Stefano Tempia

SARS-CoV-2 evolution enhanced viral fitness and immune evasion, extending the COVID-19 pandemic and resulting in millions of excess deaths. Viral diversity is generated within infected individuals, yet the timing and interplay of viral and immunological forces that drive transmissible evolution are incompletely understood. We developed a multi-scale within host phylodynamic (WiPhy) model of SARS-CoV-2 infection which couples viral replication, innate and acquired immune responses, and viral mutation. We then validated the model against quantitative viral and phylodynamic metrics. Model output predicts that typical acute infections rapidly generate genetic diversity due to accumulation of minor variants which in most cases do not achieve sufficient concentrations for transmission. Delayed innate immune responses correlate with higher peak viral load and diversification, allowing higher transmission risk of the founder virus or with a novel variant that is equally or less fit. In contrast, the risk of transmitting a fitter variant is highest during the ~10% of infections in which viral loads remain sufficiently high for transmission after 10-14 days. In these cases, non-sustained innate and/or weak acquired immune responses allow sufficient time for selection of a variant with one or more fitness enhancing non-synonymous mutations. Across a simulated cohort of ~1500 individuals, 5% of transmission risk came from variants with enhanced fitness from nonsynonymous mutations, and 13% of simulated infections accounted for 90% of fitter variant transmission risk. Our results highlight how the timing and interplay of viral and immunological forces within a host create bottlenecks that severely limit between host evolution.

Background: Accurate detection of RSV infections is important to understand epidemiology. We estimated symptomatic fraction and shedding duration of reverse‐transcription polymerase chain reaction (RT‐PCR)‐confirmed cases and compared RSV detection through molecular and serologic techniques. Methods: We enrolled healthy children aged 6–23 months in a prospective cohort study, from May to October 2022, collecting thrice‐weekly mid‐turbinate nasal swabs for RSV RT‐PCR testing. We collected serum at baseline and end of follow‐up and detected anti‐RSV IgG using enzyme‐linked immunosorbent assay (ELISA) and multipathogen bead‐based immunoassay (MIA). We ascertained symptoms by twice‐weekly nurse visits, and daily caregiver symptom diaries. We calculated sensitivity, specificity, and positive (PPV) and negative (NPV) predictive value of RT‐PCR, ELISA, and MIA compared to a standard (two or more assays‐positive) among children with paired sera and baseline blood preceding an RT‐PCR–confirmed episode. Results: The RSV season started mid‐February 2022. We enrolled 93 participants; 87 (94%) followed to the final study visit. Forty individuals had one or more RT‐PCR–confirmed RSV infection, and six of them had a repeat episode. One‐or‐more symptom was reported from 54% (25/46) of RT‐PCR–confirmed episodes, fever in 26% (12/46), and cough in 37% (17/46). Median RNA shedding duration was 7 days (IQR = 4–11 days). Among 80 children meeting criteria, ELISA and MIA each had > 92% sensitivity, specificity, PPV, and NPV while RT‐PCR had 78% (95% CI = 61%–90%) sensitivity, 98% (95% CI = 88–100%) specificity, 97% (95% CI = 82%–100%) PPV, and 84% (95% CI = 71%–93%) NPV. Discussion: Approximately half of RSV episodes were symptomatic. Serology had a high sensitivity and specificity for infection identification.

Protective immunity against influenza transmission remains poorly understood due to the high prevalence of undetected asymptomatic infections. To address this, we analyze 1518 individuals and 623 infection episodes from a three-year, rural and urban, South African household cohort study that combines pre-season serum collection with twice-weekly virological testing regardless of symptoms. By developing a subtype/lineage-specific household transmission model and incorporating time-resolved viral shedding kinetics for all observed infections, we disentangle household and community exposure, pre-season immunity, and age effects. After adjusting for exposure intensity, pre-season hemagglutination inhibition (HAI) titers ≥1:40 are associated with a reduced infection risk for A(H1N1)pdm09, A(H3N2), and B/Victoria, but not B/Yamagata. However, children exhibit higher susceptibility and longer viral shedding durations than adults across all subtypes/lineages, even after accounting for pre-season HAI titers. Here, we show persistent age-related effects on influenza susceptibility and viral shedding, underscoring the need to explore immune mechanisms beyond HAI-based correlates of protection.

Households play a crucial role in the propagation of infectious diseases due to the frequent and prolonged interactions that typically occur between their members. Recent studies have emphasized the need to include socioeconomic variables in epidemic models to account for the heterogeneity induced by human behavior. While sub-Saharan Africa suffers the highest burden of infectious disease diffusion, few studies have investigated the mixing patterns in the countries and their relation with social indicators. This work analyzes household contact matrices measured with wearable proximity sensors in a rural and an urban village in South Africa. Leveraging a rich data collection describing additional individual and household attributes, we investigate how the household contact matrix varies according to the household type (whether it is composed only of a familiar nucleus or by a larger group), the gender of its head (the primary decision-maker), the rural or urban context, and the season in which it was measured. We show the household type and the gender of its head induce differences in the interaction patterns between household members, particularly regarding child caregiving, suggesting they are relevant attributes to include in epidemic modeling.

