Editing Epidemic (section)

==Causes==
There are several factors that may contribute (individually or in combination) to causing an epidemic. There may be changes in a [[pathogen]], in the population that it can infect, in the environment, or in the interaction between all three. Factors include the following:<ref name="Principles of Epidemiology"/>{{rp|§1:72|location=}}

=== Antigenic Change ===
[[File:Differences-Between-Antigenic-Shift-and-Antigenic-Drift.webp|thumb|Illustration depicting the different mechanisms of antigenic shift and antigenic drift]]
An [[antigen]] is a [[protein]] on the [[virus]]' surface that host [[Antibody|antibodies]] can recognize and attack. Changes in the [[Antigenic variation|antigenic characteristics]] of the agent make it easier for the changed virus to spread throughout a previously immune population. There are two natural mechanisms for change - [[antigenic drift]] and [[antigenic shift]]. '''Antigenic drift''' arises over a period of time as an accumulation of [[mutation]]s in the [[Virus#Genome|virus genes]], possibly through a series of hosts, and eventually gives rise to a new strain of virus which can evade existing immunity. '''Antigenic shift''' is abrupt - in this, two or more different strains of a [[virus]], [[Coinfection|coinfecting]] a single host, combine to form a new subtype having a mixture of characteristics of the original strains. The best known and best documented example of both processes is [[influenza]].<ref>{{Cite web |last=CDC |date=12 December 2022 |title=How Flu Viruses Can Change |url=https://www.cdc.gov/flu/about/viruses/change.htm |access-date=9 September 2023 |website=Centers for Disease Control and Prevention |language=en-us}}</ref> [[SARS-CoV-2|SARS-CoV2]] has demonstrated antigenic drift and possibly shift as well.<ref>{{Cite journal |last1=Carabelli |first1=Alessandro M. |last2=Peacock |first2=Thomas P. |last3=Thorne |first3=Lucy G. |last4=Harvey |first4=William T. |last5=Hughes |first5=Joseph |last6=de Silva |first6=Thushan I. |last7=Peacock |first7=Sharon J. |last8=Barclay |first8=Wendy S. |last9=de Silva |first9=Thushan I. |last10=Towers |first10=Greg J. |last11=Robertson |first11=David L. |date=March 2023 |title=SARS-CoV-2 variant biology: immune escape, transmission and fitness |journal=Nature Reviews Microbiology |language=en |volume=21 |issue=3 |pages=162–177 |doi=10.1038/s41579-022-00841-7 |pmid=36653446 |pmc=9847462 |issn=1740-1534}}</ref>

=== Drug resistance ===
[[Antimicrobial resistance|Antibiotic resistance]] applies specifically to [[bacteria]] that become resistant to [[antibiotic]]s.<ref name="WHO2014">{{cite web |date=April 2014 |title=Antimicrobial resistance Fact sheet N°194 |url=https://www.who.int/mediacentre/factsheets/fs194/en/ |url-status=live |archive-url=https://web.archive.org/web/20150310081111/http://www.who.int/mediacentre/factsheets/fs194/en/ |archive-date=10 March 2015 |access-date=7 March 2015 |website=who.int}}</ref> Resistance in bacteria can arise naturally by [[genetic mutation]], or by one species acquiring resistance from another through [[horizontal gene transfer]].<ref>{{Cite web |title=General Background: About Antibiotic Resistance |url=http://www.tufts.edu/med/apua/about_issue/about_antibioticres.shtml |url-status=dead |archive-url=https://web.archive.org/web/20151023035356/http://www.tufts.edu/med/apua/about_issue/about_antibioticres.shtml |archive-date=23 October 2015 |access-date=30 October 2015 |website=www.tufts.edu}}</ref> Extended use of antibiotics appears to encourage selection for mutations which can render antibiotics ineffective. This is especially true of [[tuberculosis]], with increasing occurrence of [[Multi-drug-resistant tuberculosis|multiple drug-resistant tuberculosis]] (MDR-TB) worldwide.<ref name="WHO2015Fact">{{Cite web |title=Tuberculosis (TB) |url=https://www.who.int/news-room/fact-sheets/detail/tuberculosis |url-status=live |archive-url=https://web.archive.org/web/20200730165218/https://www.who.int/news-room/fact-sheets/detail/tuberculosis |archive-date=30 July 2020 |access-date=8 May 2020 |website=who.int |language=en}}</ref><ref>{{cite journal |vauthors=Dabour R, Meirson T, Samson AO |date=December 2016 |title=Global antibiotic resistance is mostly periodic |journal=Journal of Global Antimicrobial Resistance |volume=7 |pages=132–134 |doi=10.1016/j.jgar.2016.09.003 |pmid=27788414}}</ref>

