Modeling viral evolution:A novel SIRSVIDE framework with application to SARS-CoV-2 dynamics

Understanding evolutionary trends in emerging viruses,such as severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),is crucial for effective public health management and response.Nonetheless,extensive debates have arisen concerning viral evolutionary trends,particularly the interplay between transmissibility,pathogenicity,and immune escape.In this context,we have developed a novel computational model named SIRSVIDE(Susceptible-Infected-Recovered-Susceptible-Variation-Immune Decay-Immune Escape)to simulate the transmission and evolutionary dynamics of viral populations.Our simulation results indicate that under conditions of high mutation rates,elevated transmission rates,and larger susceptible host populations,viral populations exhibit prolonged increases in transmissibility and immune escape,accompanied by reductions in pathogenicity and noticeable short-term fluctuations.However,when the total susceptible population size and mutation rate decrease,substantial uncertainty in the evolutionary trends of viral populations becomes apparent.In summary,the SIRSVIDE model establishes a comprehensive framework for generating both short-and long-term viral epidemiological and evolutionary dynamics.The simulation outcomes align with existing evidence indicating that SARS-CoV-2 is undergoing selection for heightened transmissibility,decreased pathogenicity,and enhanced immune escape.Furthermore,the model sheds light on the possible evolutionary dynamics of other viruses.

Evolution of HBV Viral Load during Clinical and Biological Follow-Up of Chronic Hepatitis B Patients at the Saint Camille Hospital in Ouagadougou

Hepatitis B virus (HBV) infection is a major public health problem worldwide. The aim of this study was to document the dynamics of HBV viral load during the follow-up of chronic hepatitis B patients at the Saint Camille Hospital in Ouagadougou (HOSCO) from 2017 to 2021. This descriptive retrospective study was carried out in the Hepato-Gastro-Enterology Department of HOSCO and focused on patients who were undergoing treatment for chronic viral hepatitis B. A total of 260 cases of chronic hepatitis B were included in the study. The most affected age group was 21 to 30 years, accounting for 48.08% of the cases. Lifestyle factors included alcohol consumption (3.08%) and tobacco use (2.69%). Major risk factors for transmission included lack of vaccination (98.46%), family history of HBV infection (68.00%) and engagement in high-risk activities (28.00%). Patients requiring treatment were prescribed Tenofovir 300 mg tablets. FibroScan® showed the presence of stage F3-F4 fibrosis (2.14%) and S3 steatosis (13.33%). After one year of follow-up, 6.92% of patients achieved an undetectable viral load with normalized transaminase levels. The majority of other patients had a detectable viral load but below 20,000 IU/mL. The prevalence of viral hepatitis B remains significant worldwide. Although effective and well-monitored treatment can lead to undetectable viremia, prevention remains the most effective strategy for successful management of this disease.

Ongoing Positive Selection Drives the Evolution of SARS-CoV-2 Genomes

SARS-CoV-2 is a new RNA virus affecting humans and spreads extensively throughout the world since its first outbreak in December,2019.Whether the transmissibility and pathogenicity of SARS-CoV-2 in humans after zoonotic transfer are actively evolving,and driven by adaptation to the new host and environments is still under debate.Understanding the evolutionary mechanism underlying epidemiological and pathological characteristics of COVID-19 is essential for predicting the epidemic trend,and providing guidance for disease control and treatments.Interrogating novel strategies for identifying natural selection using within-species polymorphisms and 3,674,076 SARSCoV-2 genome sequences of 169 countries as of December 30,2021,we demonstrate with population genetic evidence that during the course of SARS-CoV-2 pandemic in humans,1)SARS-CoV-2 genomes are overall conserved under purifying selection,especially for the 14 genes related to viral RNA replication,transcription,and assembly;2)ongoing positive selection is actively driving the evolution of 6 genes(e.g.,S,ORF3a,and N)that play critical roles in molecular processes involving pathogen–host interactions,including viral invasion into and egress from host cells,and viral inhibition and evasion of host immune response,possibly leading to high transmissibility and mild symptom in SARS-CoV-2 evolution.According to an established haplotype phylogenetic relationship of 138 viral clusters,a spatial and temporal landscape of 556 critical mutations is constructed based on their divergence among viral haplotype clusters or repeatedly increase in frequency within at least 2 clusters,of which multiple mutations potentially conferring alterations in viral transmissibility,pathogenicity,and virulence of SARS-CoV-2 are highlighted,warranting attention.