The evolution of the COVID-19 pandemic in Chile during 2020: a data perspective
Gonzalo A. Benavides, Francisca Larach, Vicente Marchant, Joaquín Fernández, Fredy Montoya, Sebastián Domínguez, Camilo Mejías
TThe evolution of the COVID-19 pandemic in Chile during2020: a data perspective ∗ Gonzalo A. Benavides † , § Francisca Larach ‡ Vicente Marchant § Joaqu´ın Fern´andez ¶ , † Fredy Montoya ‖ Sebasti´an Dom´ınguez ∗∗ Camilo Mej´ıas †† , ‡‡ February 24, 2021
Abstract
The COVID-19 pandemic has had a great impact in most countries worldwide,in particular impacting Chile greatly to become one of the worst hit countries in theworld, despite its low population compared to other affected countries around theworld. In this study we report the evolution of the COVID-19 pandemic and thespread of the SARS-CoV-2 virus in Chile since the first positive case was announcedon March 3, 2020, and until November 30, 2020. We provide a detailed description ofthe data provided by the Chilean Ministry of Science per administrative region on thenumber of new cases, tests per capita, and deaths in the country.
Keywords : SARS-CoV-2, COVID-19, Chile, PCR
In December 2019, a group of patients from Wuhan, China, developed a respiratory set ofsymptoms, including atypical pneumonia and respiratory failure. A novel coronavirus, theSARS-CoV-2, was later found to be the cause of this new disease [11, 19]. It was namedCOVID-19 by the World Health Organization (WHO) [35]. A warning on the risk that thisdisease could create to the global health was sent around the world as early as January14, 2020 [20, 5]. The virus rapidly spread to most countries in the world. The WHOdeclared the COVID-19 disease a global pandemic on March 11, 2020 [34]. Most countrieshave suffered severely from the COVID-19 pandemic. Spreads of the virus shifted fromits original epicenter in China, to Europe, then the US, and later to Latin America. Inmid-July, just over five months after the virus emerged in Wuhan, the Latin America’sdeath toll from coronavirus surpassed North America’s one, with Peru and Brazil as theepicenters accounting for most of the deaths in the region. ∗ This work was partially supported by Hibring Ingenier´ıa. † Centro de Investigaci´on en Ingenier´ıa Matem´atica, Universidad de Concepci´on, Concepci´on, Chile ‡ Cl´ınica Las Condes, Santiago de Chile, Chile § Departamento de Ingenier´ıa Matem´atica, Universidad de Concepci´on, Concepci´on, Chile ¶ Departamento de Ingenier´ıa Mec´anica, Universidad del B´ıo-B´ıo, Concepci´on, Chile ‖ Departamento de Medicina, Universidad de Concepci´on, Concepci´on, Chile ∗∗ Department of Mathematics and Statistics, University of Saskatchewan, Saskatoon, Canada †† Hibring Ingenier´ıa, Concepci´on, Chile ‡‡ Corresponding author: [email protected] a r X i v : . [ q - b i o . P E ] F e b OVID-19 in Chile
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The RT-PCR test (Reverse Transcription Polymerase Chain Reaction) has been themain tool to diagnose COVID-19 active infection. It is highly specific with no false positiveresults, but its sensitivity has not been well studied [10, 31]; it may present false negativeresults, depending on the stage and severity of the disease, and the quality of the sample[12, 18, 33]. False negative results may have serious consequences, as infected people, whomight be asymptomatic, may not be isolated, and therefore continue to propagate theinfection.This virus can be transmitted by presymptomatic, symptomatic, or asymptomaticindividuals [28, 2, 21]. Super-spreaders may transmit the virus to hundreds or even thou-sands of people [22]; in some places it has been estimated that 19% of the cases seeded asmuch as 80% of all local transmission [1]. The mean incubation time for this disease is5 days [4, 27]. Between 5% to 20% of the ill individuals are hospitalized within 14 daysfrom contagion; see, e.g. [32].Chile, with a population of approximately 19 million, is divided in 16 administrativeregions with a centralized government. The majority of its inhabitants reside in theMetropolitan, Valpara´ıso and Biob´ıo regions; these concentrate approximately 60,3% ofthe national population (see [26]). The first COVID-19 case in Chile, a 33-year old manreturning from vacations outside Chile, was reported in Talca in the