=== Changes in transmission ===
[[File:Anopheles gambiae mosquito feeding 1354.p lores.jpg|thumb|Anopheles mosquito, the vector of malaria]]
[[Pathogen transmission]] is a term used to describe the mechanisms by which a disease-causing agent (virus, bacterium, or parasite) spreads from one host to another. Common modes of transmission include:<ref>{{Cite web |title=FAQ: Methods of Disease Transmission |url=https://eportal.mountsinai.ca/Microbiology/faq/transmission.shtml |access-date=10 January 2024 |website=Department of Microbiology, Mount Sinai Hospital}}</ref> -
* [[Airborne transmission|airborne]] (as with influenza and COVID-19),
* [[Fecal–oral route|fecal-oral]] (as with cholera and typhoid),
* [[vector-borne]] (malaria, Zika) and
* [[Sexually transmitted infection|sexual]] (syphilis, HIV)

The first three of these require that pathogen must survive away from its host for a period of time; an evolutionary change which increases survival time will result in increased virulence.<ref>{{Cite news |last=Mandavilli |first=Apoorva |date=1 October 2021 |title=Is the Coronavirus Getting Better at Airborne Transmission? |language=en-US |work=The New York Times |url=https://www.nytimes.com/2021/10/01/health/coronavirus-aerosols-airborne.html |access-date=12 September 2023 |issn=0362-4331}}</ref>

Another possibility, although rare, is that a pathogen may adapt to take advantage of a new mode of transmission<ref>{{Cite journal |last=Alcamí |first=Antonio |date=2023-03-28 |title=Pathogenesis of the circulating mpox virus and its adaptation to humans |journal=Proceedings of the National Academy of Sciences |language=en |volume=120 |issue=13 |pages=e2301662120 |doi=10.1073/pnas.2301662120 |issn=0027-8424 |pmc=10068839 |pmid=36940331|bibcode=2023PNAS..12001662A }}</ref><ref>{{Cite journal |last1=Antonovics |first1=Janis |last2=Wilson |first2=Anthony J. |last3=Forbes |first3=Mark R. |last4=Hauffe |first4=Heidi C. |last5=Kallio |first5=Eva R. |last6=Leggett |first6=Helen C. |last7=Longdon |first7=Ben |last8=Okamura |first8=Beth |last9=Sait |first9=Steven M. |last10=Webster |first10=Joanne P. |date=2017-05-05 |title=The evolution of transmission mode |journal=Philosophical Transactions of the Royal Society B: Biological Sciences |language=en |volume=372 |issue=1719 |pages=20160083 |doi=10.1098/rstb.2016.0083 |issn=0962-8436 |pmc=5352810 |pmid=28289251}}</ref>

