1932

Abstract

The coronavirus disease 2019 (COVID-19) pandemic challenged the workings of human society, but in doing so, it advanced our understanding of the ecology and evolution of infectious diseases. Fluctuating transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) demonstrated the highly dynamic nature of human social behavior, often without government intervention. Evolution of SARS-CoV-2 in the first two years following spillover resulted primarily in increased transmissibility, while in the third year, the globally dominant virus variants had all evolved substantial immune evasion. The combination of viral evolution and the buildup of host immunity through vaccination and infection greatly decreased the realized virulence of SARS-CoV-2 due to the age dependence of disease severity. The COVID-19 pandemic was exacerbated by presymptomatic, asymptomatic, and highly heterogeneous transmission, as well as highly variable disease severity and the broad host range of SARS-CoV-2. Insights and tools developed during the COVID-19 pandemic could provide a stronger scientific basis for preventing, mitigating, and controlling future pandemics.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-ecolsys-102320-101234
2023-11-02
2024-05-08
Loading full text...

Full text loading...

/deliver/fulltext/ecolsys/54/1/annurev-ecolsys-102320-101234.html?itemId=/content/journals/10.1146/annurev-ecolsys-102320-101234&mimeType=html&fmt=ahah

Literature Cited

  1. Abraham JO, Mumma MA. 2021. Elevated wildlife-vehicle collision rates during the COVID-19 pandemic. Sci. Rep. 11:20391
    [Google Scholar]
  2. Aguilar-Bretones M, Fouchier RA, Koopmans MP, van Nierop GP. 2023. Impact of antigenic evolution and original antigenic sin on SARS-CoV-2 immunity. J. Clin. Investig. 133:e162192
    [Google Scholar]
  3. Althaus CL, Baggio S, Reichmuth ML, Hodcroft EB, Riou J et al. 2021. A tale of two variants: spread of SARS-CoV-2 variants Alpha in Geneva, Switzerland, and Beta in South Africa. medRxiv 2021.06.10.21258468. https://doi.org/10.1101/2021.06.10.21258468
    [Crossref]
  4. Alwan NA, Burgess RA, Ashworth S, Beale R, Bhadelia N et al. 2020. Scientific consensus on the COVID-19 pandemic: We need to act now. Lancet 396:e71–72
    [Google Scholar]
  5. Andrejko KL, Pry JM, Myers JF, Fukui N, DeGuzman JL et al. 2022. Effectiveness of face mask or respirator use in indoor public settings for prevention of SARS-CoV-2 infection—California, February–December 2021. Morb. Mortal. Wkly. Rep. 71:212
    [Google Scholar]
  6. Andrews N, Stowe J, Kirsebom F, Toffa S, Rickeard T et al. 2022a. COVID-19 vaccine effectiveness against the omicron (B.1.1.529) variant. N. Engl. J. Med. 386:1532–46
    [Google Scholar]
  7. Andrews N, Tessier E, Stowe J, Gower C, Kirsebom F et al. 2022b. Duration of protection against mild and severe disease by COVID-19 vaccines. N. Engl. J. Med. 386:340–50
    [Google Scholar]
  8. Armando F, Beythien G, Kaiser FK, Allnoch L, Heydemann L et al. 2022. SARS-CoV-2 Omicron variant causes mild pathology in the upper and lower respiratory tract of hamsters. Nat. Commun. 13:3519
    [Google Scholar]
  9. Arsenault C, Gage A, Kim MK, Kapoor NR, Akweongo P et al. 2022. COVID-19 and resilience of healthcare systems in ten countries. Nat. Med. 28:1314–24