Maule region, onMarch 3, 2020. Soon after this first positive case, preventive measures were put in place:on March 14, 2020 in-person classes in schools and universities were suspended, non-essential businesses were mandated to close, and overnight curfews were established alongthe country. On March 18, 2020 incoming international flights were restricted to onlyreturning citizens, and domestic traffic decreased greatly.Until now the Chilean government’s strategy to control the epidemic has consisted intesting, tracing, and isolating positive and suspicious cases, the TTA (for its acronym inSpanish) strategy. The government defines positive cases as people whose RT-PCR testresult is positive and suspicious cases as those who showed symptoms or were a closecontact with a confirmed positive case. This has also been combined with partial or totallockdowns, applied by municipalities. Despite all these measures, on the 10th week afterthe first case, Chile started to suffer a rapid growth in new reported cases, reaching 300,000cases in the first week of July, overtaking, for example, badly-hit European countries suchas Italy and Spain. Soon Chile became one of the most affected countries in the world interms of confirmed cases and number of deaths; see, e.g., [30]. As of November 30, 2020,Chile reached 551,743 infected individuals, and the total number of virus-related fatalitiesis 15,410, according to official reports.The objective of this work is to describe the evolution of the epidemic in the Chileanterritory during the first nine months, from March 2020 to November 2020, following thefirst reported case. We analyze the situation of each region independently and compar-atively, in terms of the main statistical parameters used in epidemiology. These includetime evolution of new daily cases, testing capacity and fatality rate, providing several anddiverse charts that illustrate the data.The rest of this paper is organized as follow: in Section 2 we describe the methodologyused in this study. In Section 3 we present our results and provide brief comments onthese. In Section 4 we provide a discussion on the data we present. We finally arrive atsome conclusions in Section 5. 2OVID-19 in Chile
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We utilized Python 3.8 to handle the data and generate all figures presented in this study.
The Chilean Ministry of Health reports new cases on a daily basis. A new case is defined asa patient who tested positive for COVID-19 with an RT-PCR test. Since April 29, 2020Chile began to report both symptomatic and asymptomatic positive cases separately.All of this information is available at the Github repository from the Chilean Ministryof Sciences [29]. We consider data corresponding since the first case was reported inthe country, until November 30, 2020. This data does not specify the number of testedindividuals.Regarding to the nature of the data, we point out that both daily new cases anddaily RT-PCR tests exhibit oscillatory behaviours. We ascribe this to the fact that manylaboratories that analyze RT-PCR tests in the country do not operate during weekends.Hence, in order to facilitate the analysis, we smooth out the data by considering a 7-day central moving average. Both the original and smoothed curves are shown in thecorresponding figures presented throughout this article, the former in lighter tones.
The notification system
Epivigila is a surveillance system utilized by physicians and spe-cialists in Chile. It includes the results for positive cases of all notifiable diseases in Chile.COVID-19 was considered a disease within this surveillance system by the Chilean law onFebruary 7, 2020 [25]. Epivigila has received all RT-PCR positive results for COVID-19 inthe country every day since then. New COVID-19 cases are only counted when the corre-sponding RT-PCR test results are positive. The identification of positive cases is managedwith the personal identification number (or R.U.N. for its acronym in Spanish), prevent-ing duplication. The statistics on fatalities, on the other hand, include not only RT-PCRconfirmed patients, but also those who were suspected to have died from COVID-19 orthose who had COVID-19 and died from other pathologies, according to the doctor thatfilled out the death certificate.
