Detection and quantification of sars-cov-2 wastewater treatment plants from different cities in chile, towards to a permanent sentinel surveillance.

Background: The quantification of SARS-CoV-2 in wastewater is a tool that allows determining the trend of viral circulation in a particular geographical area. Aim(s): To quantify the SARS-CoV-2 virus in 15 wastewater treatment plants in different Chilean cities to establish a comparison with the variables of: I) Active cases per 100,000 inhabitants;ii) daily positivity (novel cases);and iii) phases of the lockdown strategy. Method(s): SARS-CoV-2 was concentrated from wastewater samples. To obtain the number of virus genomes per liter, absolute quantification was performed using qRT-PCR. Result(s): Between January and June 2021, 253 samples were processed, all of which were positive for the presence of the virus. Likewise, it will be determined that the rate of active cases per 100,000 inhabitants is the variable that best fits the trends obtained with the quantification of the viral load in wastewater. Conclusion(s): The quantification of SARS- CoV-2 in wastewater as a continuous strategy is an efficient tool to determine the trend of the viral circulation in a delimited geographical area and, combined with genomic surveillance, it can constitute an ideal sentinel surveillance alert on future outbreaks.Copyright © 2022, Sociedad Chilena de Infectologia. All rights reserved.

A Hybrid Grey Wolf-Whale Optimization Algorithm for Classification of Corona Virus Genome Sequences using Deep Learning

Genome sequence data is widely accepted as complex data and is still growing in an exponential rate. Classification of genome sequences plays a crucial role as it finds its applications in the area of biology, medical and forensics etc. For classification, Genome sequences can be represented in terms of features. More number of less significant features leads to lower accuracy in classification task. Feature selection addresses this issue by selecting the most important features which aids to improve the accuracy and lessens the computational complexity. In this research, Hybrid Grey Wolf-Whale Optimization Algorithm (HGWWOA) is proposed for Genome sequence classification. The proposed algorithm is evaluated using 23 benchmark objective functions along with Convolutional Neural Network classifier and its efficiency is verified using a novel metric namely "Feature Reduction Rate”. The proposed optimization algorithm can be applied for any optimization problems. In this research work, the proposed algorithm is used for classification of Corona Virus genome sequences. Performance comparison of the proposed and existing algorithms was carried out and it is evident that the performance of proposed algorithm exceeds the previous algorithms with an accuracy of 98.2%. © 2023, Zarka Private University. All rights reserved.

On-Site Whole-Genome Sequencing of Sars-Cov-2 Reveals C3037t Mutation in Patient with Atrioventricular Nodal Reentry Tachycardia (Avnrt)

Intro: The spike protein of the SARS-CoV-2 virus targets the human cell receptor of angiotensin-converting enzyme (ACE2), including the myocardium and heart's conduction system. Patients diagnosed with COVID-19 have also been found to exhibit cardiac arrhythmia. Here, a whole-genome sequencing analysis using long-read sequencing was proposed to evaluate the virus genome in a patient who presented with AVNRT as a main presentation of COVID-19. Method(s): The sample was recovered from nasopharyngeal and oropharyngeal swab specimens of a 46-year-old female with no comorbidities who presented with palpitation, and ECG showed typical AVNRT features. The RT-qPCR of SARS- CoV-2 was confirmed positive with a CT-value of 15.82. The total RNAs were extracted and proceeded for RT-qPCR and proceeded with Oxford Nanopore Flongle sequencing. The genomics data of the virus was deposited in GISAID (EPI_ISL_3241561) and further analysed using online bioinformatics tools such as Nextclade CLI 2.3.0. Ethical approval (IREC 2021-080) for the study was obtained from IIUM Research Ethics Committee. Finding(s): Here, we reported a total of 29,775 bp near-complete whole-genome belonging to clade 21J (Delta) of AY.79 lineage (also known as B.1.617.2.79), which formed a dominant variant in Malaysia during the time of sampling. Discussion(s): While a previous study showed an association between Delta variant infection with fulminant myocarditis, the present study reported the benign AVNRT as the main presentation of SARS-CoV-2 infection. Furthermore, we observed the presence of the C3037T mutation previously described in the endomyocardial biopsy of a patient with persistent arrhythmia. Conclusion(s): Even though SARS-CoV-2 targets the respiratory tract, the present study supports the evidence that the ACE2 receptors are present in the heart. In addition, COVID19 is causing more and more damage to heart tissue, and viral transcription has been confirmed on cardiomyocytes. Further functional studies are needed to explore the associated mutations and their relation to cardiac manifestation.Copyright © 2023