    [Google Scholar]
  10. Aylward B, Barboza P, Bawo L, Bertherat E, Bilivogui P et al. 2014. Ebola virus disease in West Africa—the first 9 months of the epidemic and forward projections. N. Engl. J. Med. 371:1481–95
    [Google Scholar]
  11. Baker RE, Yang W, Vecchi GA, Metcalf CJE, Grenfell BT. 2020. Susceptible supply limits the role of climate in the early SARS-CoV-2 pandemic. Science 369:315–19
    [Google Scholar]
  12. Bates AE, Primack RB, Biggar BS, Bird TJ, Clinton ME et al. 2021. Global COVID-19 lockdown highlights humans as both threats and custodians of the environment. Biol. Conserv. 263:109175
    [Google Scholar]
  13. Bjornstad ON, Finkenstadt BF, Grenfell BT. 2002. Dynamics of measles epidemics: estimating scaling of transmission rates using a time series SIR model. Ecol. Monogr. 72:169–84
    [Google Scholar]
  14. CDC (Cent. Dis. Control) 2022a. Table 1: Estimated Flu Disease Burden, by Season—United States, 2010–2011 through 2021–2022 Flu Seasons Disease burden of flu: CDC Atlanta, GA: updated Oct. 2022, accessed Jan. 31, 2023. https://www.cdc.gov/flu/about/burden/index.html
  15. CDC (Cent. Dis. Control) 2022b. RSV-NET interactive dashboard. RSV-NET: Respiratory Syncytial Virus Hospitalization Surveillance Network: CDC Atlanta, GA: updated Oct. 2022, accessed Jan. 31, 2023. https://www.cdc.gov/rsv/research/rsv-net/dashboard.html
  16. Choi B, Choudhary MC, Regan J, Sparks JA, Padera RF et al. 2020. Persistence and evolution of SARS-CoV-2 in an immunocompromised host. N. Engl. J. Med. 383:2291–93
    [Google Scholar]
  17. Chu DK, Akl EA, Duda S, Solo K, Yaacoub S et al. 2020. Physical distancing, face masks, and eye protection to prevent person-to-person transmission of SARS-CoV-2 and COVID-19: a systematic review and meta-analysis. Lancet 395:1973–87
    [Google Scholar]
  18. Chua KB, Bellini WJ, Rota PA, Harcourt BH, Tamin A et al. 2000. Nipah virus: a recently emergent deadly paramyxovirus. Science 288:1432–35
    [Google Scholar]
  19. Davies NG, Jarvis CI, Edmunds WJ, Jewell NP, Diaz-Ordaz K, Keogh RH. 2021. Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7. Nature 593:270–74
    [Google Scholar]
  20. Del Fava E, Cimentada J, Perrotta D, Grow A, Rampazzo F et al. 2021. Differential impact of physical distancing strategies on social contacts relevant for the spread of SARS-CoV-2: evidence from a cross-national online survey, March–April 2020. BMJ Open 11:e050651
    [Google Scholar]
  21. Derryberry EP, Phillips JN, Derryberry GE, Blum MJ, Luther D. 2020. Singing in a silent spring: Birds respond to a half-century soundscape reversion during the COVID-19 shutdown. Science 370:575–79
    [Google Scholar]
  22. Donnelly CA, Ghani AC, Leung GM, Hedley AJ, Fraser C et al. 2003. Epidemiological determinants of spread of causal agent of severe acute respiratory syndrome in Hong Kong. Lancet 361:1761–66
    [Google Scholar]
  23. Dube K, Nhamo G, Chikodzi D. 2021. COVID-19 cripples global restaurant and hospitality industry. Curr. Issues Tourism 24:1487–90
    [Google Scholar]
  24. Eales O, Haw D, Wang H, Atchison C, Ashby D et al. 2023. Dynamics of SARS-CoV-2 infection hospitalisation and infection fatality ratios over 23 months in England. PLOS Biol. 21:e3002118