During the following 8 weeks after the first reported case, only few more cases were foundin the country. In Figure 1 we observe a first small outbreak during March and thefirst days of April, mainly in the ˜Nuble, Arica y Parinacota, Araucan´ıa, and Magallanesregions, with an incidence number greater than 5 per 100,000 inhabitants. Magallanesreached about 20 daily new cases at the beginning of April, then slowly decreased itsincidence number during the following two months. Smaller outbreaks were seen in theBiob´ıo, Los Lagos and Los R´ıos regions, with an incidence number of less than 5 per100,000 inhabitants. Meanwhile, the rest of the regions of the country experimented nosignificant rise in the number of positive cases.The country’s main wave started within the first days of May. It affected principallythe Metropolitan, Tarapac´a, and Antofagasta regions. During this wave, Chile reached apeak of 35 daily new cases per 100,000 inhabitants at mid-June, the highest recorded up3OVID-19 in Chile
Benavides et al. to date. The Metropolitan region reached about 60 daily new cases per 100,000 inhab-itants, whereas Tarapac´a’s maximum incidence number was roughly 35 daily new casesper 100,000 inhabitants. On the other hand, the region of Antofagasta culminated duringthe second half of June in almost 40 daily new cases per 100,000 inhabitants. By the endof May, the Arica y Parinacota, Valpara´ıso, Maule, and O’Higgins regions saw the begin-ning of their first important waves of infection, reaching a maximum incidence numberof approximately 15, 15, 15, and 25 daily new cases per 100,000 inhabitants at mid-July,respectively. The Coquimbo, Biob´ıo, and ˜Nuble regions took a minor role in the country’smain wave, all of them reaching around 10 daily new cases per 100,000 inhabitants startingJune.During July, the incidence number grew in the Arica y Parinacota and Atacama region,and in a lesser extent in the region of Coquimbo. They reached about 45, 40, and 15 dailynew cases per 100,000 inhabitants at the end of the month. Starting September, newwaves were observed in Arica y Parinacota, and Maule regions. At the same time, atthe beginning of this month, a considerable increment of daily new cases took place inthe southern regions of Araucan´ıa, Los R´ıos, Los Lagos, Ays´en, and Magallanes. As ofNovember 30, 2020 the incidence number in the Araucan´ıa, Los R´ıos, and Los Lagosregions appear to have peaked at 15, 20, and 20 daily new cases per 100,000 inhabitants,respectively. In the Ays´en region, on the other hand, the incidence number decreasedto under 10 daily new cases per 100,000 inhabitants. In the region of Magallanes theincidence number surpassed the 100 daily new cases per 100,000 inhabitants—the highestincidence number seen so far in a region of Chile—and appeared to have stabilized ataround 40 daily new cases per 100,000 inhabitants starting mid-October.During the whole period of study, the incidence number in ˜Nuble has remained lowcompared to other the regions mentioned above and erratically between 5 and 15 dailynew cases per 100,000 inhabitants since mid-May, with no clear waves. The Biob´ıo region,on the other hand, also presents a special behaviour, with an incidence number increasingslowly and consistently from 10 daily new cases per 100,000 inhabitants at the end of June,to 15 by the end of November.Figure 2 and Figure 3 show the evolution of both the testing capacity and daily newcases in Chile as a whole, and for each of the 16 major administrative regions in the coun-try. In Figure 2 we observe that the testing capacity of the Chilean healthcare systemremained under 0.5 daily RT-PCR tests per 1,000 inhabitants until the end of March. Atthe beginning of April, it started to increase steadily, and reached approximately 0.8 inthe first days of June during the peak of new daily new cases in Chile (cf. Figure 1). Themajority of these tests were made in the Metropolitan Region (cf. Figure 3). After remain-ing almost constant for about a month, daily RT-PCR started to increase rapidly againup to roughly 1.5 in mid-August. The testing capacity continued to increase slowly toreach a stable value of approximately 1.7 daily tests per 1,000 inhabitants in mid-October.There is a remarkable exception in the increase of number of tests performed daily duringthe national holidays, celebrated September 18 to September 20, 2020 where the testingcapacity decreased momentarily. The northern regions Arica y Parinacota, Tarapac´a, At-acama, and Antofagasta, and the southern regions, Los Lagos, and Magallanes, showeda rapid increase in testing capacity during July, surpassing 1.5 daily RT-PCR tests per1000 inhabitants at the end of the month. Some of these regions, Arica y Parinacota,Antofagasta, Los Lagos and Magallanes were even able to keep over 2 daily RT-PCRper 1000 inhabitants until the end of the period of study. Of the latter, the Magallanesregion has attained the highest testing capacity among all the 16 regions of Chile, surpass-ing 3 daily RT-PCR per 1000 inhabitants since late August. The regions Los R´ıos and4OVID-19 in Chile