SARS-CoV-2 VARIANTS' TEMPORAL AND VL DISTRIBUTIONS IN IMMUNOCOMPROMISED PATIENTS

Background: The COVID-19 pandemic has been striking for three years and, despite the regular arise of new variants, populations are now widely immune and protected from severe symptoms. However, immunocompromised patients still have worse clinical outcomes, higher mortality and rarely develop effective immunity through vaccination or infection. Here, we studied the temporal distribution of infections, viral loads (VL) as well as the viral genetic diversity among an immunocompromised patient cohort, between January 2021 and September 2022. Method(s): Overall, 478 immunocompromised patients (solid organ transplant, HIV positive, cancer, autoimmune disease) and 234 controls (healthcare workers) from Pitie-Salpetriere and Bichat Claude-Bernard University hospitals (Paris, FRANCE) were diagnosed with SARS-CoV-2 infection by RT-qPCR. Whole genome sequencing was performed according to ARTIC protocol on Oxford Nanopore platform. All 712 full viral genomes were used to determine lineages and mapped to Wuhan-Hu-1 reference to produce a maximum likelihood phylogenetic tree (IQTree, 1000 bootstraps). Differences in temporal distributions of infections and VL were assessed using nonparametric statistical tests. Result(s): According to phylogenetic analysis, genomes from SARS-CoV- 2 infecting immunocompromised patients and those infecting healthy individuals are distributed in a similar way. No significant genetic differences can be observed between viral genomes from patients and controls within the different lineages. Temporal distribution of COVID-19 infections were also similar between immunocompromised patients and controls, with the exception of BA.2 variant for which controls were infected earlier (p< 0.001). VL were significantly lower in immunocompromised patients infected with Omicron variants (p=0.04). No differences in VL were observed for Alpha and Delta variants. Conclusion(s): At diagnosis, no intrinsic genetic divergence was observed in virus infecting immunocompromised patients compared to those circulating in the general population. Similarities in temporal distribution of infections between controls and patients suggest that these different groups become infected concomitantly. VL appeared to be lower for Omicron variants in immunocompromised patients. An earlier VL peak of Omicron and a testing of immunocompromised patients hospitalized once severe symptoms have appeared could indicate a delayed testing in these patients, once the replicative phase over. (Figure Presented).

Higher Spike Genetic Diversity of Delta/Omicron Variants in Immunocompromised Hosts

Background: Immunocompromised hosts with prolonged SARS-CoV-2 infections have been associated with the emergence of novel mutations, especially in the Spike protein, a key target for vaccines and therapeutics. Here, we conducted a case-control study to measure the genetic diversity of SARSCoV- 2 and to search for immunocompromised-specific minority variants. Method(s): SARS-CoV-2-positive patients with lung/cardiac/kidney transplant, HIV-positive, or treated with high doses of corticosteroids for auto-immune diseases were considered as immunocompromised hosts. SARS-CoV-2-positive healthcare workers with no auto-immune disease were used as controls. Samples were analyzed by RT-qPCR at Pitie-Salpetriere and Bichat Claude-Bernard university hospitals (Paris, France). Samples with Cycle threshold < 30 were selected for SARSCoV- 2 whole-genome sequencing using Oxford Nanopore protocol. Raw sequence data were mapped onto the Wuhan-Hu-1 reference genome, and consensus sequences were produced to determine the lineage. Only sequences covering at least 95% at >=50X depth of the Spike gene were investigated. In-house algorithms were developed to identify all majority and minority mutations in Spike. We defined a minority variant when it was present in >=6% and < 50% of the reads;and a majority variant when it was present in >50%. Result(s): We sequenced SARS-CoV-2 genome from 478 COVID-19- positive immunocompromised patients and 234 controls. More minority non-synonymous mutations in Spike were detected in viruses from immunocompromised hosts, compared to viral genomes from controls, in both Delta (p=0.001) and Omicron (p< 0.001) lineages, but not in Alpha (p=0.66) (Figure 1). Interestingly, among the 52 patients infected with the Delta variant, we concomitantly detected at low frequencies the mutations H655Y, N764K, D796Y, in three patients (associated with different auto-immune disease), that are part of Omicron variants signature mutations. Similarly, some patients (n=7) infected by Omicron BA.1 lineage had R346T at low-frequency, later fixed in Omicron BA.4.6 and BQ.1.1 lineages. None of these mutations were observed in the viral genomes from controls. Conclusion(s): Here, we report a higher genetic diversity in Spike gene among SARS-CoV-2 sequences from immunocompromised hosts for Delta and Omicron lineages. These results suggest that immunocompromised patients are more likely to allow viral genetic diversification and are associated with a risk of emergence of novel SARS-CoV-2 variants. (Figure Presented).

