This is a small summary for the course Advanced Medical Microbiology from the master Biomedical Sciences at the UvA. It includes all the information you need for the first test of this course including lectures from Tonja van der Kuyl and Lia van der Hoek. I finished this course with a 9 and i hope...
Bacterial and viral zoonoses, the one health concept
Big to small: Helminths, protozoa, fungi, bacteria, viruses, prions.
Protozoa: Unicellular eukaryotic parasite.
Prions: Misfolded infectious proteins (probably).
Little bit more than 1415 species of infectious organisms.
Discovery of viruses: Tobacco plants were dying. To find out if it were bacteria they used filters
(porcelain with pores). Filter size that should retain bacteria plants inoculated with filtrate still
infectious infectious agent smaller than bacteria.
Viruses are classified according to type of genome, symmetry of the particle, the possession of an
envelope (extra layer around the capsid, viral proteins and host cell membrane) or not and having a
segmented genome or not.
Every life form on earth have their own viruses, even viruses have viruses (the big ones). Hepatitis D
can infect hepatitis B (depending upon another virus). Viruses do not have a single prehistoric virus,
but multiple common ancestors.
RNA viruses remains of RNA world.
DNA viruses spin off of eukaryotic cells.
Viruses comprise the smallest and most abundant biological agents. Most are bacteriophages,
infecting bacteria.
Virome: All the viruses in the body or in a certain organ. Detection by deep sequencing.
Polyomaviruses, papillomaviruses (HPV, warts cervical cancer), circoviruses.
There are also microorganisms under your skin, they do no harm. They reside deep in the
hair and glands.
Zoonosis: Infections that we get directly from animals, either wild or domestic. They can be
transmitted by uncooked animal products, contact with live animals (grooming, petting, bites,
scratches) or contact/inhalation of (dried) urine or faeces.
One Health Concept: Human and animal diseases should not be seen as separate entities.
Novel zoonoses: Increase in human population worldwide & increasing numbers of livestock to feed
this population declines in natural habitats of wild animals more contact (more domesticated,
wild animals are overcrowded by us & travel of us and food) more vulnerable to pathogens
transmitted by animals.
Flying is a great way to disperse pathogens over large distances
(birds/bats/insects/airplanes).
Climate changes contribute to spread of arboviruses.
Mosquitos can live somewhere else due to the temperature.
Virus submitted to other mosquito species that can live somewhere else.
A zoonosis is an infectious disease transmitted from animals to humans, sometimes with the help of
a (insect) vector. Examples:
West Nile virus: Replicates in bird (reservoir), mosquito (vector) transmits it to humans and
horses (dead end hosts, cannot be transmitted anymore). Viruses are probably not
completely adapted to humans and horses in much lower numbers than in the bird. There
is very little chance that mosquito picks up virus particle from horse if it bites it.
MERS-COV: From camels to humans, probably with a bat in between.
Virus discovery 😊
Viromics: Sequence everything.
Make a library:
Conditions:
Low host/bacteria DNA, low in ribosomal RNA
Sequence all viruses
High sensitivity/efficiency (< 0.01 ng DNA, need 5-10 ng).
Robust
High throughput
VIDISCA: Virus discovery cDNA-AFLP. Restriction enzyme digestion for
fragmentation and all steps are optimized for detecting viruses.
DNase treatment on supernatant with viruses & naked DNA
2 characteristics of viruses: small (remain in supernatant) &
protected by capsid.
Nucleic acid isolation: Boom isolation.
Reverse transcription into cDNA second stand synthesis.
Main competitor are ribosomes, they look like viruses (protein
capsid, same size, 30 nm). You need to decrease ribosomal RNA
sequences endoh primers, do not anneal to ribosomal RNA.
(random is 4096, endoh is 96), 97% ribosomal RNA is gone. Viruses
are still there, but need to sequence in way less depth.
Digestion machines can only handle 250 bp (max 400).
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