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Region Population Total Cases Total Deaths CFRas of 11-03 as of 11-03Arica y Parinacota 252,110 10,239 207 2.0Tarapac´a 382,773 13,876 258 1.9Antofagasta 691,854 22,226 562 2.5Atacama 314,709 8,161 106 1.3Coquimbo 836,096 13,132 270 2.1Valpara´ıso 1,960,170 32,441 1151 3.5Metropolitana 8,125,072 305,218 10,342 3.4O’Higgins 991,063 19,857 544 2.7Maule 1,131,939 21,095 489 2.3˜Nuble 511,551 8,812 178 2.0Biob´ıo 1,663,696 36,599 607 1.7Araucan´ıa 1,014,343 17,531 229 1.3Los R´ıos 405,835 6,105 55 0.9Los Lagos 891,440 20,667 203 1.0Ays´en 107,297 1,269 14 1.1Magallanes 178,362 14,470 194 1.3Total 19,458,310 551,698 15,409 2.8Table 1: Total fatalities and CFR per region as of November 30.Ays´en experimented later rises in testing capacity starting from the end of August, theyattained and maintained values over 1.5 daily RT-PCR tests per 1000 inhabitants sincethe beginning of October. On the other hand, the central regions Coquimbo, Valpara´ıso,Metropolitan, O’Higgins and Maule have also experimented an increment in their testingcapacity, but in a more conservative way reaching approximately 1.3 daily RT-PCR testsper 1000 inhabitants. Finally, the Biob´ıo and ˜Nuble regions have shown a sustained in-crement in their testing capacity since the beginning of the epidemic in Chile, attainingapproximately 2 daily RT-PCR tests per 1000 inhabitants, respectively, at the beginningand end of November.The total fatalities and Case Fatality Ratio (CFR) per region as of November 30, arepresented in Table 1. The Metropolitan region concentrates the majority of the fatalitieswith approximately 67% of the total deaths related to COVID-19. The Valpara´ıso andMetropolitan regions have the highest CFR, with 3.5 and 3.4, respectively.
Chile has been one of the most affected countries in the world by the COVID-19 disease,in terms of number of cases and fatalities per capita. By July, 2020 Chile had the highestnumber of total cases per capita in the world. It was also the ninth country in theworld in terms of fatalities per capita; [30]. In addition, Chile became the sixth countryin the world by means of number of confirmed cases [13]. One of the reasons for thisphenomenon could be the weather, since the first wave of COVID-19 arrived to Chile atbeginning of the autumn season, similarly to what it was recently reported in Norway;see, e.g. [24]. From Section 3 it transpires that the epidemic in Chile can be described asasynchronous and diverse in nature in each of its 16 major administrative regions. Thesedifferences may be explained by several factors. Some of them are the great differences in5OVID-19 in Chile
Benavides et al. geography, population density, and urbanization of each region. While the northernmostregions are mainly dominated by arid weather, the central regions enjoy Mediterraneanweather. The rest of the country, on the other hand, is ruled by an oceanic and colderweather. Moreover, some regions are highly urbanized (e.g. Metropolitan region), whereasothers still have a great amount of people living in rural areas (e.g. ˜Nuble region); see, forinstance, [26]. Differences in transport connectivity between regions may have also playeda major role in the evolution of the epidemic. The Chilean territory from the north to theLos Lagos region is well connected by land, whereas Ays´en and Magallanes regions arevirtually isolated in this sense. With respect to air traffic, the major airports of the countrylocated in the Arica y Parinacota, Metropolitan, Biob´ıo and Tarapac´a regions. They haveserved as important focuses of infection at the beginning of the spread; the restrictionsin international and domestic flights were only applied after 11 days after the report ofthe first confirmed case. We highlight that the Metropolitan region’s main airport as themain source of imported contagions, as it is the principal international airport in Chile.Regardless of these restrictions, many routine flights, considered essential for the nation,continued operating during the whole period of study.The first contagions of the country were most probably of imported origin. In fact, thefirst confirmed case of COVID-19 in Chile was an individual returning from vacations inSoutheast Asia. The majority of the subsequent cases along the country during March andApril, 2020 corresponded to returning citizens, foreign