Etiology of acute viral respiratory infections common in Pakistan: A review

Acute Respiratory and Influenza Viruses Circulating in Kazakhstan During 2018-2024

Respiratory tract infections cause serious morbidity and mortality and are a major public health problem. The objective of our study was detection of the prevalence of viral respiratory diseases in the territory of Kazakhstan during the epidemic period of 2018-2024. The presence of respiratory viruses in nasopharyngeal swabs was analyzed using real-time polymerase chain reaction. The level of specific antibodies in the blood serum was determined by hemagglutination inhibition assay and enzyme-linked immunosorbent assay. In rtRT-PCR, patients were diagnosed with non-influenza viral respiratory tract infections as well as influenza viruses A(H1N1), A(H3N2), and B. Antibodies were detected against A(H1N1)pdm09, influenza A(H3N2), and influenza B viruses and with simultaneous detection of both viruses. The circulation of influenza A(H3N2) viruses belonging to the 3C.2a1b.2a.2a.3a.1 clade was confirmed by whole-genome sequencing. According to the results, in the period 2018-2024, the spread of influenza A and B viruses and non-influenza respiratory tract infections was observed. The data of this study confirm the role of known causative agents of epidemic infection and indicate the need to continue monitoring their spread in Kazakhstan, which may add to the general quality of the health system.

Antimicrobial Use Among Hospitalized Neonates and Children; Findings and Implications from a Comprehensive Point Prevalence Survey Among General Tertiary Hospitals in Pakistan

Purpose

Antimicrobial resistance is a global health crisis exacerbated by excessive and inappropriate use of antibiotics, especially among low- and middle-income countries including Pakistan. The paediatric population is a key area in view of their vulnerability and excessive prescribing of antibiotics in Pakistan. Consequently, there is an urgent need to robustly assess antimicrobial use among hospitalized neonates and children in tertiary hospitals in Pakistan as they are generally the training centres for new physicians subsequently treating children.

Patients and Methods

A point prevalence survey (PPS) was conducted in the children's wards of 14 tertiary care hospitals in Punjab Province, covering over 50% of the population of Pakistan. This builds on a previous PPS among tertiary care hospitals treating exclusively neonates and children.

Results

A total of 1811 neonates and children were surveyed with 1744 patients prescribed antibiotics, a prevalence of 96.3%. A total of 2747 antibiotics were prescribed to these 1744 neonates and children, averaging 1.57 antibiotics per patient. Overall, 57.7% of the patients were prescribed one antibiotic and 27.2% two antibiotics, with 85.6% of antibiotics administered parenterally. Over a third (34.4%) of the antibiotics were prescribed prophylactically, with 44.7% of them for surgical procedures. Among those prescribed antibiotics for surgical procedures, 75.2% were prescribed for more than one day. Overall, 92.2% of antibiotics were prescribed empirically, with 86.2% prescribed without mentioning the rationale for their choice in the notes, with 77.6% having no stop date. Respiratory tract infections were the most common indication (43.4%). Staphylococcus species (36.0%) were the most common pathogen with limited Culture and Sensitivity Testing performed. Three quarters (75.2%) of antibiotics were from the Watch list, and 24.4% were Access antibiotics.

Conclusion

A very high prevalence of antibiotic use among neonates and children in tertiary hospitals in Pakistan, including Watch antibiotics, mirroring previous studies. Consequently, initiatives including antimicrobial stewardship programmes are urgently needed to address current inappropriate prescribing.

Global epidemiological trends in the incidence and deaths of acute respiratory infections from 1990 to 2021