    [Google Scholar]
  25. Elliott P, Eales O, Steyn N, Tang D, Bodinier B et al. 2022. Twin peaks: the omicron SARS-CoV-2 BA.1 and BA.2 epidemics in England. Science 376:eabq4411
    [Google Scholar]
  26. Endo A, Cent. Math. Model. Infect. Dis. COVID-19 Work. Group, Abbott S, Kucharski AJ, Funk S. 2020. Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China. Wellcome Open Res. 5:67
    [Google Scholar]
  27. Epstein JH, Anthony SJ, Islam A, Kilpatrick AM, Ali Khan S et al. 2020. Nipah virus dynamics in bats and implications for spillover to humans. PNAS 117:29190–201
    [Google Scholar]
  28. Ferretti L, Ledda A, Wymant C, Zhao L, Ledda V et al. 2020. The timing of COVID-19 transmission. medRxiv 2020.09.04.20188516. https://doi.org/10.1101/2020.09.04.20188516
    [Crossref]
  29. Flaxman S, Mishra S, Gandy A, Unwin HJT, Mellan TA et al. 2020. Estimating the effects of non-pharmaceutical interventions on COVID-19 in Europe. Nature 584:257–61
    [Google Scholar]
  30. Fleming-Davies AE, Williams PD, Dhondt AA, Dobson AP, Hochachka WM et al. 2018. Incomplete host immunity favors the evolution of virulence in an emergent pathogen. Science 359:1030–33
    [Google Scholar]
  31. Forster PM, Forster HI, Evans MJ, Gidden MJ, Jones CD et al. 2020. Current and future global climate impacts resulting from COVID-19. Nat. Clim. Chang. 10:913–19
    [Google Scholar]
  32. Fraser C, Riley S, Anderson RM, Ferguson NM. 2004. Factors that make an infectious disease outbreak controllable. PNAS 101:6146–51
    [Google Scholar]
  33. Frieden TR, Buissonnière M, McClelland A. 2021. The world must prepare now for the next pandemic. BMJ Glob. Health 6:e005184
    [Google Scholar]
  34. Funk S, Gilad E, Watkins C, Jansen VAA. 2009. The spread of awareness and its impact on epidemic outbreaks. PNAS 106:6872–77
    [Google Scholar]
  35. Galvani AP. 2003. Epidemiology meets evolutionary ecology. Trends Ecol. Evol. 18:132–39
    [Google Scholar]
  36. Gao F, Bailes E, Robertson DL, Chen Y, Rodenburg CM et al. 1999. Origin of HIV-1 in the chimpanzee Pan troglodytes. Nature 397:436–41
    [Google Scholar]
  37. Gardner BJ, Kilpatrick AM. 2021a. Estimates of reduced vaccine effectiveness against hospitalization, infection, transmission and symptomatic disease of a new SARS-CoV-2 variant, Omicron (B.1.1.529), using neutralizing antibody titers. medRxiv 2021.12.10.21267594. https://doi.org/10.1101/2021.12.10.21267594
    [Crossref]
  38. Gardner BJ, Kilpatrick AM. 2021b. Third doses of COVID-19 vaccines reduce infection and transmission of SARS-CoV-2 and could prevent future surges in some populations: a modeling study. medRxiv 2021.10.25.21265500. https://doi.org/10.1101/2021.10.25.21265500
    [Crossref]
  39. Gatto M, Bertuzzo E, Mari L, Miccoli S, Carraro L et al. 2020. Spread and dynamics of the COVID-19 epidemic in Italy: effects of emergency containment measures. PNAS 117:10484–91
    [Google Scholar]
  40. Gilbert GS, Webb CO. 2007. Phylogenetic signal in plant pathogen–host range. PNAS 104:4979–83
    [Google Scholar]
  41. Giovanetti M, Fonseca V, Wilkinson E, Tegally H, San EJ et al. 2022. Replacement of the Gamma by the Delta variant in Brazil: impact of lineage displacement on the ongoing pandemic. Virus Evol. 8:veac024
