Last Update 2020-12-03

This is the daily updated version of "Understanding Epidemic Data and Statistics: A case study of COVID-19".
Click For preprint version: arxiv ; medrxiv.
More detailed map for Iran: Iran(Last Update on 2020-03-22, the detailed data was not provided after that date).

# A case study of COVID-19¶

## Abstract¶

The 2019-Novel-Coronavirus (COVID-19) has affected 191 countries and out of about 64508175 confirmed cases. Understanding the transmission dynamics of the infection in each country which affected on a daily basis and evaluating the effectiveness of control policies is critical for our further actions. To date, the statistics of COVID-19 reported cases show more than 80 percent of infected had a mild case of disease, while around 14 percent of infected experienced a severe one and about 5 percent are categorized as critical disease victims. Today's report (2020-12-02; daily updates in the prepared website) shows the confirmed cases of COVID-19 in US, India, Brazil, and Russia are 13921374, 9534964 , 6436650 and 2327105; respectively. Calculating the total Case Fatality Rate (CFR) of Italy (2020-03-04), about 3.561853050224969% of confirmed cases passed away. Compared to South Korea's rate of 1.546738399462004% (2.3028154285584908 times lower than Italy) and China's 5.129369533015451% (-44.00845460739815% lower than Italy), the CFR of Italy is too high. There are some effective policies that yield significant changes in the trend of cases. The lockdown policy in China and Italy (the effect observed after 11 days), Shutdown of all non-essential companies in Hubei (the effect observed after 5 days), combined policy in South Korea and reducing working hours in Iran.

## Introduction¶

Human coronaviruses (HCoV) which causes gastrointestinal and respiratory tract infections, were first introduced by the discovery of HCoV-229E and HCoV-OC43, from the nasal cavities of human patients with the common cold, in 1960s (Myint, 199419; Tyrrell & Bynoe, 196627). Other discovered human coronaviruses, which have involved serious respiratory tract infections, include SARS-CoV (2003), HCoV NL63 (2004), HKU1 (2005), MERS-CoV (2012), and the latest one, SARSCoV-2 (2019) resulting in Coronavirus disease (COVID-19) (Lim, Ng, Tam, & Liu, 201615; Syed, 202026). The name refers to the morphology of the virus, when viewed under 2D transmission electron microscopy (large pleomorphic spherical particles with bulbous surface) and stems from the Latin word "corona", meaning "crown"(Goldsmith et al., 20049). Concerning the risk factor, HCoVs vary significantly; from the relatively harmless ones (i.e., common cold) to the most lethal ones (MERS-CoV, with more than 30% mortality rate in the infected) (Fehr & Perlman, 20156). CoVs spread during cold seasons and cause colds with major symptoms, i.e., fever, sore throat, and less commonly pneumonia and bronchitis for the more aggressive strains. To date, there are no vaccines or antiviral drugs capable of preventing or treating HCoV infections (Fehr & Perlman, 2015 6; Forgie & Marrie, 2009 8; Liu et al., 2017 16).
To date, several outbreaks of coronavirus-related diseases have been reported. Severe acute respiratory syndrome- or SARS was the first coronavirus-related outbreak, starting in Guangdong, China, in November 2002, and spread to a total of 29 territories, including Hong Kong, Taiwan, Canada, Singapore, Vietnam, and the United States, within 9 months. It infected a total of 8,098 people and killed 774 worldwide (Smith, 200625). The second coronavirus-related outbreak happened in the Middle East in April 2012, officially named Middle East Respiratory Syndrome or MERS. This virus was first identified in a patient from Saudi Arabia, and later, MERS affected several other countries, including Saudi Arabia, South Korea, the United Arab Emirates, Jordan, Qatar, and Oman. Overall resulting with infections in 24 countries, with over 1,000 cases and over 400 deaths (Organization23). The outbreak of MERS happened again in South Korea, supposedly from a traveler from Middle East. It happened during May and July 2015, and infected a total of 186 individuals, with a death toll of 36 (Organization, 201524). After 3 years in August 2018, the next MERS outbreak happened in countries on the Arabian Peninsula, and resulted in almost 147 infected people and the death of 47. The MERS outbreak had been reported in Saudi Arabia, United Kingdom, and South Korea.
In Dec 2019, a pneumonia outbreak was reported in Wuhan, China, and on Dec 31, it was attributed to a new strain of HCoV, first named as 2019-nCoV by World Health Organization (WHO), and later renamed to SARS-CoV-2 by the International Committee on Taxonomy of Viruses. Almost 2 weeks later, on Jan. 11, 2020, Chinese state media reported the first fatality from the new discovered virus, that led to infection of dozens more (https://www.nytimes.com/2020/01/10/world/asia/china-virus-wuhan-death.html). As of Jan 20, multiple countries reported their first cases, including Japan, South Korea and Thailand. The first confirmed case in the United States came the very next day in Washington State. Continuing its spread, Coronavirus presence was confirmed throughout the month of February in the Philippines (Feb 2), France (Feb 14), Iran (Feb 21), and as reports started in Italy on Feb 23; many more Europeans countries followed suit, reporting their first confirmed cases. As of this writing, the coronavirus has affected 191 countries, out of about 64508175 confirmed cases, around 4,000 people have lost their lives. With China, Italy, Iran, and South Korea experiencing the worst cases of outbreaks and showing no sign of alleviation, the 2019-2020 outbreak of COVID-19 is now officially recognized as a pandemic by WHO. An outbreak or epidemic often refers to a sudden increase in the occurrence of an infectious disease, in a particular time and place. Pandemics are near-global epidemic outbreaks, where multiple countries across the world are involved (Green et al., 200211).
The mentioned rapid trend of spread prompts a lot of concerns and questions such as; "How fast is the virus spreading?", "which policies or efforts could control the disease better?", and "what is the main difference of COVID-19 outbreak with pervious epidemics?" Fortunately, the daily case detection changes are available and can be tracked almost in real time on the website provided by authors (http://iuwa.ir/corona/). The aim of this study is to provide the transmission trend from China to other countries and to report the daily confirmed cases, case fatalities and surveillance in every countries from the first day of outbreak until (2020-12-02). Also, to evaluate the effect of each government policies in controlling the outbreak of COVID-19.