The aim of this study was to investigate the global epidemiological trends in the incidence and deaths of acute respiratory infections (ARIs), encompassing both upper respiratory infections (URIs) and lower respiratory infections (LRIs), from 1990 to 2021. Using data from the Global Burden of Disease study 2021 (GBD 2021), we utilized the average annual percentage change (AAPC) to examine the trends in the age-standardized incidence rate and deaths rate (ASIR and ASDRs) of URIs and LRIs. In 2021, the global ASIR of URIs and LRIs were 166,770.73 (95 % UI: 148,098.16-189,487.93) per 100,000 and 4283.61 (95 % UI: 4057.03-4524.89) per 100,000, respectively. The highest ASIR of URIs occurred in high-sociodemographic index (SDI) regions (232744.64, 95 % UI: 206887.07-261694.81) per 100,000, whereas LRIs occurred in low-SDI regions (9261.1, 95 % UI: 8741.61-9820.86) per 100,000. In 2021, the global ASDRs of URIs and LRIs were 0.28 (95 % UI: 0.09-0.61) per 100,000 and 28.67 (95 % UI: 25.92-31.07) per 100,000, respectively. The highest ASDRs of both URIs and LRIs were observed in low-SDI regions, with 1.1 (95 % UI: 0.08-2.78) per 100,000 and 70.68 (95 % UI: 62.56-78.62) per 100,000, respectively. From 1990 to 2021, the global ASIR for URIs and LRIs decreased, with AAPCs of -0.17 % (95 % CI: 0.17 % to -0.16 %) and -1.28 % (95 % CI: -1.37 % to -1.22 %), respectively. The global ASDRs also decreased (-3.39 % for URIs; -2.46 % for LRIs). However, during the COVID-19 pandemic, the ASIR of URIs increased in many countries, especially in high-SDI regions (rate difference before and during the COVID-19 pandemic in ASIR was 2210.19 per 100,000.) and low-SDI regions (rate difference in ASIR: 111.26 per 100,000). The global incidence and deaths related to ARIs have decreased over the past 32 years. However, it remains a significant public health concern, particularly due to the notable incidence of URIs in high SDI regions and the deaths associated with both URIs and LRIs in low SDI regions. Furthermore, an increase in the incidence of URIs was observed in both high- and low-SDI regions during the COVID-19 pandemic, highlighting the need for increased attention.

Molecular characterization of human adenoviruses associated with pediatric respiratory infections in Karachi, Pakistan

Human adenoviruses (HAdVs) are a diverse group of viruses associated with respiratory infections in humans worldwide. However, there is a lack of research on the genetic diversity and epidemiology of HAdVs in Pakistan. This study characterized HAdVs in pediatric patients with respiratory tract infections in Karachi, Pakistan, between 2022 and 2023. We analyzed 762 nasopharyngeal samples of children ≤ 5 years. DNA extraction, followed by PCR targeting E2B and hexon genes, was carried out. Data analysis was performed on SPSS 25.0, and phylogenetic analysis of hexon gene was performed on MEGA 11. HAdV was detected in 7.34% (56/762) of patients round the year, but at a significantly higher rate during the winter season. Age was insignificantly associated with HAdV incidence (p = 0.662), but more than 62.5% (35/56) of positive cases were younger than 10 months. The circulating HAdVs were identified as six different types from species B (78.57%) and C (21.42%), with the majority of isolates found to be like B3. HAdV was found to be co-infected with bocavirus (5.4%) and measles (7.14%). These findings revealed a high frequency and genetic diversity of respiratory HAdVs in Karachi, Pakistan. We conclude that periodic and continuous surveillance of adenoviruses and other respiratory pathogens is necessary to improve the prognosis and management of respiratory diseases, thereby reducing the child mortality rate in Pakistan.

Experimental trials of predicted CD4+ and CD8+ T-cell epitopes of respiratory syncytial virus

Background

Respiratory syncytial virus (RSV) is the most common cause of viral lower respiratory tract infections (LRTIs) in young children around the world and an important cause of LRTI in the elderly. The available treatments and FDA-approved vaccines for RSV only lessen the severity of the infection and are recommended for infants and elderly people.

Methods

We focused on developing a broad-spectrum vaccine that activates the immune system to directly combat RSV. The objective of this study is to identify CD4+ and CD8+ T-cell epitopes using an immunoinformatics approach to develop RSV vaccines. The efficacy of these peptides was validated through in-vitro and in-vivo studies involving healthy and diseased animal models.

Results

For each major histocompatibility complex (MHC) class-I and II, we found three epitopes of RSV proteins including F, G, and SH with an antigenic score of >0.5 and a projected SVM score of <5. Experimental validation of these peptides on female BALB/c mice was conducted before and after infection with the RSV A2 line 19f. We found that the 3RVMHCI (CD8+) epitope of the F protein showed significant results of white blood cells (19.72 × 103 cells/μl), neutrophils (6.01 × 103 cells/μl), lymphocytes (12.98 × 103 cells/μl), IgG antibodies (36.9 µg/ml), IFN-γ (86.96 ng/L), and granzyme B (691.35 pg/ml) compared to control at the second booster dose of 10 µg. Similarly, 4RVMHCII (CD4+) of the F protein substantially induced white blood cells (27.08 × 103 cells/μl), neutrophils (6.58 × 103 cells/μl), lymphocytes (16.64 × 103 cells/μl), IgG antibodies (46.13 µg/ml), IFN-γ (96.45 ng/L), and granzyme B (675.09 pg/ml). In-vitro studies showed that 4RVMHCII produced a significant level of antibodies in sera on day 45 comparable to mice infected with the virus. 4RVMHCII also induced high IFN-γ and IL-2 secretions on the fourth day of the challenge compared to the preinfectional stage.