    [Google Scholar]
  42. Glynn JR, Moss PAH. 2020. Systematic analysis of infectious disease outcomes by age shows lowest severity in school-age children. Sci. Data 7:329
    [Google Scholar]
  43. Goldberg AR, Langwig KE, Marano J, Sharp AK, Brown KL et al. 2022. Wildlife exposure to SARS-CoV-2 across a human use gradient. bioRxiv 2022.11.04.515237. https://doi.org/10.1101/2022.11.04.515237
    [Crossref]
  44. Haas EJ, Angulo FJ, McLaughlin JM, Anis E, Singer SR et al. 2021. Impact and effectiveness of mRNA BNT162b2 vaccine against SARS-CoV-2 infections and COVID-19 cases, hospitalisations, and deaths following a nationwide vaccination campaign in Israel: an observational study using national surveillance data. Lancet 397:1819–29
    [Google Scholar]
  45. Hale VL, Dennis PM, McBride DS, Nolting JM, Madden C et al. 2022. SARS-CoV-2 infection in free-ranging white-tailed deer. Nature 602:481–86
    [Google Scholar]
  46. He X, Lau EHY, Wu P, Deng XL, Wang JA et al. 2020. Temporal dynamics in viral shedding and transmissibility of COVID-19. Nat. Med. 26:672–75
    [Google Scholar]
  47. Heikkinen T, Järvinen A. 2003. The common cold. Lancet 361:51–59
    [Google Scholar]
  48. Holmes EC, Goldstein SA, Rasmussen AL, Robertson DL, Crits-Christoph A et al. 2021. The origins of SARS-CoV-2: a critical review. Cell 184:4848–56
    [Google Scholar]
  49. Hosseini P, Sokolow SH, Vandegrift KJ, Kilpatrick AM, Daszak P. 2010. Predictive power of air travel and socio-economic data for early pandemic spread. PLOS ONE 5:e12763
    [Google Scholar]
  50. Hsiang S, Allen D, Annan-Phan S, Bell K, Bolliger I et al. 2020. The effect of large-scale anti-contagion policies on the COVID-19 pandemic. Nature 584:262–67
    [Google Scholar]
  51. Ives AR, Bozzuto C. 2021. Estimating and explaining the spread of COVID-19 at the county level in the USA. Commun. Biol. 4:60
    [Google Scholar]
  52. Jiang X, Liu J, Zhang C, Liang W. 2020. Face masks matter: Eurasian tree sparrows show reduced fear responses to people wearing face masks during the COVID-19 pandemic. Glob. Ecol. Conserv. 24:e01277
    [Google Scholar]
  53. Johns Hopkins Univ 2023. Coronavirus Resource Center. Johns Hopkins Univ. updated Mar. 10, accessed Jan. 31. https://coronavirus.jhu.edu/
  54. Karlinsky A, Kobak D. 2021. Tracking excess mortality across countries during the COVID-19 pandemic with the World Mortality Dataset. eLife 10:e69336
    [Google Scholar]
  55. Karmakar M, Lantz PM, Tipirneni R. 2021. Association of social and demographic factors with COVID-19 incidence and death rates in the US. JAMA Netw. Open 4:e2036462
    [Google Scholar]
  56. Ke R, Martinez PP, Smith RL, Gibson LL, Mirza A et al. 2022. Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness. Nat. Microbiol. 7:640–52
    [Google Scholar]
  57. Kerr PJ, Cattadori IM, Sim D, Liu J, Holmes EC, Read AF. 2022. Divergent evolutionary pathways of myxoma virus in Australia: virulence phenotypes in susceptible and partially resistant rabbits indicate possible selection for transmissibility. J. Virol. 96:e00886-22
    [Google Scholar]
  58. Khoury DS, Cromer D, Reynaldi A, Schlub TE, Wheatley AK et al. 2021. Neutralizing antibody levels are highly predictive of immune protection from symptomatic SARS-CoV-2 infection. Nat. Med. 27:1205–11
