BACKGROUND: Chronic lung disease is a major cause of morbidity in African children with HIV infection; however, the microbial determinants of HIV-associated chronic lung disease (HCLD) remain poorly understood. We conducted a case-control study to investigate the prevalence and densities of respiratory microbes among pneumococcal conjugate vaccine (PCV)-naive children with (HCLD +) and without HCLD (HCLD-) established on antiretroviral treatment (ART).
METHODS: Nasopharyngeal swabs collected from HCLD + (defined as forced-expiratory-volume/second < -1.0 without reversibility postbronchodilation) and age-, site-, and duration-of-ART-matched HCLD- participants aged between 6-19 years enrolled in Zimbabwe and Malawi (BREATHE trial-NCT02426112) were tested for 94 pneumococcal serotypes together with twelve bacteria, including Streptococcus pneumoniae (SP), Staphylococcus aureus (SA), Haemophilus influenzae (HI), Moraxella catarrhalis (MC), and eight viruses, including human rhinovirus (HRV), respiratory syncytial virus A or B, and human metapneumovirus, using nanofluidic qPCR (Standard BioTools formerly known as Fluidigm). Fisher\'s exact test and logistic regression analysis were used for between-group comparisons and risk factors associated with common respiratory microbes, respectively.
RESULTS: A total of 345 participants (287 HCLD + , 58 HCLD-; median age, 15.5 years [IQR = 12.8-18], females, 52%) were included in the final analysis. The prevalence of SP (40%[116/287] vs. 21%[12/58], p = 0.005) and HRV (7%[21/287] vs. 0%[0/58], p = 0.032) were higher in HCLD + participants compared to HCLD- participants. Of the participants positive for SP (116 HCLD + & 12 HCLD-), 66% [85/128] had non-PCV-13 serotypes detected. Overall, PCV-13 serotypes (4, 19A, 19F: 16% [7/43] each) and NVT 13 and 21 (9% [8/85] each) predominated. The densities of HI (2 × 104 genomic equivalents [GE/ml] vs. 3 × 102 GE/ml, p = 0.006) and MC (1 × 104 GE/ml vs. 1 × 103 GE/ml, p = 0.031) were higher in HCLD + compared to HCLD-. Bacterial codetection (≥ any 2 bacteria) was higher in the HCLD + group (36% [114/287] vs. (19% [11/58]), (p = 0.014), with SP and HI codetection (HCLD + : 30% [86/287] vs. HCLD-: 12% [7/58], p = 0.005) predominating. Viruses (predominantly HRV) were detected only in HCLD + participants. Lastly, participants with a history of previous tuberculosis treatment were more likely to carry SP (adjusted odds ratio (aOR): 1.9 [1.1 -3.2], p = 0.021) or HI (aOR: 2.0 [1.2 - 3.3], p = 0.011), while those who used ART for ≥ 2 years were less likely to carry HI (aOR: 0.3 [0.1 - 0.8], p = 0.005) and MC (aOR: 0.4 [0.1 - 0.9], p = 0.039).
CONCLUSIONS: Children with HCLD + were more likely to be colonized by SP and HRV and had higher HI and MC bacterial loads in their nasopharynx. The role of SP, HI, and HRV in the pathogenesis of CLD, including how they influence the risk of acute exacerbations, should be studied further.
BACKGROUND: The BREATHE trial (ClinicalTrials.gov Identifier: NCT02426112 , registered date: 24 April 2015).

Jamestown Canyon virus (JCV) is a mosquitoborne orthobunyavirus in the California serogroup that circulates throughout Canada and the United States. Most JCV exposures result in asymptomatic infection or a mild febrile illness, but JCV can also cause neurologic diseases, such as meningitis and encephalitis. We describe a case series of confirmed JCV-mediated neuroinvasive disease among persons from the provinces of British Columbia, Alberta, Quebec, and Nova Scotia, Canada, during 2011-2016. We highlight the case definitions, epidemiology, unique features and clinical manifestations, disease seasonality, and outcomes for those cases. Two of the patients (from Quebec and Nova Scotia) might have acquired JCV infections during travel to the northeastern region of the United States. This case series collectively demonstrates JCV\'s wide distribution and indicates the need for increased awareness of JCV as the underlying cause of meningitis/meningoencephalitis during mosquito season.

Orthohantaviruses cause hantavirus cardiopulmonary syndrome; most cases occur in the southwest region of the United States. We discuss a clinical case of orthohantavirus infection in a 65-year-old woman in Michigan and the phylogeographic link of partial viral fragments from the patient and rodents captured near the presumed site of infection.

We report an imported Crimean-Congo hemorrhagic fever case in Senegal. The patient received PCR confirmation of virus infection 10 days after symptom onset. We identified 46 patient contacts in Senegal; 87.7% were healthcare professionals. Strengthening border crossing and community surveillance systems can help reduce the risks of infectious disease transmission.

The cacao swollen shoot virus disease (CSSVD) is among the most economically damaging diseases of cacao trees and accounts for almost 15-50% of harvest losses in Ghana. This virus is transmitted by several species of mealybugs (Pseudococcidae, Homoptera) when they feed on cacao plants. One of the mitigation strategies for CSSVD investigated at the Cocoa Research Institute of Ghana (CRIG) is the use of mild-strain cross-protection of cacao trees against the effects of severe strains. In this study, simple deterministic, delay, and stochastic ordinary differential equation-based models to describe the dynamic of the disease and spread of the virus are suggested. Model parameters are estimated using detailed empirical data from CRIG. The modeling outcomes demonstrate a remarkable resemblance between real and simulated dynamics. We have found that models with delay approximate the data better and this agrees with the knowledge that CSSVD epidemics develop slowly. Also, since there are large variations in the data, stochastic models lead to better results. We show that these models can be used to gain useful informative insights about the nature of disease spread.