tourists, and people who interactedwith them. In mid-March, an outbreak was declared at a gymnasium in the city of Chill´an,in the ˜Nuble region [23]; 21 people were confirmed to have been infected by a foreignvisitor. Another 6 people were later linked to this same outbreak. By the end of Marchand the beginning of April, the Magallanes region suffered its first wave. The Chileangovernment soon conjectured that the outbreak was due to the arrival of several cruiseships transporting tourists of diverse nationalities [9, 7]. After the report of 155 confirmedcases in the country, the Chilean government acknowledged community transmission of theSARS-CoV-2 virus along the country, and announced the closure of the Chilean bordersin March 16, 2020 [15].In mid-May, about two weeks after the beginning of the main wave in the Metropolitanregion, the neighboring regions of Coquimbo, Valparaiso, O’Higgins and Maule also initi-ated their main waves. Much probably, they got heavily contaminated by the Metropolitanregion due to land proximity and easy land connectivity, as they do not have importantairports. The Coquimbo region, interestingly, was able to initially contain this outbreakduring mid-June, which later resurfaced in July and August.Simultaneously to the aforementioned regions, the northern regions of Tarapac´a andAntofagasta, distant from the Metropolitan Region, also suffered rapid outbreaks. Thisbehavior is probably due to maintained air traffic with the Metropolitan region for miningactivity issues, which did not stop for being considered essential. The Atacama region,also with important mining activity, was able to initially avoid rapid increments in dailynew cases. Although, during July and August, a violent increment in new cases was seen.On the other hand, the northernmost region Arica y Parinacota also started to suffera rapid increase in its daily new cases at the end of May. This outbreak was controlledduring June, to then heavily reappeared during July and August. Despite not havingimportant mining centers, the region possesses one of the fourth most important airportsin the country, strongly connected with the one of the Metropolitan region and the virtuallyonly way of passenger transport to central Chile. Most surely, the virus reached the regionthrough this airport.The southern regions of Los R´ıos and Araucan´ıa managed to keep the incidence below 56OVID-19 in Chile
Benavides et al. daily new cases per 1000 inhabitants until mid-August. The Los Lagos region accomplishedsimilar results until the beginning of July. These behaviors are fairly impressive as wintersthere are usually rough. We assume this slow spread was due to better isolation andpreparation, thanks to the experience gained from the central and northern Chile.The Ays´en region, the least-populated and second vastest region of the country, hadreported only 124 cases in total (about 0.1% of its population) until the beginning ofSeptember, when a rapid outbreak started. We consider that the region managed topractically seclude from the virus for a long period of time due to its virtual land-isolationand low rates of stranger arrivals. It is important to notice that, in pre-pandemic times,the region characterizes for receiving a great amount of foreign tourists every year.The ˜Nuble region, has evidenced the most erratic behaviour among all the 16 regionsof Chile, with constant increases and decreases in the number of daily new cases. Weexplain this phenomenon based on the fact that approximately 30.6 % of the populationin the ˜Nuble region lives in rural areas, making it the most rural region of the country[26]. We speculate that great part of small waves presented during the period of studycorrespond to localized outbreaks, which were effectively contained mainly due to thefacility in isolation that rurality provides. The fact that there is no airport in the regionmay have also served to prevent further spread.With about 9% of its population already infected and an incidence above 110 daily newcases per 1000 inhabitants during mid-September, the Magallanes region has been the mostaffected region of the country. The majority of the epidemic in the region is explained byits capital Punta Arenas, which concentrates approximately 75% of the population of theMagallanes region. We speculate that, after the recovery from the outbreak experimentedin June-July—which was part of the national’s main wave—and due to the consequentresumption of great part of flights connecting with the rest of the regions (especiallythe Metropolitan region), Magallanes received a considerable number of imported cases.This, combined with the fact that the principal trading and administrative activity ofthe region are concentrated in a few