=== Seasonality ===
Seasonal diseases arise due to the change in the environmental conditions, especially such as humidity and temperature, during different seasons. Many diseases display [[seasonality]],<ref>{{Cite journal |last=Martinez |first=Micaela Elvira |date=8 November 2018 |title=The calendar of epidemics: Seasonal cycles of infectious diseases |journal=PLOS Pathogens |language=en |volume=14 |issue=11 |pages=e1007327 |doi=10.1371/journal.ppat.1007327 |issn=1553-7374 |pmc=6224126 |pmid=30408114 |doi-access=free }}</ref><ref>{{Cite web |date=8 November 2018 |title=Mark Your Calendar: All Infectious Diseases Are Seasonal |url=https://www.publichealth.columbia.edu/news/mark-your-calendar-all-infectious-diseases-are-seasonal |access-date=13 September 2023 |website=Columbia University Mailman School of Public Health |language=en}}</ref> This may be due to one or more of the following underlying factors: -<ref>{{Cite journal |last1=Grassly |first1=Nicholas C |last2=Fraser |first2=Christophe |date=7 October 2006 |title=Seasonal infectious disease epidemiology |journal=Proceedings of the Royal Society B: Biological Sciences |volume=273 |issue=1600 |pages=2541–2550 |doi=10.1098/rspb.2006.3604 |issn=0962-8452 |pmc=1634916 |pmid=16959647}}</ref>
* The ability of the pathogen to survive outside the host - e.g. [[Waterborne diseases|water-borne]] cholera<ref>{{Cite journal |last=Leitzell |first=Katherine |date=20 November 2011 |title=The Time of Cholera |url=https://www.earthdata.nasa.gov/learn/sensing-our-planet/the-time-of-cholera |journal=NASA Earthdata |language=en}}</ref> which becomes prevalent in [[Monsoon|tropical wet]] seasons, or influenza which peaks in temperate regions during winter.<ref>{{Cite web |last=CDC |date=2022-09-20 |title=Learn more about the flu season |url=https://t.cdc.gov/C03 |access-date=2023-09-13 |website=Centers for Disease Control and Prevention |language=en-us}}</ref><ref>{{Cite journal |last1=Marr |first1=Linsey C. |last2=Tang |first2=Julian W. |last3=Van Mullekom |first3=Jennifer|author3-link=Jennifer Van Mullekom |last4=Lakdawala |first4=Seema S. |date=January 2019 |title=Mechanistic insights into the effect of humidity on airborne influenza virus survival, transmission and incidence |journal=Journal of the Royal Society Interface |language=en |volume=16 |issue=150 |pages=20180298 |doi=10.1098/rsif.2018.0298 |issn=1742-5689 |pmc=6364647 |pmid=30958176}}</ref>
* The behaviour of people susceptible to the disease - such as spending more time in close contact indoors.<ref>{{Cite web |last=Robson |first=David |date=19 October 2015 |title=The real reason germs spread in the winter |url=https://www.bbc.com/future/article/20151016-the-real-reason-germs-spread-in-the-winter |access-date=14 September 2023 |website=www.bbc.com |language=en}}</ref>
* Changes in immune function during winter - one possibility is a reduction in vitamin D, and another is the effect of cold on mucous membranes in the nose.<ref>{{Cite web |last=Kashef |first=Ziba |date=2019-05-13 |title=Flu virus' best friend: low humidity |url=https://news.yale.edu/2019/05/13/flu-virus-best-friend-low-humidity |access-date=2023-09-13 |website=YaleNews |language=en}}</ref><ref>{{Cite web |last=LaMotte |first=Sandee |date=6 December 2022 |title=Scientists finally know why people get more colds and flu in winter |url=https://www.cnn.com/2022/12/06/health/why-winter-colds-flu-wellness/index.html |access-date=2023-09-14 |website=CNN |language=en}}</ref>
* Abundance of vectors such as mosquitoes.<ref>{{Cite book |last1=Medicine |first1=Institute of |url=https://books.google.com/books?id=lDClwYeJdCEC |title=Vector-Borne Diseases: Understanding the Environmental, Human Health, and Ecological Connections: Workshop Summary |last2=Health |first2=Board on Global |last3=Threats |first3=Forum on Microbial |date=2008-03-18 |publisher=National Academies Press |isbn=978-0-309-17770-2 |language=en}}</ref>

=== Human behaviour ===
[[File:Punch-A_Court_for_King_Cholera.png|thumb|''A Court for King Cholera.'' Illustration from ''[[Punch (magazine)|Punch]]'' (1852).]]
Changes in behaviour can affect the likelihood or severity of epidemics. The classic example is the [[1854 Broad Street cholera outbreak]], in which a cholera outbreak was mitigated by removing a supply of contaminated water - an event now regarded as the foundation of the science of [[epidemiology]].<ref>{{Cite journal |last=Tulchinsky |first=Theodore H. |date=2018 |title=John Snow, Cholera, the Broad Street Pump; Waterborne Diseases Then and Now |journal=Case Studies in Public Health |pages=77–99 |doi=10.1016/B978-0-12-804571-8.00017-2 |pmc=7150208|isbn=9780128045718 }}</ref> Urbanisation and overcrowding (e.g. in [[refugee camp]]s) increase the likelihood of disease outbreaks.<ref>{{Cite journal |last=Neiderud |first=Carl-Johan |date=2015-06-24 |title=How urbanization affects the epidemiology of emerging infectious diseases |journal=Infection Ecology & Epidemiology |volume=5 |issue=1 |pages=10.3402/iee.v5.27060 |doi=10.3402/iee.v5.27060 |issn=2000-8686 |pmc=4481042 |pmid=26112265|bibcode=2015InfEE...527060N }}</ref><ref>{{Cite journal |last1=Altare |first1=Chiara |last2=Kahi |first2=Vincent |last3=Ngwa |first3=Moise |last4=Goldsmith |first4=Amelia |last5=Hering |first5=Heiko |last6=Burton |first6=Ann |last7=Spiegel |first7=Paul |date=1 September 2019 |title=Infectious disease epidemics in refugee camps: a retrospective analysis of UNHCR data (2009-2017) |url=https://www.joghr.org/article/12009-infectious-disease-epidemics-in-refugee-camps-a-retrospective-analysis-of-unhcr-data-2009-2017 |journal=Journal of Global Health Reports |language=en |volume=3 |pages=e2019064 |doi=10.29392/joghr.3.e2019064|s2cid=207998081 |doi-access=free }}</ref> A factor which contributed to the initial rapid increase in the [[Western African Ebola virus epidemic|2014 Ebola virus epidemic]] was [[Bathing the dead|ritual bathing]] of (infective) corpses; one of the control measures was an education campaign to change behaviour around funeral rites.<ref>{{Cite web |last=Maxmen |first=Amy | author-link=Amy Maxmen|date=30 January 2015 |title=How the Fight Against Ebola Tested a Culture's Traditions |url=https://www.nationalgeographic.com/adventure/article/150130-ebola-virus-outbreak-epidemic-sierra-leone-funerals-1 |archive-url=https://web.archive.org/web/20210308231136/https://www.nationalgeographic.com/adventure/article/150130-ebola-virus-outbreak-epidemic-sierra-leone-funerals-1 |url-status=dead |archive-date=March 8, 2021 |access-date=14 September 2023 |website=National Geographic |language=en}}</ref>