    [Google Scholar]
  59. Kilpatrick AM. 2011. Globalization, land use, and the invasion of West Nile virus. Science 334:323–27
    [Google Scholar]
  60. Kissler SM, Tedijanto C, Goldstein E, Grad YH, Lipsitch M. 2020. Projecting the transmission dynamics of SARS-CoV-2 through the postpandemic period. Science 368:860–68
    [Google Scholar]
  61. Kistler KE, Huddleston J, Bedford T. 2022. Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2. Cell Host Microbe 30:545–55.e4
    [Google Scholar]
  62. Koutsakos M, Wheatley AK, Laurie K, Kent SJ, Rockman S. 2021. Influenza lineage extinction during the COVID-19 pandemic?. Nat. Rev. Microbiol. 19:741–42
    [Google Scholar]
  63. Larremore DB, Wilder B, Lester E, Shehata S, Burke JM et al. 2021. Test sensitivity is secondary to frequency and turnaround time for COVID-19 screening. Sci. Adv. 7:eabd5393
    [Google Scholar]
  64. Laughner JL, Neu JL, Schimel D, Wennberg PO, Barsanti K et al. 2021. Societal shifts due to COVID-19 reveal large-scale complexities and feedbacks between atmospheric chemistry and climate change. PNAS 118:e2109481118
    [Google Scholar]
  65. Leclerc QJ, Fuller NM, Knight LE, CMMID COVID-19 Work. Group, Funk S, Knight GM. 2020. What settings have been linked to SARS-CoV-2 transmission clusters?. Wellcome Open Res. 5:83
    [Google Scholar]
  66. Lewnard JA, Liu VX, Jackson ML, Schmidt MA, Jewell BL et al. 2020. Incidence, clinical outcomes, and transmission dynamics of severe coronavirus disease 2019 in California and Washington: prospective cohort study. BMJ 369:m1923
    [Google Scholar]
  67. Li WD, Shi ZL, Yu M, Ren WZ, Smith C et al. 2005. Bats are natural reservoirs of SARS-like coronaviruses. Science 310:676–79
    [Google Scholar]
  68. Li Y, Qian H, Hang J, Chen X, Cheng P et al. 2021. Probable airborne transmission of SARS-CoV-2 in a poorly ventilated restaurant. Build. Environ. 196:107788
    [Google Scholar]
  69. Liu Z, Ciais P, Deng Z, Lei R, Davis SJ et al. 2020. Near-real-time monitoring of global CO2 emissions reveals the effects of the COVID-19 pandemic. Nat. Commun. 11:5172
    [Google Scholar]
  70. Lloyd-Smith JO, Schreiber SJ, Kopp PE, Getz WM. 2005. Superspreading and the effect of individual variation on disease emergence. Nature 438:355–59
    [Google Scholar]
  71. Lu L, Sikkema RS, Velkers FC, Nieuwenhuijse DF, Fischer EA et al. 2021. Adaptation, spread and transmission of SARS-CoV-2 in farmed minks and associated humans in the Netherlands. Nat. Commun. 12:6802
    [Google Scholar]
  72. Luis AD, Hayman DT, O'Shea TJ, Cryan PM, Gilbert AT et al. 2013. A comparison of bats and rodents as reservoirs of zoonotic viruses: Are bats special?. Proc. R. Soc. B 280:20122753
    [Google Scholar]
  73. Lyngse FP, Kirkeby CT, Denwood M, Christiansen LE, Mølbak K et al. 2022. Household transmission of SARS-CoV-2 Omicron variant of concern subvariants BA.1 and BA.2 in Denmark. Nat. Commun. 13:5760
    [Google Scholar]
  74. Lytras S, Xia W, Hughes J, Jiang X, Robertson DL. 2021. The animal origin of SARS-CoV-2. Science 373:968–70
    [Google Scholar]