## Basic Statistics¶

COVID-19 has currently spread to 191 countries and most national authorities have failed to keep it's rapid spread contained 32. WHO (World Health Organization) reports that it began in Wuhan city, located in Hubei Province of China, first reported on 21 January 20. COVID-19 categorizes in three distinctions concerning it's infected host's severity of disease 10,17. To date, the statistics of its reported cases shows more than 80 percent of infected had a mild case of disease, while around 14 percent of infected experienced a severe one, suffering from breathlessness and pneumonia. And about 5 percent are categorized as critical disease patients, their symptoms include septic shock, respiratory failure, and the failure of more than one organ.
Today's (2020-12-02) reports show that US has the most confirmed, fatal and also recovered cases. The order of confirmed cases after China's, is followed respectively by India, Brazil, and Russia; which could be found in the table1.

### Table 1¶

Top 10 total Confirmed, Deaths & Recovered cases

Country/Region Confirmed Deaths Recovered
0 US 13921374 273799 5322128
1 India 9534964 138648 8973373
2 Brazil 6436650 174515 5759294
3 Russia 2327105 40630 1814442
4 France 2275677 52822 167915
5 Spain 1665775 45784 150376
6 United Kingdom 1663467 59796 3602
7 Italy 1641610 57045 823335
8 Argentina 1440103 39156 1268358
9 Colombia 1334089 37117 1225635

Confirmed death cases caused by COVID-19 are also observed in 176 different countries, lead in numbers by US, Brazil, India, and Mexico respectively. About 18.338983073552452% of death cases are located in US, 21.58079034168925 % of confirmed cases are located in US (12.930667486771652% of recovered cases are located in India) were also present table1. Countries reported that all infected cases were recovered and there are no active cases that exist in their databases table2.

### Table 2¶

Countries with no active cases

Country/Region Confirmed Recovered Deaths

The overall stats states that there are 64508175 confirmed, 1492989 deaths and 41158958 recovered cases.
Figure 1 also shows that the COVID-19 spread exists in all continents.

### Figure 1¶

Transmission of Coronavirus Disease 2019-2020 (COVID-19); Blue nodes represents regions with confirmed COVID-19 cases, and Red nodes represents the regions with COVID 19 causes deaths

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ValueError                                Traceback (most recent call last)
<ipython-input-22-21b393daf982> in <module>
13                     '<li><bold>Deaths : '+str(full_latest.iloc[i]['Deaths'])+
14                     '<li><bold>Recovered : '+str(full_latest.iloc[i]['Recovered']),
16 for i in range(0, len(full_latest[full_latest["Deaths"]>0])):
17     folium.Circle(

