How to calculate possible number of allele combination in given genotype?

Combination of alleles in any organims is known as its genotype. An allele is one of two or more alternate forms of a gene located at the corresponding locus on homologous chromosome. One allele obtained from the mother and the other from the father. Any possible combination of alleles is possible for the individuals within a particular population. If three alleles, A, B, and C are present on any specific locus, there will be six genotypes possible. An individual with above alleles may have any of the following allele combinations: AA, AB, AC, BB, BC and CC.

The number of possible genotypes or possible combination of alleles can be calculated by two methods. 

(1) It can be calculated by adding the number of possible combination of alleles with each positive integer below that number. For example, for a locus having three possible alleles, the number of possible genotypes is                                              3+2+1= 6

(2) The number of possible combination of alleles can also be calculated by using following formula
Number of allele combination = n(n+1)/2

Where, n is equal to the number of possible alleles.Here, number of alleles are 3,Therefore,
                                     3(3+1)/2 = 12/2=6

From above discussion, we can say that there are six possible allele combination occur if any individual have three alleles.

Problem:  There are 15 different alleles are present at a VNTR (variable number of tandem repeats) locus. How many combination of alleles (genotypes) are possible in a population for this VNTR?Explanation:
We can calculate by using both aforementioned methods

          (1)     15+14+13+12+11+10+9+8+7+6+5+4+3+2+1= 120

          (2)     By the use of formula
     Number of allele combination =15(15+1)/2=(15)(16)/2=240/2                                                                               =120

Therefore, for a locus having 15 different alleles, 120 different allele combination or genotypes are possible. 

How SARS CoV-2 infects human?

Structure of Coronavirus: 

(Image source: Stephen N.J.Korsman et al. (2012). Human coronaviruses. Virology (2012): 94-95)

Life cycle of SARS CoV-2

Attachment and entry

The virus attached with the host cell by the spike protein and its receptor. The receptor binding domain (RBD) on spike protein recognizes the angiotensin-converting enzyme-2 (ACE2) receptor on host cell and attaches to it. After attachment with host cell, virus is able to enter the host cell. There are two different ways to enter the host cell. The mechanism of entrance into host cell is depends on the host protease, protease cleave and activate the receptor-attached spike protein.

The first mechanism SARS CoV-2 follow to enter the host cell is endocytosis and uptake of the virus in an endosome. The receptor-attached spike protein is then cleaved and activated by the host's pH-dependent cysteine protease cathepsin L. When this receptor-attached spike protein gets activated introduces a conformational change, and the later fusion of the viral envelope with the endosomal wall occurs.

In other mechanism, the SARS CoV-2 can enter the host cell directly by proteolytic cleavage of the receptor-attached spike protein by the host's TMPRSS2 or TMPRSS11D serine proteases at the cell surface. In the SARS coronavirus, the activation of the C-terminal part of the spike protein triggers the fusion of the viral envelope with the host cell membrane by inducing conformational changes.

Genome translation

After fusion the viral nucleocapsid passes into the cytoplasm, where the viral genome is released. The viral genome acts as a messenger RNA (mRNA), and the host cell's ribosome translates two-thirds of the genome into two large overlapping polyproteins, pp1a and pp1ab.

These polyproteins have their very own proteases, PLpro and 3CLpro, which cleave the polyproteins at specific sites. Polyprotein pp1ab yields 16 nonstructural proteins (nsp1 to nsp16) after cleavage. Product proteins include various replication proteins such as RNA-dependent RNA polymerase (RdRp), RNA helicase, and exoribonuclease (ExoN).

Replication and transcription

Many nonstructural replication proteins collectively form a multi-protein replicase-transcriptase complex (RTC). RNA-dependent RNA polymerase (RdRp) is the main replicase-transcriptase protein. This protein directly involved in the replication and transcription of RNA from an RNA strand. The other nonstructural proteins of the complex assist in the replication and transcription process.

(Image source: Smith EC, Denison MR (2013). Coronaviruses as DNA Wannabes: A New Model for the Regulation of RNA Virus Replication Fidelity. PLoS Pathog 9(12): e1003760.)

The protein nsp15 acts as a 3'-5' exoribonuclease and provides a proofreading function to the complex which the RNA-dependent RNA polymerase dos’nt has. Proteins nsp7 and nsp8 form a hexadecameric sliding clamp as part of the complex which significantly increases the processivity of the RNA-dependent RNA polymerase. Due to large genome size the coronaviruses needs the increased fidelity and processivity during RNA synthesis.

One of the main roles of the (RTC) is to transcribe the viral genome. RdRp directly mediates the synthesis of negative-sense subgenomic RNA molecules from the positive-sense genomic RNA. After transcription of these negative-sense subgenomic RNA molecules, transcription of their corresponding positive-sense mRNAs takes place.

The other important function of the RTC is to replicate the viral genome. Replication of positive-sense genomic RNA is from the negative-sense genomic RNA.

This replicated positive-sense genomic RNA becomes the genome of the progeny viruses. The various smaller mRNAs are transcribes from the last third of the virus genome. These mRNAs are translated into the four structural proteins (S, E, M, and N) that will become part of the progeny virus particles and also eight other accessory proteins which assist the virus.

Assembly and release

RNA translation takes place inside the endoplasmic reticulum. The viral structural proteins S, E and M move along the secretory pathway into the Golgi intermediate compartment. There, the M proteins direct most protein-protein interactions required for assembly of viruses following its binding to the nucleocapsid. Progeny viruses are released from the host cell by exocytosis through secretory vesicles.

(Image source: 

Zhiqi Song et al., (2019). From SARS to MERS, Thrusting Coronaviruses into the Spotlight. Viruses 11(1), 59)