数据 (The data)
With the number of cases steadily rising day by day, COVID-19 has been pretty much in the headlines of every newspaper known to man. Despite the massive amount of attention, a topic that has remained mostly untouched (some exceptions being the reports of farm and domestic animals getting infected) by the mainstream media is how animals are hit by the disease too. To cite the information provided by the government of Canada¹ “There is currently limited information on animals and COVID-19, especially on whether an animal can spread the virus if they become infected. “
随着案件数量每天稳步上升，COVID-19几乎已成为每个人所熟知的报纸的头条新闻。 尽管引起了极大的关注，但主流媒体仍未触及到这个话题(动物和家畜受到感染的报道除外)，这也是动物如何受到这种疾病袭击的话题。 引用加拿大政府提供的信息¹“目前关于动物和COVID-19的信息有限，尤其是关于动物如果被感染是否可以传播病毒的信息。 “
There have been admirable efforts by the scientific community to understand how the virus develops, both in animal and human hosts and the research about it grows by the day. Open data regarding animal infections is, however, not so easy to find.
科学界做出了令人钦佩的努力，以了解该病毒在动物和人类宿主中如何发展，并且对它的研究日趋增长。 但是，关于动物感染的公开数据并不是那么容易找到。
To that effect, the World Organisation for Animal Health frequently publishes a report of new cases in animals around the world at this page². However, compiling information from this source is hard work, and not everyone is willing/has the time to extract the data from each statement and make a dataset out of them. One of the few sources of data open to the public is the one in the United States Department of Agriculture website³. The table lists cases of SAR-CoV-2 (the virus that causes COVID-19 in humans) in animals that have been confirmed by the United States Department of Agriculture’s National Veterinary Services Laboratories. Though in each case, only the first animal of a species reported in a facility or home makes it to the table, and it is, therefore, a rough estimate of how many animals have the virus in the US.
为此，世界动物卫生组织经常在此页面 ²上发布世界各地动物新病例的报告。 但是，从此来源编译信息是一项艰苦的工作，并不是每个人都愿意/有时间从每个语句中提取数据并从中提取数据集。 公开数据的少数来源之一是美国农业部网站 ³中的一种。 该表列出了由美国农业部国家兽医服务实验室确认的动物中SAR-CoV-2(在人类中引起COVID-19的病毒)的病例。 尽管在每种情况下，只有设施或家中报告的该物种的第一只动物才会出现在桌子上，因此，它是对美国有多少动物感染该病毒的粗略估计。
Despite its small size (around 30 data points) For each case, the table notes the type of animal infected, where and when it got infected, the method used to detect the virus and whether or not it was in contact with a human infected. The table is not available to download, but it is easy enough to either copy or scrape if you want it. To make things more interesting, I decided to scrap it instead of copying it into an Excel file using the following code:
尽管其体积很小(大约30个数据点)，但表中仍注明了每种动物的感染类型，感染时间和地点，用于检测病毒的方法以及是否与感染者接触。 该表不可下载，但如果需要，可以轻松复制或刮取。 为了使事情变得更有趣，我决定使用以下代码来对其进行剪贴，而不是将其复制到Excel文件中：
import pandas as pd
from bs4 import BeautifulSoup
import requests
#URL
URL = 'https://www.aphis.usda.gov/aphis/ourfocus/animalhealth/sa_one_health/sars-cov-2-animals-us'
#Final list of results
list_of_results = []
#Scraping the data
animals = requests.get(URL)
animals_content = animals.content
parser = BeautifulSoup(animals_content, 'html.parser')
results1 = parser.find_all('tbody')
for x in results1:
element = x.find_all('td')
for y in element:
list_of_results.append(y.text.replace('\n', '').strip())
#Separating the data into different lists
animals = list_of_results[0::4]
date = list_of_results[1::4]
state = list_of_results[2::4]
method = list_of_results[3::4]
#Making a dataframe to work from
data = pd.DataFrame()
data[animals[0]] = animals[1:]
data[date[0]] = date[1:]
data[state[0]] = state[1:]
data[method[0]] = method[1:]
#Original dataset that will remain untouched through the analysis
original = data
#Adding a column that checks whether or not the animal had contact with
def human_checker(row):
if '~' in row:
return 'Yes'
else:
return 'No'
data['Contact with infected Human'] = data['Type of Animal'].apply(human_checker)While this is, admittedly a pretty long snip of code for its intended purpose, it does its job and results in a table that you can work with using Python if that’s your choice. Its usability, of course, depends on the table staying just as it is while they add cases (which I doubt will happen as the table should be able to grow in size and complexity with more data coming in). If you’d like to look more closely at the preparation process, you are welcome to visit my Github page and the NBViewer which hosts the whole process.
尽管诚然，这是达到预期目的的一长段代码，但它确实可以完成工作，并且会生成一个表，您可以选择使用该表来使用Python。 当然，它的可用性取决于表在添加案例时保持原样的状态(我怀疑这种情况会发生，因为表应该能够随着更多数据的输入而增加大小和复杂性)。 如果您想更仔细地了解准备过程，欢迎访问我的Github页面和托管整个过程的NBViewer 。
分析 (The Analysis)
Most animals in the data until now (over 90%) had exposure to a confirmed or probable infected human. However, according to the information published in the CDC’s official website⁴:
到目前为止，数据中的大多数动物(超过90％)都暴露于确诊或可能感染的人类。 但是，根据CDC官方网站上发布的信息the：
“The virus that causes COVID-19 spreads mainly from person to person through respiratory droplets from coughing, sneezing, and talking. Recent studies show that people who are infected but do not have symptoms likely also play a role in the spread of COVID-19. At this time, there is no evidence that animals play a significant role in spreading the virus that causes COVID-19. Based on the limited information available to date, the risk of animals spreading COVID-19 to people is considered low”.