=== Changes in the host population ===
The level of immunity to a disease in a population - [[herd immunity]] - is at its peak after a disease outbreak or a vaccination campaign. In the following years, immunity will decline, both within individuals and in the population as a whole as older individuals die and new individuals are born. Eventually, unless there is another vaccination campaign, an outbreak or epidemic will recur.<ref>{{Cite journal |last1=Yang |first1=Luojun |last2=Grenfell |first2=Bryan T |last3=Mina |first3=Michael J |date=February 2020 |title=Waning immunity and re-emergence of measles and mumps in the vaccine era |url=https://linkinghub.elsevier.com/retrieve/pii/S1879625720300304 |journal=Current Opinion in Virology |language=en |volume=40 |pages=48–54 |doi=10.1016/j.coviro.2020.05.009|pmid=32634672 |s2cid=220414525 }}</ref>

It's also possible for disease which is endemic in one population to become epidemic if it is introduced into a novel setting where the host population is not immune. An example of this was the introduction European diseases such as smallpox into indigenous populations during the 16th century.<ref>{{cite web |title=Stacy Goodling, "Effects of European Diseases on the Inhabitants of the New World" |url=http://www.millersville.edu/~columbus/papers/goodling.html |url-status=dead |archive-url=https://web.archive.org/web/20080510163413/http://www.millersville.edu/~columbus/papers/goodling.html |archive-date=10 May 2008}}</ref>

=== Zoonosis ===
[[File:Figure 3- Examples of Zoonotic Diseases and Their Affected Populations (6323431516).jpg|thumb|Possibilities for zoonotic disease transmissions]]
A [[zoonosis]] is an [[infectious disease]] of humans caused by a pathogen that can [[Cross-species transmission|jump]] from a non-human host to a human.<ref>{{Cite web |date=29 July 2020 |title=Zoonoses |url=https://www.who.int/news-room/fact-sheets/detail/zoonoses |access-date=14 September 2023 |website=World Health Organization |language=en}}</ref> Major diseases such as [[Ebola virus disease]] and [[salmonellosis]] are zoonoses. [[HIV]] was a zoonotic disease transmitted to humans in the early part of the 20th century, though it has now evolved into a separate human-only disease.<ref name="Orgin2011">{{cite journal |vauthors=Sharp PM, Hahn BH |date=September 2011 |title=Origins of HIV and the AIDS pandemic |journal=Cold Spring Harbor Perspectives in Medicine |volume=1 |issue=1 |pages=a006841 |doi=10.1101/cshperspect.a006841 |pmc=3234451 |pmid=22229120}}</ref> Some strains of [[Influenza A virus subtype H5N1|bird flu]] and [[Influenza A virus subtype H1N1|swine flu]] are zoonoses; these viruses occasionally recombine with human strains of the flu and can cause [[pandemic]]s such as the [[1918 Spanish flu]] or the [[2009 swine flu]].<ref>{{cite journal |vauthors=Scotch M, Brownstein JS, Vegso S, Galusha D, Rabinowitz P |date=September 2011 |title=Human vs. animal outbreaks of the 2009 swine-origin H1N1 influenza A epidemic |journal=EcoHealth |volume=8 |issue=3 |pages=376–380 |doi=10.1007/s10393-011-0706-x |pmc=3246131 |pmid=21912985}}</ref>