~/anaconda/anaconda3/lib/python3.7/site-packages/folium/vector_layers.py in __init__(self, location, radius, popup, tooltip, **kwargs)
265
266     def __init__(self, location, radius, popup=None, tooltip=None, **kwargs):
--> 267         super(Circle, self).__init__(location, popup=popup, tooltip=tooltip)
268         self._name = 'circle'

~/anaconda/anaconda3/lib/python3.7/site-packages/folium/map.py in __init__(self, location, popup, tooltip, icon, draggable, **kwargs)
275         super(Marker, self).__init__()
276         self._name = 'Marker'
--> 277         self.location = validate_location(location)
278         self.options = parse_options(
279             draggable=draggable or None,

~/anaconda/anaconda3/lib/python3.7/site-packages/folium/utilities.py in validate_location(location)
63                              .format(coord, type(coord)))
64         if math.isnan(float(coord)):
---> 65             raise ValueError('Location values cannot contain NaNs.')
66     return [float(x) for x in coords]
67

ValueError: Location values cannot contain NaNs.

### Heatmap of Death Cases¶

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-23-c72e593c8e31> in <module>
6 stationArr = full_latest[['Lat', 'Long', 'Deaths']].values
7 # plot heatmap
9 m

~/anaconda/anaconda3/lib/python3.7/site-packages/folium/plugins/heat_map.py in __init__(self, data, name, min_opacity, max_zoom, max_val, radius, blur, gradient, overlay, control, show, **kwargs)
65         data = if_pandas_df_convert_to_numpy(data)
66         self.data = [[*validate_location(line[:2]), *line[2:]]  # noqa: E999
---> 67                      for line in data]
68         if np.any(np.isnan(self.data)):
69             raise ValueError('data may not contain NaNs.')

~/anaconda/anaconda3/lib/python3.7/site-packages/folium/plugins/heat_map.py in <listcomp>(.0)
65         data = if_pandas_df_convert_to_numpy(data)
66         self.data = [[*validate_location(line[:2]), *line[2:]]  # noqa: E999
---> 67                      for line in data]
68         if np.any(np.isnan(self.data)):
69             raise ValueError('data may not contain NaNs.')

~/anaconda/anaconda3/lib/python3.7/site-packages/folium/utilities.py in validate_location(location)
63                              .format(coord, type(coord)))
64         if math.isnan(float(coord)):
---> 65             raise ValueError('Location values cannot contain NaNs.')
66     return [float(x) for x in coords]
67

ValueError: Location values cannot contain NaNs.

## Global Daily Statistics¶

### Figure 2¶

COVID-19 global epidemic data and statistics of. a) confirmed, recovered and death COVID-19 cases, b) normalized confirmed, recovered and death COVID-19 cases, c) New confirmed, recovered and death COVID-19 cases, and d) Normalized new confirmed, recovered and death COVID-19 cases

Figure 2 shows the global confirmed, deaths and recovered cases' trend for COVID-19 form Jan 22 to 2020-12-02. Death cases are excessively lower than confirmed ones, so we normalized (By dividing the value of Confirmed, Deaths and Recovered cases to their maximum respectively.) it in above Fig. to investigate all three trends of cases. For the confirmed cases, there is a huge increase since Feb 11, the increase tones down from Feb 11 to the next day, Furthermore on Feb 13 another sharp increase is reported. It could be observed in Fig. 2 which shows new cases for each day (and normalized in Fig. 2 ). The most reliable speculation for this jump is that in that day, China (the country with the most confirmed cases) for the first time, reported the clinically diagnosed cases in addition to laboratory-confirmed cases 21, in which 13332 clinically diagnosed cases are added to 1148 laboratory-confirmed ones. Since then, China has kept the same reporting method for the confirmed cases. On 23rd and 24th of Feb, again the decrease of new cases subsided and new cases increased as before. As shown in Fig. 2 the reduction trend is continued (approximately) and the cause of the increase was other countries' growing numbers. So, for more accurate analysis each country will be investigated separately.

## China Daily Statistics¶

### Figure 3¶

COVID-19 epidemic data and statistics of China (main land), Hubei province, and China excluding Hubei a-c) New confirmed, recovered and death COVID-19 cases, d-f) Normal data for confirmed, recovered and death COVID-19 cases, g-i) Confirmed and Death cases, and j-l) Normal data of confirmed and death cases

### Figure 4¶

Confirmed death and Confirmed recovered Regression MAE data for COVID-19 transmission through a,b) China (main land), c,d) Hubei province, and e,f) China excluding Hubei.