“导致COVID-19的病毒主要通过咳嗽，打喷嚏和说话的呼吸道飞沫在人与人之间传播。 最近的研究表明，被感染但没有症状的人也可能在COVID-19的传播中起作用。 目前，没有证据表明动物在传播引起COVID-19的病毒方面起着重要作用。 根据迄今为止可获得的有限信息，认为动物传播COVID-19到人的风险较低。
Furthermore, the CDC continues in the same report by adding:
此外，疾控中心在同一份报告中继续增加以下内容：
“We are still learning about this virus, but it appears that it can spread from people to animals in some situations, especially after close contact with a person sick with COVID-19”.
“我们仍在研究这种病毒，但在某些情况下，它似乎可以从人传播到动物，尤其是在与患有COVID-19的患者密切接触后”。
Therefore, it is highly likely that the cases in the data had this origin, though it is not the only possible explanation, and it could have other roots too.
因此，数据中的案例很有可能是起源于此的，尽管这不是唯一可能的解释，它也可能具有其他根源。
Moving on from the possible origin to the animals that contracted the disease, the species of animals infected are of a relatively small variety, as shown in the graph below:
从可能的起源转到感染该疾病的动物，被感染的动物种类相对较小，如下图所示：
Bar a couple of exceptions (notably the tigers and the lions which contracted the disease at the Bronx Zoo⁵ and a couple of minks), the overwhelming majority of cases recorded belong to cats and dogs. Likewise, the distribution of cases through the United States is limited to a small number of states, with only twelve states out of the fifty have reported cases so far.
除少数例外(特别是在布朗克斯动物园 ⁵感染这种疾病的老虎和狮子以及几只水貂)外，记录的绝大多数病例都属于猫和狗。 同样，通过美国分配的案件仅限于少数几个州，迄今为止，在五十个州中只有十二个州报告了案件。
New York with nine cases and Utah with eight are the states with the most cases reported so far, followed by Texas with three. The other nine states only have one contagion each.
纽约是九例，犹他州是八例，是迄今为止报告最多的州，其次是德克萨斯州，是三例。 其他九个州每个州只有一个传染病。
Until now, July is the month with most infections reported, with the current month as a relatively close second despite it not being finished yet, which makes it likely that the trend upward will keep on its course. Lastly, it is worth noting the methods used for diagnosis of the disease so far, as plotted below:
到目前为止，7月是报告感染最多的月份，尽管还没有结束，但本月仍是第二个月，这使得上升趋势可能会继续下去。 最后，值得注意的是，到目前为止，该疾病的诊断方法如下图所示：
Most of the conditions were recognised using the PCR-test, which, on the authority of the FDA⁶, serves to test if there is an active coronavirus infection. The other test administered most regularly detects antibodies (Ab) produced by the immune system to stop the sickness.
大多数条件是通过PCR试验识别的，该试验是根据FDA the的授权进行的 ，用于检验是否存在活动性冠状病毒感染。 进行的另一项测试最定期地检测由免疫系统产生的抗体(Ab)，以阻止疾病。
结论 (Conclusion)
While there is little data to say anything decisive just yet, there are a couple of starting trends that are worth looking at:
尽管目前尚无数据可以说出决定性的内容，但是有几个值得关注的起始趋势：
- For as long as three months, cases of COVID-19 in animals have been steadily rising, and the number of cases in August so far suggests that it may continue. 在长达三个月的时间里，动物中的COVID-19病例一直在稳步上升，到目前为止，八月份的病例数表明这种情况可能会持续下去。
While the full list of species that can contract the virus is still unknown, the scientific community has been working non-stop to understand whether or not farm animals can contract the sickness too. So far, according to this source¹, ducks, chicken and pigs have resistance to the virus.
尽管尚不清楚可感染该病毒的物种的完整列表，但科学界一直在不停地努力了解农场动物是否也可感染该病。 到目前为止， 根据该来源 ¹，鸭，鸡和猪对这种病毒具有抗药性。
- A good percentage of the animals tested have had the infection in the past and developed antibodies to fight it. 过去测试过的动物中，有很大一部分曾经感染过这种病毒，并开发出抗击它的抗体。
Most of this information depends on what the near future might hold, and the listed trends can either be reversed or proved correct.
这些信息大部分取决于不久的将来会怎样，列出的趋势可以逆转或证明是正确的。
[1]: Government of Canada, Coronavirus disease (COVID-19) > Prevention and risks, (2020)
[1]：加拿大政府， 冠状病毒病(COVID-19)>预防和风险 ，(2020年)
[2]: World Organisation for Animal Health, Event in animals, (2020)
[2]：世界动物卫生组织， 动物事件 ，(2020年)
[3]: United States Department of Agriculture (USDA), Confirmed cases of SARS-CoV-2 in Animals in the United States, (2020)
[3]：美国农业部(USDA)，美国确诊为动物的SARS-CoV-2病例 ，(2020年)
[4]: Centers for Disease Control and Prevention (CDC), COVID-19 and Animals, (2020)
[4]：疾病预防控制中心(CDC)， COVID-19和动物 ，(2020年)
[5]: N. Daly, Seven more big cats test positive for coronavirus at Bronx Zoo, National Geographic, (2020)
[5]：戴利(N. Daly) ，《国家地理》 ， 布朗克斯动物园，另外七只大猫的冠状病毒测试呈阳性 ，(2020年)
[6]: U.S Foods and Drugs Administration (FDA), Coronavirus Testing Basics, (2020)
[6]：美国食品和药物管理局(FDA)， 冠状病毒检测基础知识 (2020)
翻译自: https://towardsdatascience.com/exploring-the-data-of-animals-infected-with-covid-19-50ce1ed16edd
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