blocks of Punta Arenas, might have triggered theenormous outbreak.Chile has done an outstanding effort in enhancing the current molecular biology lab-oratories and opening new public, private, university-based laboratories. The countryhas shown a sustained increase in testing capacity during the whole period of study. Asof October 23, 2020, this has allowed Chile to have the first place in testing per capitacapacity in Latin America [8], keeping over 1 daily RT-PCR per 1,000 inhabitants sincethe beginning of August and stabilizing in about 1.8 daily RT-PCR per 1,000 inhabitantsduring November (see Figure 2). At the same time, the utilization of the unified patientdatabase notification system Epivigila, have made it possible to ensure a faithful andstrong database.Nevertheless, we stress that much probably there was a significant subreport during thethe beginning of the pandemic, especially during the main wave that took place in May-June; the testing capacity there was below 1 daily RT-PCR per 1,000 inhabitants. Thisinitial deficit in testing capacity, due to lack of proper instalments and equipment, resultedin that testing was performed predominantly in symptomatic cases, leaving virtually apartclose contacts and with scarce active search strategies.During the peak period of the first wave (mid May to end of June) the rapid growthin testing capacity caused delays in rendering times due to both delay in the processing ofRT-PCR tests and the subsequent rendering of results to available centralized databases.For this reason, in this study we do not consider active cases for our reports due to thedifferences in waiting time for RT-PCR results, with delays that could result in many new7OVID-19 in Chile
Benavides et al. cases counted as such only after their 14 days isolation period had ended.The results of containment strategies have varied significantly among the country.Most of the regions required lockdowns at a municipality level, with the exception of theMetropolitan Region that required an early complete lockdown for 2 months, and waseven longer for certain municipalities within it. Highest population density and densetransportation system could explain the biggest outbreak in Metropolitan Region and thedifficulty of containing/restraining it. We analyze outbreak dynamics at a regional level,so we cannot see inter municipality differences. According to [3], different socioeconomicconditions and mobility can play an important role in differences in lockdown effective-ness that are seen when comparing municipalities from one same region. Despite thecountry’s preparedness, and the good development status of ICUs in Chile, a high CFRwas observed as of November 30, 2020 (see Table 1)—the CFR of the A/H1N1 influenzaepidemic in Chile in 2009 is estimated in 0.9 % [17]. The cause for this is probably mul-tifactorial: High incidence of comorbidities such as overweight and obesity (about 74 %of the adult population are overweight or obese [14]), hypertension (approximately 27.6% of the population suspects of suffering hypertension [16]), and smoking (33.3 % of thepopulation smoke regularly [16]), among others; health system saturation during peakperiod, especially emergency rooms, and delay in consultation of severe cases due to pop-ulation’s ignorance about the severity of the sickness. In [6] it was found that increasingCOVID-19 caseloads were associated with countries with higher obesity, higher medianpopulation age and longer time to border closures from the first reported case and in-creased mortality per million was significantly associated with higher obesity prevalence.On the contrary, per capita gross domestic product and reduced income dispersion re-duced mortality. Rapid border closures, full lockdowns, and wide-spread testing were notassociated with COVID-19 mortality per million people.
We presented notable differences in behaviour of outbreak dynamics—incidence, testingcapacity and fatalities—among all 16 major administrative regions of Chile. We argued ongeographical and demographics differences as possible explanations to this behavior. Wedecided to leave out the data corresponding to December 2020 as the holidays impactedthe behaviour of the pandemic in a great manner due to the holidays (including shopping,gatherings, travelling, and more).
Conflict of interest
The authors declare no conflicts of interest.
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Figure 1: New cases normalized by 100,000 inhabitants, per region.13OVID-19 in Chile
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Figure 2: RT-PCR and daily cases per capita.14OVID-19 in Chile
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Figure 3: Evolution of RT-PCR testing by region.15OVID-19 in Chile