  75. Madewell ZJ, Yang Y, Longini IM, Halloran ME, Dean NE. 2020. Household transmission of SARS-CoV-2: a systematic review and meta-analysis. JAMA Netw. Open 3:e2031756
    [Google Scholar]
  76. Makela MJ, Puhakka T, Ruuskanen O, Leinonen M, Saikku P et al. 1998. Viruses and bacteria in the etiology of the common cold. J. Clin. Microbiol. 36:539–42
    [Google Scholar]
  77. Manenti R, Mori E, Di Canio V, Mercurio S, Picone M et al. 2020. The good, the bad and the ugly of COVID-19 lockdown effects on wildlife conservation: insights from the first European locked down country. Biol. Conserv. 249:108728
    [Google Scholar]
  78. Martinez ME. 2018. The calendar of epidemics: seasonal cycles of infectious diseases. PLOS Pathog. 14:e1007327
    [Google Scholar]
  79. Meekins DA, Gaudreault NN, Richt JA. 2021. Natural and experimental SARS-CoV-2 infection in domestic and wild animals. Viruses 13:1993
    [Google Scholar]
  80. Meslé MM, Brown J, Mook P, Hagan J, Pastore R et al. 2021. Estimated number of deaths directly averted in people 60 years and older as a result of COVID-19 vaccination in the WHO European Region, December 2020 to November 2021. Eurosurveillance 26:2101021
    [Google Scholar]
  81. Mollentze N, Streicker DG. 2020. Viral zoonotic risk is homogenous among taxonomic orders of mammalian and avian reservoir hosts. PNAS 117:9423–30
    [Google Scholar]
  82. Moriyama M, Hugentobler WJ, Iwasaki A. 2020. Seasonality of respiratory viral infections. Annu. Rev. Virol. 7:83–101
    [Google Scholar]
  83. Nadeau SA, Vaughan TG, Scire J, Huisman JS, Stadler T. 2021. The origin and early spread of SARS-CoV-2 in Europe. PNAS 118:e2012008118
    [Google Scholar]
  84. New York Times 2023. COVID-19 data, New York, NY. updated Mar 24, 2023, accessed Jan. 13, 2023. https://github.com/nytimes/covid-19-data/blob/master/live/us-states.csv
  85. Nextstrain 2023. Genomic epidemiology of SARS-CoV-2 with subsampling focused globally since pandemic start Seattle, WA: updated Jun. 24, 2023, accessed Jan. 31, 2023. https://nextstrain.org/ncov/gisaid/global/all-time?l=clock
    [Google Scholar]
  86. Nikolay B, Salje H, Hossain MJ, Khan A, Sazzad HMS et al. 2019. Transmission of Nipah virus—14 years of investigations in Bangladesh. N. Engl. J. Med. 380:1804–14
    [Google Scholar]
  87. Nouvellet P, Bhatia S, Cori A, Ainslie KE, Baguelin M et al. 2021. Reduction in mobility and COVID-19 transmission. Nat. Commun. 12:1090
    [Google Scholar]
  88. Nyberg T, Ferguson NM, Nash SG, Webster HH, Flaxman S et al. 2022. Comparative analysis of the risks of hospitalisation and death associated with SARS-CoV-2 omicron (B.1.1.529) and delta (B.1.617.2) variants in England: a cohort study. Lancet 399:1303–12
    [Google Scholar]
  89. O'Driscoll M, Ribeiro Dos Santos G, Wang L, Cummings DA, Azman AS et al. 2021. Age-specific mortality and immunity patterns of SARS-CoV-2. Nature 590:140–45
    [Google Scholar]
  90. Olival KJ, Hosseini PR, Zambrana-Torrelio C, Ross N, Bogich TL, Daszak P. 2017. Host and viral traits predict zoonotic spillover from mammals. Nature 546:646–50
    [Google Scholar]
  91. Our World in Data 2023. COVID-19 dataset Oxford, UK: updated Jun. 28, accessed Jan. 31. https://github.com/owid/covid-19-data/tree/master/public/data
    [Google Scholar]
