1、病毒基因组特点：Viral genomes are often quite small, with the smallest having only three genes
2、病毒为什么很难放入进化树内：no genes are conserved among all viruses, or between all viruses and all cells; hence it may be impos- sible to ever place viruses into the tree of life or build a universal viral phylogenetic tree that includes all viruses.
3、病毒不都是很小的，there are also unusually large viruses such as the Pandoraviruses
4、病毒特点
Intracellular细胞内, rely on a suitable living cell to carry out their replication cycle.
Extracellular细胞外, virion. Metabolically inert.新陈代谢不活跃
5、如何区分质粒和病毒？
质粒：环状双链DNA，在细菌与真菌细胞内，独立于染色体复制，没有外壳；细胞子在特殊状态下也可以吸收质粒，或者在细胞间进行接合；
病毒：有单链/双链DNA或RNA，也有逆转录病毒，一般有蛋白质外壳；专一性寄生特定细胞，更多会使细胞裂解死亡
6、基本概念
Nucleic acid+Capsid=Naked virus
Naked virus+Envelope包膜=Enveloped virus包膜病毒
7、Virions中也有酶
-Lysozyme溶菌酶
- Nucleic acid polymerases 或者reverse transcriptase逆转录酶 -enzyme help for release 比如Neuraminidase（NA）神经氨酸酶
8、Virus replication：One-Step Growth一步生长曲线
经过latent period潜伏期后，直接assembly和release
与细菌四步生长曲线比较：
病毒一步生长曲线有一段潜伏期，在此期间检测不到感染性病毒，潜伏期后就直接是成熟期，在此期间病毒量急剧上升，但不是细菌那种log期，也不是指数增长，如果受到细胞数限制，病毒数就会不在增长，但是没有dead期
9、检测和进行病毒计数：Plaque Assay噬菌斑试验
滴度Titer：the number of “plaque-forming units” per milliliter每毫升斑块形成单位
PFU/ml
但滴度反映的不是absolute量（不是绝对量）
10、Efficiency of plating转染平板效率
空斑形成单位的数量PFU总是低于用电子显微镜制作的病毒悬液的计数。
有时培养效率低只是意味着在所用的条件下，一些病毒粒子没有成功地感染细胞。
细菌病毒>50%，动物病毒0.1-1%
11、replication cycle复制循环
Attachment吸附receptor、Penetration侵入、Packaging装配、lysis裂解
侵入：Endocytosis (内吞作用)、Uncoated at the cytoplasm、Uncoated at the cytoplasmic membrane、Nuclear membrane (influenza)
细菌也有抵御外源DNA入侵的机制：TA模式、CRISPR、限制性内切酶
防止限制性内切酶：Glucosylation葡糖基化、Methylation甲基化、Proteins inhibit the host restriction蛋白抑制、Restriction systems破坏宿主DNA
12、T4的基因组形成：Circular permutation (环状排列)。复制的基因组被重组形成串联体，用内切酶将其切成片段。
13、infection早期形成的更多是病毒核酸复制所需的酶，后期是更多结构蛋白
14、temperate phage温和噬菌体：some double-stranded DNA bacterial viruses, although capable of a virulent cycle, can also infect their host and establish a long-term stable relationship
Lysogeny溶原性：most virus genes are not transcribed and instead, the virus genome is replicated in synchrony with the host chromosome and passed to daughter cells at cell division.与宿主染色体同步复制并传递给子细胞
Lysogen溶原性细菌：A cell that harbors a temperate virus
Prophage原噬菌体：病毒DNA
Maintenance of the lysogenic state is due to a phage-encoded repressor protein.溶原状态的维持是由于病毒的阻遏蛋白
15、Rolling circle replication：the λ genome
16、Virulent viruses 烈性噬菌体lyse or kill their hosts after infection
Temperate viruses温和噬菌体 replicate their genomes in tandem with the host genome and without killing their hosts
17、Viroids类病毒
small (the smallest known pathogens, 246-399);
circular, ssRNA molecules;
lack a protein coat;
stable extracellular form;
cause plant diseases.