature Microbiology.

[29]  J. Quick,et al.  COVID-19 ARTIC v3 Illumina library construction and sequencing protocol - short amplicons (275bp) v1 , 2020 .

[30]  J. R. Giles,et al.  Sample size calculation for phylogenetic case linkage , 2020, medRxiv.

[31]  Pardis C Sabeti,et al.  Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant , 2020, bioRxiv.

[32]  Rochelle P. Walensky,et al.  Assessment of SARS-CoV-2 Screening Strategies to Permit the Safe Reopening of College Campuses in the United States , 2020, JAMA network open.

[33]  Yongsheng Wu,et al.  Epidemiology and transmission of COVID-19 in 391 cases and 1286 of their close contacts in Shenzhen, China: a retrospective cohort study , 2020, The Lancet Infectious Diseases.

[34]  Laura Matrajt,et al.  Evaluating the Effectiveness of Social Distancing Interventions to Delay or Flatten the Epidemic Curve of Coronavirus Disease , 2020, Emerging infectious diseases.

[35]  A. Vespignani,et al.  Evolving epidemiology and transmission dynamics of coronavirus disease 2019 outside Hubei province, China: a descriptive and modelling study , 2020, The Lancet Infectious Diseases.

[36]  Olga Chernomor,et al.  IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era , 2019, bioRxiv.

[37]  Karthik Gangavarapu,et al.  An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar , 2018, Genome Biology.

[38]  Patricia Quinlisk,et al.  Mumps Outbreak in a Highly Vaccinated University-Affiliated Setting Before and After a Measles-Mumps-Rubella Vaccination Campaign—Iowa, July 2015–May 2016 , 2018, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[39]  Dennis Andersson,et al.  A retrospective cohort study , 2018 .

[40]  Trevor Bedford,et al.  Nextstrain: real-time tracking of pathogen evolution , 2017, bioRxiv.

[41]  Richard A Neher,et al.  TreeTime: Maximum-likelihood phylodynamic analysis , 2017, bioRxiv.

[42]  Trevor Bedford,et al.  Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples , 2017, Nature Protocols.

[43]  Abigail Stone,et al.  Poor hand hygiene by college students linked to more occurrences of infectious diseases, medical visits, and absence from classes. , 2016, American journal of infection control.

[44]  T. Nolan,et al.  Vaccination with a multicomponent meningococcal B vaccine in prevention of disease in adolescents and young adults. , 2015, Vaccine.

[45]  M. Taha,et al.  Meningococcal carriage during a clonal meningococcal B outbreak in France , 2013, European Journal of Clinical Microbiology & Infectious Diseases.

[46]  A. Wilm,et al.  LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets , 2012, Nucleic acids research.

[47]  Sanyi Tang,et al.  Campus quarantine (Fengxiao) for curbing emergent infectious diseases: lessons from mitigating A/H1N1 in Xi'an, China. , 2012, Journal of theoretical biology.

[48]  Laura M. Glass,et al.  Targeted Social Distancing Designs for Pandemic Influenza , 2006, Emerging infectious diseases.

[49]  N. Andrews,et al.  Social Behavior and Meningococcal Carriage in British Teenagers , 2006, Emerging infectious diseases.

[50]  J. Oosterheert,et al.  Frequent Detection of Human Coronaviruses in Clinical Specimens from Patients with Respiratory Tract Infection by Use of a Novel Real-Time Reverse-Transcriptase Polymerase Chain Reaction , 2004, The Journal of infectious diseases.

[51]  M. Newman Assortative mixing in networks. , 2002, Physical review letters.

[52]  Susan W. Jeansonne Risk of Meningococcal Infection in College Students , 2000 .

[53]  L. Harrison,et al.  Risk of meningococcal infection in college students. , 1999, JAMA.

[54]  S P Azen,et al.  OBTAINING CONFIDENCE INTERVALS FOR THE RISK RATIO IN COHORT STUDIES , 1978 .

[55]  A. Savitzky,et al.  Smoothing and Differentiation of Data by Simplified Least Squares Procedures. , 1964 .

[56]  Edsger W. Dijkstra,et al.  A note on two problems in connexion with graphs , 1959, Numerische Mathematik.