  92. Paredes MI, Lunn SM, Famulare M, Frisbie LA, Painter I et al. 2022. Associations between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants and risk of coronavirus disease 2019 (COVID-19) hospitalization among confirmed cases in Washington state: a retrospective cohort study. Clin. Infect. Dis. 75:e536–44
    [Google Scholar]
  93. Pekar J, Worobey M, Moshiri N, Scheffler K, Wertheim JO. 2021. Timing the SARS-CoV-2 index case in Hubei province. Science 372:412–17
    [Google Scholar]
  94. Pekar JE, Magee A, Parker E, Moshiri N, Izhikevich K et al. 2022. The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2. Science 377:960–66
    [Google Scholar]
  95. Qu P, Evans JP, Faraone JN, Zheng Y-M, Carlin C et al. 2023. Enhanced neutralization resistance of SARS-CoV-2 omicron subvariants BQ.1, BQ.1.1, BA.4.6, BF.7, and BA.2.75.2. Cell Host Microbe 31:9–17.e3
    [Google Scholar]
  96. RECOVERY Collab. Group 2021. Dexamethasone in hospitalized patients with COVID-19. N. Engl. J. Med. 384:693–704
    [Google Scholar]
  97. Rickards CG, Kilpatrick AM. 2023. Age-specific SARS-CoV-2 infection fatality rates derived from serological data vary with income and income inequality. PLOS ONE 18:e0285612
    [Google Scholar]
  98. Riley S, Ainslie KE, Eales O, Walters CE, Wang H et al. 2021. Resurgence of SARS-CoV-2: detection by community viral surveillance. Science 372:990–95
    [Google Scholar]
  99. Riley S, Kwok KO, Wu KM, Ning DY, Cowling BJ et al. 2011. Epidemiological characteristics of 2009 (H1N1) pandemic influenza based on paired sera from a longitudinal community cohort study. PLOS Med. 8:e1000442
    [Google Scholar]
  100. Rothenburg S, Brennan G. 2020. Species-specific host–virus interactions: implications for viral host range and virulence. Trends Microbiol. 28:46–56
    [Google Scholar]
  101. Rudan I. 2021. Evaluating different national strategies to contain the COVID-19 pandemic before mass vaccination. J. Glob. Health 11:01004
    [Google Scholar]
  102. Russell TW, Wu JT, Clifford S, Edmunds WJ, Kucharski AJ, Jit M. 2021. Effect of internationally imported cases on internal spread of COVID-19: a mathematical modelling study. Lancet Public Health 6:e12–20
    [Google Scholar]
  103. Rutz C, Loretto M-C, Bates AE, Davidson SC, Duarte CM et al. 2020. COVID-19 lockdown allows researchers to quantify the effects of human activity on wildlife. Nat. Ecol. Evol. 4:1156–59
    [Google Scholar]
  104. Schrimpf MB, Des Brisay PG, Johnston A, Smith AC, Sánchez-Jasso J et al. 2021. Reduced human activity during COVID-19 alters avian land use across North America. Sci. Adv. 7:eabf5073
    [Google Scholar]
  105. Shaman J, Pitzer VE, Viboud C, Grenfell BT, Lipsitch M. 2010. Absolute humidity and the seasonal onset of influenza in the continental United States. PLOS Biol. 8:e1000316
    [Google Scholar]
  106. Sheikh A, McMenamin J, Taylor B, Robertson C. 2021. SARS-CoV-2 Delta VOC in Scotland: demographics, risk of hospital admission, and vaccine effectiveness. Lancet 397:2461–62
    [Google Scholar]
  107. Shi A, Gaynor S. 2023. Visualization of COVID-19 spread metrics. Updated Apr. 14, 2023, accessed Jan. 13, 2023. https://github.com/lin-lab/COVID19-Viz/tree/master/clean_data_pois