SARS-CoV-2 USES ENDOSOMAL MEMBRANES TO BUILD REPLICATION ORGANELLES

Background: The health emergency caused by the COVID-19 pandemic has evidenced that the frequency of spillover episodes of viruses infecting bats to other species, including humans, has significantly increased compared to previous decades. Besides SARS-CoV-2, six other human coronaviruses (NL63, 229E, OC43, HKU1, SARS-CoV and MERS-CoV) emerged in the 20th and 21st century, most likely because of cross-species transmission events from bats. While many of these coronaviruses cause mild respiratory infections, MERS-CoV, SARS-CoV and SARS-CoV-2 can cause severe respiratory distress, particularly in immunocompromised individuals. However, unlike SARS-CoV and MERS-CoV, SARS-CoV-2 is highly contagious, very stable, with many person-to-person transmissions, which can occur even before individuals exhibit any symptoms. While vaccines are readily available, the emergence of new SARS-CoV-2 variants along with the increasing incidence of individuals developing long COVID urge to develop antivirals specific to treat COVID-19. To reach this goal, we need to have a working knowledge of the host-SARS-CoV-2 interactions to identify targets for therapeutic intervention. Method(s): Following that rationale, we focused on understanding how SARSCoV- 2 generates replication organelles (ROs). All coronaviruses need to remodel cellular membranes to create these structures to allow the active replication and transcription of their genome. Due to their relevance for virus replication, disabling RO formation represents a promising strategy to fight SARS-CoV-2. However, the biogenesis mechanism, the origin, and type of these replication organelles are still a major focus of debate. To identify the cellular membranes that SARS-CoV-2 uses to generate ROs we used multiple cell lines and primary cells that were evaluated by fluorescence microscopy, genetic engineering, compounds that specifically inhibit cellular processes, and immunoprecipitation assays to validate protein-protein interactions. We also used RT-qPCR to assess viral genome replication. Result(s): SARS-CoV-2 uses the viral protein NSP6 to remodel endosomal membranes juxtaposed to the ER to generate replication organelles. Specifically, the virus depends on Clathrin, COPB1, and Rab5 for efficient SARSCoV- 2 RNA synthesis. Conclusion(s): Uncovering the origins and mechanism(s) by which SARS-CoV-2 assembles ROs opens new avenues to develop strategies to interfere with RO biogenesis and halt virus replication.

Abstracts of the papers presented in the International Conference of Indian Virological Society, VIROCON 2022 on "Emerging and Re-emerging Viral Infections Impacting Humans, Animals, Plants, Fish and Environment"

The proceedings contain 206 papers. The topics discussed include: influenza: experiences from Kashmir;outbreaks of different viral etiologies amidst COVID-19 pandemic;development of a colorimetric isothermal (LAMP) assay for rapid detection of monkeypox virus;circulation of genetically diverse non-polio enteroviruses in respiratory samples during COVID-19 pandemic period (2021-22);evolutionary analysis of all eleven genes of species C rotaviruses circulating in humans and domestic animals;molecular characterization of dengue viruses circulating in Pune district, Maharashtra from 2009-2022;isolation and genomic characterization of cell fusing agent virus from aedes aegypti mosquitoes from Assam, India;structure-based identification and evaluation of antiviral activity of potent small molecule inhibitors targeting alphavirus RNA-dependent RNA polymerase;integration of HBV receptor NTCP into hepatoma cell using grnome editing;and hepatitis B virus genome targeting using CRISPR/Cas9based gene editing tool.

SARS-CoV-2: Literature Review Focusing on Structure, Diagnosis and Vaccine Development

SARS-CoV-2 is a highly pathogenic novel ongoing-pandemic virus. It causes COVID-19. Little is known about SARS-CoV-2 biology, countermeasure, and its origin. SARS-CoV-2 is characterized by high infectiousness and sever pathogenesis. COVID-19 crosses the bounders of all continents in a high spreading manner. Here, several aspects regarding the origin and the molecular structure of this novel virus as well as the production of effective vaccines have been addressed. This article illustrated that SARS-CoV-2 was not being recombined inside laboratory and it has a complicated genome that led to sophisticated pathogenesis. Additionally, an important structural protein known as spike S was demonstrated by researchers as an important protein used by the virus for host cell entry as well as for vaccine development. However, the efforts for viral diagnosis and genomic demonstration as well as vaccine production are promising to tackle COVID-19. These perspectives will help in COVID-19 control. However, further investigations are urgently needed to figure out which controlling tactic is more efficient not only in the case of SARS-CoV-2 but also for future pandemics.Copyright © Mohammed Hamzah Abdulkadhim Al-Saadi and Wisam Hindawi Hoidy.

