The Nicaraguan Pediatric Influenza Cohort Study, 2011-2019: Influenza Incidence, Seasonality, and Transmission

Tracking the genetic diversity of SARS-CoV-2 variants in Nicaragua throughout the COVID-19 pandemic

The global circulation of SARS-CoV-2 has been extensively documented; however, the dynamics within Central America, particularly Nicaragua, remain underexplored. This study characterizes the genomic diversity of SARS-CoV-2 in Nicaragua from March 2020 through December 2022, utilizing 1064 genomes obtained via next-generation sequencing. These sequences were selected nationwide and analyzed for variant classification, lineage predominance, and phylogenetic diversity. We employed both Illumina and Oxford Nanopore Technologies for all sequencing procedures. Results indicated a temporal and spatial shift in dominant lineages, initially from B.1 and A.2 in early 2020 to various Omicron subvariants toward the study's end. Significant lineage shifts correlated with changes in COVID-19 positivity rates, underscoring the epidemiological impact of variant dissemination. Comparative analysis with regional data underscored the low diversity of circulating lineages in Nicaragua and their delayed introduction compared to other countries in the Central American region. The study also linked specific viral mutations with hospitalization rates, emphasizing the clinical relevance of genomic surveillance. This research advances the understanding of SARS-CoV-2 evolution in Nicaragua and provides valuable information regarding its genetic diversity for public health officials in Central America. We highlight the critical role of ongoing genomic surveillance in identifying emergent lineages and informing public health strategies.

Vaccination against rapidly evolving pathogens and the entanglements of memory

Immune memory determines infection risk and responses to future infections and vaccinations over potentially decades of life. Despite its centrality, the dynamics of memory to antigenically variable pathogens remains poorly understood. This Review examines how past exposures shape B cell responses to vaccinations with influenza and SARS-CoV-2. An overriding feature of vaccinations with these pathogens is the recall of primary responses, often termed 'imprinting' or 'original antigenic sin'. These recalled responses can inhibit the generation of new responses unless some incompletely defined conditions are met. Depending on the context, immune memory can increase or decrease the total neutralizing antibody response to variant antigens, with apparent consequences for protection. These effects are easier to measure experimentally than epidemiologically, but there is evidence that both early and recent exposures influence vaccine effectiveness. A few immunological interactions between adaptive immune responses and antigens might explain the seemingly discrepant effects of memory. Overall, the complex observations point to a need for more quantitative approaches to integrate high-dimensional immune data from populations with diverse exposure histories. Such approaches could help identify optimal vaccination strategies against antigenically diverse pathogens.

Increased influenza severity in children in the wake of SARS-CoV-2

The SARS-CoV-2 pandemic and subsequent interruption of influenza circulation has lowered population immunity to influenza, especially among children with few prepandemic exposures. Using data from a prospective pediatric cohort study based in Managua, Nicaragua, we compared the incidence and severity of influenza A/H3N2 and influenza B/Victoria between 2022 and two prepandemic seasons. We found a higher incidence of A/H3N2 in older children in 2022 compared with pre-2020 and a higher proportion of severe influenza in 2022, primarily among children aged 0-4, suggesting an influence of the SARS-CoV-2 pandemic on influenza incidence and severity in children.

Increased Influenza Severity in Children in the Wake of SARS-CoV-2

The SARS-CoV-2 pandemic and subsequent interruption of influenza circulation has lowered population immunity to influenza, especially among children with few pre-pandemic exposures. We compared the incidence and severity of influenza A/H3N2 and influenza B/Victoria between 2022 and two pre-pandemic seasons and found an increased frequency of severe influenza in 2022.

High Co-circulation of Influenza and Severe Acute Respiratory Syndrome Coronavirus 2

In the first 2 years of the coronavirus disease 2019 pandemic, influenza transmission decreased substantially worldwide, meaning that health systems were not faced with simultaneous respiratory epidemics. In 2022, however, substantial influenza transmission returned to Nicaragua where it co-circulated with severe acute respiratory syndrome coronavirus 2, causing substantial disease burden.

Pediatric burden and seasonality of human metapneumovirus over 5 years in Managua, Nicaragua

BACKGROUND

Human metapneumovirus (hMPV) is an important cause of pediatric respiratory infection. We leveraged the Nicaraguan Pediatric Influenza Cohort Study (NPICS) to assess the burden and seasonality of symptomatic hMPV infection in children.

METHODS

NPICS is an ongoing prospective study of children in Managua, Nicaragua. We assessed children for hMPV infection via real-time reverse-transcription polymerase chain reaction (RT-PCR). We used classical additive decomposition analysis to assess the temporal trends, and generalized growth models (GGMs) were used to estimate effective reproduction numbers.

RESULTS

From 2011 to 2016, there were 564 hMPV symptomatic infections, yielding an incidence rate of 5.74 cases per 100 person-years (95% CI 5.3, 6.2). Children experienced 3509 acute lower respiratory infections (ALRIs), of which 160 (4.6%) were associated with hMPV infection. Children under the age of one had 55% of all symptomatic hMPV infections (62/112) develop into hMPV-associated ALRIs and were five times as likely as children over one to have an hMPV-associated ALRI (rate ratio 5.5 95% CI 4.1, 7.4 p < 0.001). Additionally, symptomatic reinfection with hMPV was common. In total, 87 (15%) of all observed symptomatic infections were detected reinfections. The seasonality of symptomatic hMPV outbreaks varied considerably. From 2011 to 2016, four epidemic periods were observed, following a biennial seasonal pattern. The mean ascending phase of the epidemic periods were 7.7 weeks, with an overall mean estimated reproductive number of 1.2 (95% CI 1.1, 1.4).

CONCLUSIONS

Symptomatic hMPV infection was associated with substantial burden among children in the first year of life. Timing and frequency of symptomatic hMPV incidence followed biennial patterns.