  108. Shi A, Gaynor SM, Dey R, Zhang H, Quick C, Lin X. 2022. COVID-19 Spread Mapper: a multi-resolution, unified framework and open-source tool. Bioinformatics 38:2661–63
    [Google Scholar]
  109. Shu Y, McCauley J. 2017. GISAID: global initiative on sharing all influenza data—from vision to reality. Eurosurveillance 22:30494
    [Google Scholar]
  110. Smith DJ, Forrest S, Ackley DH, Perelson AS. 1999. Variable efficacy of repeated annual influenza vaccination. PNAS 96:14001–6
    [Google Scholar]
  111. Sonabend R, Whittles LK, Imai N, Perez-Guzman PN, Knock ES et al. 2021. Non-pharmaceutical interventions, vaccination, and the SARS-CoV-2 delta variant in England: a mathematical modelling study. Lancet 398:1825–35
    [Google Scholar]
  112. Taubenberger JK, Morens DM. 2006. 1918 Influenza: the mother of all pandemics. Rev. Biomedica 17:69–79
    [Google Scholar]
  113. Taylor LH, Latham SM, Woolhouse MEJ. 2001. Risk factors for human disease emergence. Philos. Trans. R. Soc. B 356:983–89
    [Google Scholar]
  114. Tegally H, Wilkinson E, Althaus CL, Giovanetti M, San JE et al. 2021. Rapid replacement of the Beta variant by the Delta variant in South Africa. medRxiv 2021.09. 23.21264018. https://doi.org/10.1101/2021.09.23.21264018
    [Crossref]
  115. The Lancet Infect. Dis 2022. Emerging SARS-CoV-2 variants: shooting the messenger. Lancet Infect. Dis. 22:1
    [Google Scholar]
  116. Tucker MA, Schipper AM, Adams TS, Attias N, Avgar T et al. 2023. Behavioral responses of terrestrial mammals to COVID-19 lockdowns. Science 380:1059–64
    [Google Scholar]
  117. Twohig KA, Nyberg T, Zaidi A, Thelwall S, Sinnathamby MA et al. 2022. Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study. Lancet Infect. Dis. 22:35–42
    [Google Scholar]
  118. UK Off. National Stat 2023. Coronavirus (COVID-19) latest insights: antibodies. London, UK: updated Jan. 18, 2023, accessed Jan. 31, 2023. https://www.ons.gov.uk/peoplepopulationandcommunity/healthandsocialcare/conditionsanddiseases/articles/coronaviruscovid19latestinsights/antibodies
  119. Volz E, Mishra S, Chand M, Barrett JC, Johnson R et al. 2021. Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature 593:266–69
    [Google Scholar]
  120. Webster R, Peiris M, Chen H, Guan Y. 2006. H5N1 outbreaks and enzootic influenza. Emerg. Infect. Dis. 12:3–8
    [Google Scholar]
  121. Williamson EJ, Walker AJ, Bhaskaran K, Bacon S, Bates C et al. 2020. Factors associated with COVID-19-related death using OpenSAFELY. Nature 584:430–36
    [Google Scholar]
  122. Woolhouse MEJ, Dye C, Etard JF, Smith T, Charlwood JD et al. 1997. Heterogeneities in the transmission of infectious agents: implications for the design of control programs. PNAS 94:338–42
    [Google Scholar]
  123. Worobey M, Levy JI, Malpica Serrano L, Crits-Christoph A, Pekar JE et al. 2022. The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic. Science 377:951–59
    [Google Scholar]
  124. Zhang JJ, Litvinova M, Liang YX, Wang Y, Wang W et al. 2020. Changes in contact patterns shape the dynamics of the COVID-19 outbreak in China. Science 368:1481–86
    [Google Scholar]
/content/journals/10.1146/annurev-ecolsys-102320-101234
Loading
/content/journals/10.1146/annurev-ecolsys-102320-101234
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error