Role of antiviral therapy in respiratory infections in children: Analysis of clinical and laboratory observations.

Objective. To evaluate the efficacy of therapy for acute respiratory viral infections (ARVIs) in children with antiviral medications: inosine pranobex (Groprinosin, Gedeon Richter) and Kagocel (Kagocel, Niarmedic Pharma LLC) in comparison with symptomatic treatment without etiotropic agents based on clinical and laboratory parameters. Patients and methods. The clinical and laboratory observation was conducted in an outpatient setting in the pre-COVID-19 period between 2018 and 2020. Acute respiratory infections were diagnosed using licensed testing systems by multiplex polymerase chain reaction (PCR) with detection of nucleic acid viral genomes: influenza, rhinovirus, respiratory syncytial virus, metapneumovirus, parainfluenza, seasonal coronaviruses, adenoviruses, and bocavirus). A total of 151 children aged 3 to 15 years were examined and monitored in dynamics, with 78.7% of positive and 21.3% of negative results detected by PCR in the nasopharyngeal and oropharyngeal swabs. The patients were randomized into three groups depending on the antiviral medication prescribed: group 1 (53 children) received Groprinosin;group 2 (52 children) received Kagocel;group 3 (control, 46 children) received only symptomatic therapy without antiviral agents. Results. The study demonstrated a significant positive effect in patients in group 1 treated with Groprinosin (n = 53). At the end of therapy for both mono- and mixed infections, there were 95.8% of negative results (according to PCR diagnosis, that is, the absence of viral genome). In children in group 2 (n = 52) treated with Kagocel, the absence of viral nucleic acids (NAs) was observed less frequently (in 77.3% of cases). In children in group 3 (n = 46) who did not receive etiotropic antiviral therapy, there were only 40.3% of negative results after the end of treatment, and viral NAs were detected in 59.7% of patients. In this case, a 5-day course of Groprinosin was prescribed, after which the PCR results became negative in all patients. Therefore, children with recurrent respiratory infections, mixed infections, and herpesvirus infections require longer therapy. Additionally, a high frequency of ARVI complications was noted in group 3 (5 (10.9%) patients, where otitis was observed in 1 case, sinusitis - in 2 cases, bronchitis - in 2 cases), whereas 1 (1.8%) patient taking Groprinosin had otitis, and 1 (1.9%) patient taking Kagocel had pneumonia. Conclusion. This study was the first to investigate antibody titers to respiratory viruses in dynamics at 3, 6 and 12 months after the onset of ARVI. It showed that the development of antibodies to respiratory viruses is very unstable and does not occur in all patients. Antibodies almost disappeared by the third month after ARVI and were no longer detectable by the sixth month. After 12 months, patients suffered a new ARVI and developed the corresponding antibodies. This information will be especially relevant in conditions of the rise in the incidence of ARVIs, as well as the COVID-19 pandemic observed in recent years.Copyright © 2022, Voprosy Prakticheskoi Pediatrii. All rights reserved.

Traditional herbal medicine in the treatment of patients infected with new coronavirus

The purposes of this review was in the direction of epidemiology, causative agents, symptoms, vaccine research probabilities and COVID-19 infection novel Corona viruses that was investigated in China. The COVID-19 has surrounded viruses along with a practical sensation one stranded RNA genome and a nucleocapsid of helical uniformity. The COVID-19 is an enormous family of viruses that are prevalent in a public and large number of species of animals including hens, camels, bats, cat, and cattle. Human corona viruses can cause gentle disorder identical to a common cough, cold, while others reason more acute disease MERS (Middle East Respiratory Syndrome) and SARS (Severe Acute Respiratory Syndrome). Thus spreading the COVID-19 should be closely investigated to recognize the growth of particularly virulent strains in society at an early stage and to simplify the evolution of enough preventive and therapeutic measurements.Copyright © 2021, Health Biotechnology and Biopharma. All rights reserved.

