Sequential viral introductions and spread of BA.1 across Pakistan provinces during the Omicron wave.

Background: COVID-19 waves caused by specific SARS-CoV-2 variants have occurred globally at different times. We focused on Omicron variants to understand the genomic diversity and phylogenetic relatedness of SARS-CoV-2 strains in various regions of Pakistan.

Methods: We studied 276,525 COVID-19 cases and 1,031 genomes sequenced from December 2021 to August 2022.

When a Headache Is More than the Flu: A Case Report.

Introduction: When influenza (flu) season arrives, it is easy for emergency department clinicians to anchor on the diagnosis of flu, sending patients on their way with or without anti-influenza medication. It is important not to miss the outlier - the patient who seems to have typical symptoms of influenza but with certain subtleties that should make one consider expanding the differential diagnosis.

Case Report: We describe an 11-year-old previously healthy male who presented with eight days of fever, myalgias, cough, congestion, and headache in the context of positive influenza exposure.

Origins and Evolution of Seasonal Human Coronaviruses.

Four seasonal human coronaviruses (sHCoVs) are endemic globally (229E, NL63, OC43, and HKU1), accounting for 5-30% of human respiratory infections. However, the epidemiology and evolution of these CoVs remain understudied due to their association with mild symptomatology. Using a multigene and complete genome analysis approach, we find the evolutionary histories of sHCoVs to be highly complex, owing to frequent recombination of CoVs including within and between sHCoVs, and uncertain, due to the under sampling of non-human viruses.

Projecting the SARS-CoV-2 transition from pandemicity to endemicity: Epidemiological and immunological considerations.

In this review, we discuss the epidemiological dynamics of different viral infections to project how the transition from a pandemic to endemic Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) might take shape. Drawing from theories of disease invasion and transmission dynamics, waning immunity in the face of viral evolution and antigenic drift, and empirical data from influenza, dengue, and seasonal coronaviruses, we discuss the putative periodicity, severity, and age dynamics of SARS-CoV-2 as it becomes endemic. We review recent studies on SARS-CoV-2 epidemiology, immunology, and evolution that are particularly useful in projecting the transition to endemicity and highlight gaps that warrant further research.