**2. Methods**

A scoping literature review in search for current topics associated with SARS-CoV-2 or COVID-19 viral replication, adaptations, and biological determinants known to cause variant emergence (e.g., molecular factors, animal reservoirs, immunological factors, etc.) was conducted in biomedical databases such as PubMed, MEDLINE, and Google search engine. Additionally, World Health Organization (WHO), Centers for Disease Control and Prevention (CDC), and Food and Drug Administration (FDA) websites were relied upon to get the most recent information related to content of the chapter. Papers related to the biological determinants commonly associated with viral replication, recombination, adaptation, and immunological seletion were chosen based on the scope of the chapter. Biological determinants of variant emergence and their possible or current implications on the COVID-19 pandemic are presented below.

### **3. Biological determinants of SARS-CoV-2 variants emergence**

### **3.1 Molecular determinants**

### *3.1.1 Viral replication/recombination*

SARS-CoV-2, a beta coronavirus, is a RNA virus using an error-prone RNAdependent RNA polymerase for replication [2]. The virus encodes a proofreading 3′ exonuclease (nsp140) but despite this activity, it accumulates genomic changes having a potential to create heterogenous mixture of antigenic proteins resulting in emergence of new variants [2]. The genomic mutation rate of SARS-CoV-2 in humans is estimated at 0.8–2.38 x 10−3 nucleotide substitutions per site per year with experimental data suggesting the virus capable of mutating and accumulating changes when it encounters new cell types [3, 4]. Thus, high viral load means high viral replication and thus higher potential for genomic errors due to replication. Along with the replication associated changes, dramatic changes in the virus phenotype can be observed due to genomic recombination in a cell infected with more than one coronavirus [2, 5]. Till now eight recombination events have been observed in SARS-CoV-2 but the frequency of such events is not known [6]. Random errors accumulated during replication/recombination along with population level natural and vaccine induced immunity, play an important role in Darwinian selection of these variants [2].

## **3.2 Zoonotic determinants**

Although the exact precursor of SARS-CoV-2 is unknown, it is established it is of wild origin. The initial December 2019 outbreak in Wuhan, China was linked to the seafood and live animal city market [7]. This market was reported to trade poultry, snakes, hedgehogs, and other wild animals [8].

The different SARS-CoV-2 variants detected in animals including dogs, cats, tigers, lions, minks, and gorillas all had genomes related to the human variant yet had additional mutations. The presence and infection of these animal reservoirs with SARS-CoV-2 virus also increases the possibility of viral mutations/recombinations and emergence of variants. Zoonotic reservoirs capable of carrying and providing an environment for viral multiplication are listed below.