A New Chapter in the COVID-19 Pandemic: the Characteristics of Omicron Variant and A New Step for Scientific Epidemic Prevention and Control.

Since the outbreak of COVID-19, SARS-CoV-2 has continued to evolve. As the fifth variants of concern (VOCs) announced by the World Health Organization, Omicron has significantly changed from previous VOCs in terms of genome, biological and epidemiological characteristics. Although the severe illness and mortality caused by Omicron infection are significantly lower than those caused by the previous VOCs, Omicron's strong transmission ability has continued to break through the epidemic prevention barrier and human immunity barrier established by prior infections and vaccines. Omicron has opened a new chapter in the COVID-19 pandemic. In this paper, we review the changes in genome and biological characteristics of Omicron and its subspecies as well as the differences in epidemiological characteristics between Omicron and influenza viruses in order to provide scientific basis for the optimization of epidemic prevention and control.Copyright © 2023, Peking Union Medical College Hospital. All rights reserved.

Hypothesis of a potential antiviral drug

The approval of mRNA vaccine technique against COVID-19 opens a door to research and the creation of new drugs against different infectious pathologies or even cancer, since for several diseases the therapeutic options are limited, and different viral diseases are treated only symptomatically. For these reasons, this study proposed a hypothesis supported by biological studies, that it provides a theoretical basis for the possible development of a drug that used the mRNA technique and the ribonucleolytic action of a ribonuclease for a possible antiviral therapy, and analyzed a future perspective of this technique in order to provide a bibliographic basis on this hypothesis and motivate researchers to carry out biological studies on this topic.Copyright © 2022, Health Biotechnology and Biopharma. All rights reserved.

SARS-CoV-2: Molecular Biology and Therapeutic Targets

A century after the outbreak of the Spanish flu, the world is suffering from another pandemic because of the coronavirus. The virus took a toll on more than millions of lives worldwide and continues to affect the health and socio-economic infrastructure all over the world. This study explores the epidemiology, etiology, and transmission of the virus and its phylogenetic relationship with SARS and MERS coronavirus responsible for the 2002 and 2012 viral outbreak. Furthermore, this review highlights the key features of the viral genome and essential viral proteins responsible for the viral life cycle, evading host immune response, and viral immunopathology with therapeutics from "Recovery" and "Solidarity" trials. The review culminates with a discussion on different classes of prominent vaccines and their efficacy. An overall understanding of essential viral proteins and their role in pathogenesis, repurposed drugs, and vaccine development is the rationale of the present review.Copyright © 2021 Bentham Science Publishers.

Progress on cross-species infection mechanism of 2019-nCoV and antiviral drug research.

2019-nCoV has a up to 96% homology with the gene sequence of a bat coronavirus. By comparing its 7 conserved non-structural proteins, it is found that 2019-nCoV belongs to SARS related coronaviruses(SARSr-CoV). The receptor for 2019-nCoV entering cells is the same as that for SARSr-CoV, and angiotensin-converting enzyme 2 (ACE2) is a common cross-genus receptor. This article first elaborates the interspecies transmission and genetic variation, then briefly discusses the receptors on the surface of human cells (such as ACE2 and APP4), which cause human infection and encode five proteins in the viral genome, therefore are important targets for development of antiviral drugs. The article reviews eight promising anti-coronavirus drugs, including three anti-HIV drugs (Lopinavir/Ritonavir, Danoprevir/Ritonavir, Darunavir), two anti-Ebola virus drugs (Remdesivir, Galidesivir), two anti-influenza virus drugs (Arbidol, Favipiravir) and one anti-malarial drug (chloroquine phosphate). Among them, Remdesivir, Abidol and Favipiravir have strong inhibitory effects on 2019-nCoV, they may be the most promising drugs under investigation.Copyright © 2020 by the Chinese Medical Association.

Progress on cross-species infection mechanism of 2019-nCoV and antiviral drug research.

2019-nCoV has a up to 96% homology with the gene sequence of a bat coronavirus. By comparing its 7 conserved non-structural proteins, it is found that 2019-nCoV belongs to SARS related coronaviruses(SARSr-CoV). The receptor for 2019-nCoV entering cells is the same as that for SARSr-CoV, and angiotensin-converting enzyme 2 (ACE2) is a common cross-genus receptor. This article first elaborates the interspecies transmission and genetic variation, then briefly discusses the receptors on the surface of human cells (such as ACE2 and APP4), which cause human infection and encode five proteins in the viral genome, therefore are important targets for development of antiviral drugs. The article reviews eight promising anti-coronavirus drugs, including three anti-HIV drugs (Lopinavir/Ritonavir, Danoprevir/Ritonavir, Darunavir), two anti-Ebola virus drugs (Remdesivir, Galidesivir), two anti-influenza virus drugs (Arbidol, Favipiravir) and one anti-malarial drug (chloroquine phosphate). Among them, Remdesivir, Abidol and Favipiravir have strong inhibitory effects on 2019-nCoV, they may be the most promising drugs under investigation.Copyright © 2020 by the Chinese Medical Association.