A comprehensive understanding of the dynamics of Streptococcus pneumoniae colonization in conjunction with respiratory virus infections is essential for enhancing our knowledge of the pathogenesis and advancing the development of effective preventive strategies. Therefore, a case-control study was carried out in Addis Ababa, Ethiopia to investigate the colonization rate of S. pneumoniae and its coinfection dynamics with respiratory viruses among children under the age of 5 years. Samples from the nasopharyngeal and/or oropharyngeal, along with socio-demographic and clinical information, were collected from 420 children under 5 years old (210 cases with lower respiratory tract infections and 210 controls with conditions other than respiratory infections.). A one-step Multiplex real-time PCR using the Allplex Respiratory Panel Assays 1-4 was performed to identify respiratory viruses and bacteria. Data analysis was conducted using STATA software version 17. The overall colonization rate of S. pneumoniae in children aged less than 5 years was 51.2% (215/420). The colonization rates in cases and controls were 54.8% (115/210) and 47.6% (100/210), respectively (p = 0.14). Colonization rates were observed to commence at an early age in children, with a colonization rate of 48.9% and 52.7% among infants younger than 6 months controls and cases, respectively. The prevalence of AdV (OR, 3.11; 95% CI [1.31-8.19]), RSV B (OR, 2.53; 95% CI [1.01-6.78]) and HRV (OR, 1.7; 95% CI [1.04-2.78]) tends to be higher in children who tested positive for S. pneumoniae compared to those who tested negative for S. pneumoniae. Further longitudinal research is needed to understand and determine interaction mechanisms between pneumococci and viral pathogens and the clinical implications of this coinfection dynamics.

Retrieval and visualization of biological data are essential for understanding complex systems. With the increasing volume of data generated from high-throughput sequencing technologies, effective and optimized data visualization tools have become indispensable. This is particularly relevant in the COVID-19 postpandemic period, where understanding the diversity and interactions of microbial communities (i.e., viral and bacterial) constitutes an important asset to develop and plan suitable interventions.In this chapter, we show the usage and the potentials of ExTaxsI (Exploring Taxonomy Information) tool to retrieve viral biodiversity data stored in National Center for Biotechnology Information (NCBI) databases and create the related visualization. In addition, by integrating different functions and modules, the tool generates relevant types of visualization plots to facilitate the exploration of microbial biodiversity communities useful to deep dive into ecological and taxonomic relationships among different species and identify potential significant targets.Using the Monkeypox virus as a case study, this work points out significant perspectives on biological data visualization, which can be used to gain insights into the ecology, evolution, and pathogenesis of viruses. Accordingly, we show the potentiality of ExTaxsI to organize and describe the available/downloaded data in an easy, simple, and interpretable way allowing the user to interact dynamically with the visualization plots through specific filters, zoom, and explore functions.

Measles is a highly contagious infection that leads to many serious complications. Despite the significant global effort to eradicate it, it still represents a major threat due to suboptimal vaccination coverage, especially after the coronavirus disease 2019 (COVID-19) pandemic that affected all routine childhood vaccinations. One of its fatal complications, which has been reported a few times in the literature, is hemophagocytic lymphohistiocytosis (HLH). We discuss a case of a 14-month-old unvaccinated female patient who developed measles-induced HLH and was treated with intravenous immunoglobulins (IVIG) and steroids; unfortunately, she developed multiorgan failure and passed away before chemotherapy could be initiated.

Cytomegalovirus (CMV) infection or Epstein-Barr virus (EBV) infection in immunocompetent patients usually resolves without treatment. However, it can cause severe symptoms that can last for several weeks, especially in immunocompromised patients. Indications for antiviral immunocompetent individuals with CMV disease are not well-established. Here, we report two cases who had concomitant CMV-EBV infection. The first patient ultimately received anti-CMV therapy with significant improvement in symptoms and labs. The second patient had a milder disease course and was treated conservatively.

OBJECTIVE: Nucleic acid-based molecular techniques in current laboratory practice allow the identification of a broad range of respiratory viruses. However, due to asymptomatic carriage, the detection of viruses in the respiratory tract does not necessarily indicate disease. The study aimed to investigate infections of different viruses that colonize the airways, the viral combinations in coinfection, and the viral association with the occurrence of either upper respiratory tract infection (AURTI) or lower respiratory tract infection (ALRTI) in children.
RESULTS: A matched case-case-control study included ALRTI cases, AURTI cases, and healthy controls was conducted at Kunming Children\'s Hospital. Oropharyngeal swabs from the three groups were collected for eight viral pathogens detection by multiplex RT-PCR. The association of each pathogen with disease status was determined by comparing the results between cases and controls. From 1 March 2021 through 28 February 2022, 278 participants in each group were investigated. Viral infection was detected in 54.0%, 37.1%, and 12.2% of the ALRTI cases, AURTI cases, and healthy controls, respectively. Human respiratory syncytial virus (RSV), adenovirus (ADV), and parainfluenza virus-3 (PIV-3) were the most frequently documented viruses. RSV/ADV was the most frequent combination detected in coinfection. When compared to healthy controls, RSV and PIV-3 were independently associated with both ALRTI and AURTI.
CONCLUSIONS: RSV and PIV-3 were causes of both ALRTI and AURTI cases. These results provide initial evidence of the potential of microbiota-based diagnostics for the differential diagnosis of severe acute respiratory infections using oropharyngeal swab samples.