Background: Respiratory syncytial virus (RSV), influenza, and SARS-CoV-2 are major causes of morbidity among children, yet comparative burden estimates remain limited in low- and middle-income countries in the Western Pacific Region. We estimated the burden of RSV relative to influenza and SARS-CoV-2 among children less than 24 months (<25 months) in the Philippines. Methods: We applied the World Health Organization (WHO) tiered disease burden estimation approach to estimate RSV-, influenza-, and SARS-CoV-2-associated hospitalizations from 01-May-2022 to 30-April-2024. Proportions were derived and extrapolated to national hospitalization rates using data from the hospital-based RSV Pilot Surveillance, National Health Insurance Program claims as a proxy for non-sentinel admissions, National Demographic and Health Survey data for risk factor assessment, and national population estimates. Findings: We estimated 50,909 RSV-associated hospitalizations (95% CI: 41,310–61,463; rate: 1,163·8 per 100,000), substantially exceeding the corresponding estimates for influenza and SARS-CoV-2. Infants aged 0–5 months accounted for 53·3% of RSV hospitalizations, with hospitalization rates declining with increasing age. RSV was associated with an estimated 3,244 seasonal ICU admissions (95% CI 1,432–5,050; rate 74·1 per 100,000) and 1,460 in-hospital deaths (0–2,711; 33·3 per 100,000).Interpretation: RSV contributes the highest burden of severe disease among children aged <24 months in the Philippines. Available preventive tools, including maternal RSV vaccines and long-acting monoclonal antibodies, could substantially reduce disease burden in this age group.

Brucellosis is a widespread zoonotic disease and a major contributor to febrile illness, often underdiagnosed. This study investigated the seroprevalence of brucellosis and the associated exposure factors within South African farming and animal health communities. A cross-sectional survey was conducted across 40,000 km² in the Free State and Northern Cape provinces from 2015 to 2016. Interviews and serum samples were collected from 847 volunteers on randomly selected farms and veterinary professionals listed in a regional register. Samples were tested using a commercial Brucella IgG ELISA. Risk factors were assessed using logistic regression, accounting for within-farm clustering. The seroprevalence was higher among veterinary professionals (11.6%; 16/138) than farm-based participants (7.0%; 50/711); p = 0.095. Multivariable analysis identified several exposure factors within the farm-based population: age over 40 years (aOR = 5.35; 95% CI: 1.68–17.02), White population group (aOR = 4.60; 95% CI: 1.64–12.91), contact with diseased animals (aOR = 2.01; 95% CI: 1.05–3.84), and working 4–8 h daily with ungulates (aOR = 2.90; 95% CI: 1.25–6.76). Among veterinary professionals, odds of exposure were higher with more than 5 years of work (OR = 1.82; 95% CI: 1.21–2.72) and extended ungulate contact (OR = 4.85; 95% CI: 1.27–18.52). Occupational exposure highlights the need for improved brucellosis prevention strategies.

Background Digital participatory surveillance (DPS) may provide information on non-medically attended influenza-like illnesses (ILI). Combining DPS with laboratory testing allows pathogen identification. We assessed the feasibility of DPS and home-based swabbing in South Africa. Methods We enrolled a cohort of individuals aged ≥18 years who completed weekly respiratory symptoms questionnaires from March–October 2022. We calculated the percent of weekly DPS-reports consistent with ILI and COVID-19 syndromes and compared with weekly private respiratory consultations. Symptomatic participants in 3 provinces were offered self-administered nasal swabbing for influenza and SARS-CoV-2 detection by polymerase chain reaction (PCR). We assessed six feasibility indicators: recruitment capability, representativeness, reliability, accuracy, acceptability, and usefulness. Results Recruitment capability: 26% (249/954) of participants who accessed the platform enrolled and 92% (81/88) of participants eligible for self-swabbing were enrolled. Acceptability: 84% (210/249) of participants remained enrolled until the end of follow-up, 15% (32/249) completed the acceptability questionnaire with 100% (32/32) indicating willingness to participate in future studies, whereas 16% (39/210) withdrew from the study. Representativeness: 50% (125/249) were aged 18-39 years and 50% were older than 40 years (124/249), 71% (178/249) were female and 79% (196/249) had a tertiary qualification. Reliability: median weekly participation was 23% (interquartile range (IQR): 19%-29%) and 38% (80/210) submitted >1 weekly symptoms questionnaire. Accuracy: 2% (31/1440) and 25% (359/1440) of weekly questionnaires met ILI and COVID-19 case definitions, respectively. Influenza and SARS-CoV-2 were detected in 7% (6/81) and 32% (26/81) of tested samples, respectively. There was low correlation with respiratory consultations (0.08, 95% CI -0.27–0.43) for ILI and (0.36, 95% CI 0.11–0.62) COVID19. Usefulness: symptoms were reported in 32% (459/1440) of reports and 11% (49/459) sought medical care. Conclusion The study was feasible, however, the low enrolment numbers limit power. Linkage to self-swabbing was successful and demonstrates the potential for pathogen confirmation.