Genomic characterization and phylogenetic analysis of sars-cov-2 in libya

The COVID-19 epidemic started in Libya in March 2020 and rapidly spread. To shed some light on the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) strains circulating in Libya, viruses isolated from 10 patients in this country were sequenced, characterized at the genomic level, and compared to genomes isolated in other parts of the world. As nine genomes out of 10 belonged to the SS1 cluster and one to SS4, three datasets were built. One included only African strains and the other two contained internationally representative SS1 and SS4 genomes. Genomic analysis showed that the Libyan strains have some peculiar features in addition to those reported in other world regions. Considering the countries in which the strains are genetically more similar to the Libyan strains, SARS-CoV-2 could have entered Libya from a North African country (possibly Egypt), sub-Saharan Africa (e.g., Ghana, Mali, Nigeria), the Middle East (e.g., Saudi Arabia), or Asia (India, Bangladesh).Copyright © 2021 by the authors. Licensee MDPI, Basel, Switzerland.

COVID-19: Insights into Structure-Function Relationship, Drug Targets and Drug Design Strategies for Novel-Coronavirus 2019

Background: Novel coronavirus (2019-nCov) imposed deadly health calamity with unexpected disastrous situation alarming the globe for urgent treatment regimes. World Health Organization (WHO) termed the coronavirus disease as COVID-2019 on February 11, 2020 and announced its outbreak as pandemic on 11 March 2020. The first infection was noticed in Wuhan, Hubei province, China, in December 2019, and it is believed that the corona-virus is transmitted to humans through bats as a reservoir involving human to human transfer. However, the proper intermediary transmission channel is yet to be unestablished. Method(s): Elderly populations and patients with concomitant symptoms are more at risk as compared to middle-aged patients as it may progress to pneumonia followed by severe acute respiratory syndrome (SARS) and multi-organ failure. Morbidity rates estimated in patients are less, i.e., 2-3%, but the dearth of a specific treatment strategy to prevent coronavirus infection is a major concern. Result(s): Currently, anti-viral and anti-malarial drugs are in practice for the management of COVID-19 disease along with plasma therapy in the absence of a potent vaccine. Besides, home isolation and social distancing are the precautionary measures adopted by many countries to minimize the spread of infection. Various studies have been conducted, and numerous are still going on to establish specific treatment for COVID-19. Conclusion(s): In this review, we summarized information on the structural components of COVID19 virus with special emphasis on the virus genome, life cycle, the importance of protease enzyme, the role of spike proteins in viral replication, validated drug targets, ongoing effective treatments for COVID-19 management and the latest research on drug design to develop anti-CoV drugs.Copyright © 2021 Bentham Science Publishers.

SARS-CoV-2: Evaluation and Evolution

The emerging new COVID 2019 pandemic, which started in 2019 in China (Wuhan) and is caused by SARS-CoV-2, raises critical concerns due to high morbidity and mortality. As many patients are infected and the numbers still increase, this may suggest that there are different variants of the virus and some of them are more pathogenic. Besides, the virus is suspected to have various evolutionary pathways since SARS-CoV-2 belongs to the RNA viruses' family, which is characterized by a high mutation rate. Additionally, it is crucial to understand the life cycle of the virus to be able to urge antiviral studies. Genotyping studies about viruses are also important in order to understand the transmission and evolution of the virus. The genome of SARS-CoV-2 has a furin-like cleavage site in its S protein that may affect its pathogenicity. It was found that insertions and deletions in S protein have an impact on the transmission and fusion of the virus. The single nucleotide polymorphisms (SNP) genotypes are used to track the relationship of virus isolates. Se-quence alignment revealed the presence of hundreds of inter-host mutations during person-to-per-son transmission. Furthermore, genetic recombination provided a second mechanism for virus evo-lution. In this review, we highlight the life cycle of the virus and methods of virus evolution caused by mutations or recombination of viral genomes.Copyright © 2021 Bentham Science Publishers.