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An infection is the invasion of tissues by pathogens, their multiplication, and the reaction of host tissues to the infectious agent and the toxins they produce. An infectious disease, also known as a transmissible disease or communicable disease, is an illness resulting from an infection. Infections can be caused by a wide range of pathogens, most prominently bacteria and viruses. Hosts can fight infections using their immune systems. Mammalian hosts react to infections with an innate response, often involving inflammation, followed by an adaptive response. Specific medications used to treat infections include antibiotics, antivirals, antifungals, antiprotozoals, and antihelminthics. Infectious diseases resulted in 9.2 million deaths in 2013 (about 17% of all deaths). The branch of medicine that focuses on infections is referred to as infectious diseases. Infections are caused by infectious agents (pathogens) including: Bacteria (e.g. Mycobacterium tuberculosis, Staphylococcus aureus, Escherichia coli, Clostridium botulinum, and Salmonella spp.) Viruses and related agents such as viroids. (E.g. HIV, Rhinovirus, Lyssaviruses such as Rabies virus, Ebolavirus and Severe acute respiratory syndrome coronavirus 2) Fungi, further subclassified into: Ascomycota, including yeasts such as Candida (the most common fungal infection); filamentous fungi such as Aspergillus; Pneumocystis species; and dermatophytes, a group of organisms causing infection of skin and other superficial structures in humans. Basidiomycota, including the human-pathogenic genus Cryptococcus. Parasites, which are usually divided into: Unicellular organisms (e.g. malaria, Toxoplasma, Babesia) Macroparasites (worms or helminths) including nematodes such as parasitic roundworms and pinworms, tapeworms (cestodes), and flukes (trematodes, such as schistosomes). Diseases caused by helminths are sometimes termed infestations, but are sometimes called infections.
[2]Paolo Prandoni, [3]LCAV, EPFL
In [1]:
import matplotlib.pyplot as plt
import numpy as np
import scipy.signal as sp
import seaborn as sns
sns.set()
In [2]:
plt.rcParams["figure.figsize"] = (14,4)
The basic reproduction number[4]¶
The propagation mechanism of an epidemic such as the one caused by
SARS-CoV-2 virus can be roughly modeled, at least in its inital phase,
as a process in which each infected individ