Objective: The objective of this study is to summarize the state of knowledge on the economic burden and cost of illness due to influenza, SARS‐CoV‐2, respiratory syncytial virus (RSV), and other respiratory viruses (ORV) in Latin America and the Caribbean (LAC).Methods: We performed a scoping review across three databases (PubMed‐Medline, Scielo, and Embase) without time restriction, including economic burden and cost‐of‐illness studies. We extracted and analyzed data on publication year, population, study type, perspective, costing techniques, and settings. We reported absolute and relative frequencies to summarize the results. Economic burden estimates were divided by the gross domestic product (GDP) for each country. Costs were converted into 2022 international dollars (PPP).Results: Overall, 2638 articles were retrieved; we included 44 full texts from 16 LAC countries. Twenty‐four (54.5%) studies focused on influenza, 16 (36.4%) on SARS‐CoV‐2, 3 (6.8%) on RSV, and 1 on ORV. Twenty two (50.0%) focused on cost‐effectiveness (related to vaccination)/cost–benefit analysis, and 17 (38.6%) focused on cost of illness. Most studies (n = 33, 75.0%) were conducted from the third‐party perspective. Fifty percent of the studies used a bottom‐up costing technique and 29.6% top‐down. Influenza direct medical costs ranged from I$6.6–I$300.3 for outpatients and I$62.8–I$222,920 for inpatients; for RSV from I$68.3–I$1292; and for SARS‐CoV‐2 between I$69.9 and I$38,039. The total annual costs of the influenza economic burden ranged between 0.0003% and 1.33% of the GDP.Conclusion: This study showed variability in costing methods, perspectives, and types of studies among LAC countries. This variability underscores the need for standardized methodologies in future cost studies to ensure comparability and reliability of results.

Background: Respiratory syncytial virus (RSV) and influenza infections are associated with increased pneumococcal colonization and disease risk. We assessed the impact of RSV and influenza on pneumococcal colonization density and factors influencing density changes during viral infection. Methods: Over 3 years, 1658 individuals from 325 households were enrolled, with nasopharyngeal swabs collected twice weekly for pneumococcus, RSV, and influenza A/B detection by real-time polymerase chain reaction. We analyzed samples from 2 weeks before, during, and 2 and 8 weeks after infection. Pneumococcal density was compared across infection periods by t tests, and multivariable regression identified factors influencing density changes. Results: Pneumococcal density increased during RSV infection (log mean before vs during infection, 9.3 vs 10.2 genomic copies/mL; P < .01) but showed no significant overall increase with influenza (log mean before vs during infection, 9.6 vs 9.9 genomic copies/mL; P = .2). However, the following were correlated with increased pneumococcal density: higher influenza viral loads (cycle threshold [Ct] value <25: coefficient, 2.8; 95% CI 1.4–4.2) and RSV viral loads (viral Ct value <25: coefficient, 2.5 [95% CI, 1.1–3.9; P < .01]; viral Ct value of 25–29: coefficient, 1.1 [95% CI, .1–2.2; P = .04]; vs viral Ct value of 30–34). Participants who were underweight had lower pneumococcal density differences (coefficient, −1.8; 95% CI, −3.5 to −.1; P = .04) than those with a normal body mass index. Conclusions: RSV infection, especially with higher viral loads, increases pneumococcal colonization, while individuals who are underweight exhibit lower density changes.

Our understanding of influenza transmission remains imperfect due to the high prevalence of asymptomatic infections that often go undetected. To address this challenge, we leveraged uniquely resolved data from a household cohort study spanning three consecutive years in rural and urban South Africa. The study incorporated pre-season serum collection and twice-weekly virological testing during the influenza season, regardless of symptom presence. We developed a subtype/lineage-specific influenza household transmission model that accounts for time-resolved viral shedding across the full clinical spectrum of infections, allowing us to disentangle the role of household and community exposures, pre-season immunity, and age on transmission. Our analysis revealed that viral shedding intensity, as measured by the cycle threshold (Ct) values of infected household members, significantly correlated with the risk of transmission for all four influenza subtypes/lineages. After adjusting for viral shedding, pre-season hemagglutination inhibition (HAI) titers greater than 1:40 were associated with a significantly lower risk of infection acquisition for A(H1N1)pdm09, A(H3N2), and B/Victoria, but not for B/Yamagata. Notably, children exhibited higher susceptibility and longer viral shedding durations compared to adults across all subtypes/lineages, even after adjusting for pre-season HAI titers. While our findings support that HAI titers correlate with protection, the strong residual effects of age on susceptibility and viral shedding may reflect the accumulation of additional immune responses shaped by repeated exposures over time. Our study underscores the need to explore immune mechanisms beyond HAI titers that modulate influenza susceptibility and transmission.