Genetic diversity and evolution of SARS-CoV-2 in the republic of Niger over 3 years.

Establishing wastewater-based SARS-CoV-2 variant surveillance independent of clinical isolates

Sentinel surveillance of COVID-19 in 2024-2025 shows the persistence of Omicron circulation and the introduction of the XFJ recombinant in the Republic of Guinea

Introduction several studies have shown the evolution of SARS-CoV-2 between 2020 and 2023 in Guinea. This study provides updated information on the circulation dynamics of SARS-CoV-2 from 2024 to 2025 and the variants circulating in Guinea. Methods as part of the integrated influenza/COVID-19 sentinel surveillance program, 2423 nasopharyngeal samples were analysed using RT-PCR, and those positive for SARS-CoV-2 were sequenced using the Illumina COVIDSeq Assay protocol. Results all age groups, ranging from <2 years to > 64 years, were affected by COVID-19, with an average SARS-CoV-2 positivity rate of 2.3%. The virus showed sporadic activity throughout the 2024-2025 period, with a higher level of activity during epidemiological week 42 (October) of 2024. Genomic analysis showed that only the Omicron variant circulated, along with its subvariants JN.1 and LF.7, in 2024. Subvariant LF.7 and recombinant XFJ also circulated in 2025. Conclusion SARS-CoV-2 subvariants continue to circulate sporadically in Guinea, with the XFJ recombinant having been detected in humans. Therefore, it is imperative to strengthen sentinel, genomic, and environmental surveillance for the early detection of any new COVID-19 outbreak and the potential emergence of new variants.

SARS-CoV-2 variants circulating in West and Central Africa between 2020 and 2022: A retrospective study.

OBJECTIVE The study aims to identify and characterize the SARS-Cov-2 variants circulating in West and Central Africa during the pandemic, between 2020 and 2022. METHODS From early 2020 to late 2022, naso-pharyngeal or oro-pharyngeal samples were collected in five countries: Burkina Faso, Côte d'Ivoire, Mali, Republic of Congo and Chad. SARS-CoV-2 positive samples (Ct-value < 30) were sequenced to identify the circulating variants in these countries during the different waves of the pandemic. RESULTS Overall, 793 whole genomes of SARS-Cov-2 were generated: 308 in Côte d'Ivoire, 244 in the Republic of Congo, 91 in Chad, 87 in Burkina Faso and 63 in Mali. In 2020, early variants detected included B.1 and B.1.1. Lineage A.21 was identified in both Burkina Faso and Mali, while lineages A and A.18 were detected in Côte d'Ivoire and Mali. Some variants appeared to be country-specific, such as lineage B.1.1.404 in Burkina Faso. Chad exhibited a distinct pattern compared with the other countries, with Delta variants detected earlier than in the other locations. In 2021, the diversity of circulating variants increased and differed more markedly between countries. In 2022, the variant landscape was dominated by Omicron lineages in all countries. CONCLUSION This study provides new resources concerning the SARS-CoV-2 variants circulating in West and Central Africa between 2020 and 2022, which are less represented in global datasets. The variants identified in this study were similar to the variants observed in other regions of the world.

Genetic Diversity of the ACE2 Gene and Susceptibility to COVID-19 in Morocco Population

Background: The COVID-19 was the most amazing pandemic of the early third millennium, with significant variability in infection rates across regions worldwide. Genetic factors, particularly the ACE2 gene, coding for a common receptor implicated in facilitating SARS-CoV-2 entry into human cells, could play a crucial role in susceptibility to infection. Our study aimed to analyze the allelic frequency of four SNPs in ACE2 gene (rs4646127, rs2074192, rs2285666, rs112171234) and evaluate their correlations with COVID-19 infection rates in four regional samples from Morocco. Methods: The total sample (N = 200) was obtained from: Rif (n = 50), Doukkala (n = 50), Ouarzazate (n = 49), and, Guelmim (n = 51). Genomic DNA was extracted using the GeneJET™ kit and genotyped by real-time PCR using TaqMan technology. Results: Analyses revealed significant spatial variations in the frequencies of alternative alleles of the studied SNPs, ranging from 0% to 74%. A significant positive correlation was observed between the frequency of alternative G allele of the rs4646127 and the infection rate variation (r = 0.96; p = 0.03; n = 4). Furthermore, significant differences reached 54.17% with worldwide populations (from North Africa, sub-Saharan Africa, Europe, Latino-America, East Asia, and South Asia) for the total SNP’s comparisons. Conclusions: Our results suggest a significant positive correlation between the frequency of the alternative allele of the ACE2 gene polymorphism rs4646127 and COVID-19 regional infection rates in Morocco. This property could be exploited to consider this SNP as a potential biomarker for identifying at-risk groups. However, due to the limited number of regional samples, our results for all the analyzed SNPs remain exploratory and would require confirmation through larger-scale studies.

Molecular Epidemiology of Emerging Subvariants of the SARS-CoV-2 Omicron Lineage: A Cross-sectional Study from Himachal Pradesh, India

Tracking SARS-CoV-2 variants revealed the predominance of the JN.1 sublineage of Omicron with generally mild symptoms, highlighting the need for robust, ongoing genomic surveillance integrated with epidemiological data to enable early detection of emerging variants and strengthen control strategies.

Changes in the Distribution of Respiratory Pathogens After the COVID-19 Pandemic.

BACKGROUND Diverse quarantine measures against the coronavirus disease 2019 (COVID-19) pandemic have affected the distribution patterns of respiratory pathogens. This study analyzed changes in the incidence and distribution of major respiratory pathogens during the COVID-19 pandemic and after the endemic declaration. In addition, the study aimed to provide a basis for future community-centered infectious disease response strategies by identifying co-infection patterns and whether pathogens re-emerge after mitigation. METHODS In this retrospective study, the results of 105,619 respiratory pathogen tests, including FilmArray® Respiratory Panel (BioFire Diagnostics) assay (FilmArray RP), influenza tests, and COVID-19 tests, were collected at a Korean university hospital during the COVID-19 pandemic (Period I: March 2021 through April 2023) and endemic (Period II: May 2023 through February 2025). The changes in the distribution of major pathogens, age and gender characteristics, seasonality, and co-infection patterns were compared between the two periods. RESULTS The overall positivity rate for the FilmArray RP significantly increased from 64.4% in Period I to 71.1% in Period II (p < 0.001). In the age-specific analysis, age group 3 (4 months to 2 years) had the highest positivity rate in Period II (82.7%). Human rhinovirus/enterovirus was the most frequently detected pathogen, whereas respiratory syncytial virus cases increased in number, but decreased in proportion to all positive cases in Period II. The prevalence of adenoviruses and Mycoplasma pneumoniae has significantly increased since the pandemic. Human metapneumovirus has shifted its seasonality from autumn to summer and spring, whereas parainfluenza virus 3 has shifted from autumn to spring and summer. Among all positive cases, co-infections significantly increased to 17.6% and 22.3% during Periods I and II, respectively (p < 0.001). CONCLUSIONS This study revealed significant changes in the incidence, seasonality, age characteristics, and co-infection patterns of respiratory pathogens after the mitigation of COVID-19. These changes result from the re-emergence of pathogens that were suppressed during the pandemic, immune vaccination, and the resumption of social activities, suggesting the need to establish an age- and pathogen-specific surveillance system for future infec-tious disease responses.