Conclusion

In conclusion, epitopes of the F protein showed considerable immune response and are suitable for further validation.

Spread of Pathogens Causing Respiratory Viral Diseases Before and During CoVID-19 Pandemic in Kazakhstan

Analyze clinical samples collected and determine the etiology of viral pathogens and the dynamics of their spread. Acute respiratory viral infections remain one of the key health problems worldwide. They constitute etiologically independent diseases, with similar clinical infection manifestations and a single mechanism for the transmission of pathogens. 4712 nasopharyngeal swabs were collected from people before and during the COVID-19 pandemic with acute respiratory infections that tested negative for COVID-19 and were examined in this study. The collected samples were screened by a real-time polymerase chain reaction on a Rotor-Gene Q6 plex instrument. Statistical processing of the results, tabular, and graphical data were analyzed in the MS Excel. The largest number of the nasopharyngeal swabs were collected from children under 17 years of age (60.75%). In 702 samples (9.85%) pathogens of respiratory infections of non-influenza etiology were detected, including adenovirus, bocavirus, coronavirus, metapneumovirus, paramyxovirus types I–IV, respiratory syncytial virus, and rhinovirus. At the same time, both before and during the COVID-19 pandemic, different influenza virus variants co-circulation (A/H1N1, A/H3N2, and type B) were discovered, with a predominance of viruses with the antigenic formula A/H1N1. The results of the study indicate the need for continuous monitoring of the viral pathogens spread, which will expand the existing knowledge of the viral etiology of respiratory diseases and highlight the importance of viruses in the respiratory infections occurrence.

Ethiopian Medicinal Plants Used for Respiratory Tract Disorders: Ethnomedicinal Review

Respiratory tract infections (RTIs) refer to infections in any part of the respiratory tract, which are common, with most of the world's population contracting at least one infection annually. These infections are becoming important causes of death and morbidity due to the rapid development of antimicrobial resistance that has resulted in reduced efficacy of existing drugs. Different local societies residing in Ethiopia have been reported to use traditional medicinal plants to treat RTIs. Nevertheless, up-to-date summarized data on the diversity of plants used in the traditional medicine system to treat RTIs in Ethiopia are lacking. The purpose of this review was to assess plant species used in traditional medicine to treat respiratory tract infections in Ethiopia. It attempts to compile available data required for undertaking further scientific investigations. The data were collected by searching for published scientific articles and other grey literature. Following this, medicinal plant (MP) diversity, growth forms, plant parts used, modes of remedy preparation and application, sources and distributions, and frequently treated respiratory disorders were examined. An Excel spreadsheet and SigmaPlot software were used to summarize and present the data. Two hundred twenty-nine (229) plant species that have been used to treat respiratory disorders in Ethiopia were documented. Lamiaceae was the most cited family (27 species), followed by Asteraceae (23 species), and Fabaceae (18 species), whereas cough was primarily cited as being treated by MPs and scored the highest frequency of citation (FOC = 243), followed by the common cold (FOC = 151) and asthma (FOC = 63). The top-cited plant species used in the treatment of RTIs were Eucalyptus globulus (6.8%), Allium sativum (5.5%), Zingiber officinale (4.2%), Ruta chalepensis (3.8%), and Ocimum lamiifolium (2.8%). Herbs were the dominant plant growth form (46%) used to treat respiratory diseases, and the most commonly used MP parts were leaves (37%). The leading traditional method used for preparation was decoction (25.5%), and the remedies were usually administered orally (64.6%). The MP origin reported was mainly from the wild (59%). High diversity of medicinal plants was reported as being used to treat various RTIs in Ethiopia. Information obtained from this review could be used as a reference for the selection of plants for further pharmacological, phytochemical, and toxicological investigations for their possible therapeutic applications and the development of new plant-based drugs.

Immunoinformatics-Aided Analysis of RSV Fusion and Attachment Glycoproteins to Design a Potent Multi-Epitope Vaccine

Respiratory syncytial virus (RSV) usually causes respiratory tract infections of upper airways in infants and young children. Despite recent medical advances, no approved vaccine is available to control RSV infections. Therefore, we conducted an immunoinformatics study to design and evaluate a potential multi-epitope vaccine against RSV. Sequence-based analyses of the glycoproteins F and G revealed a total of eight CD8 T-cell and three CD4 T-cell epitopes after considering antigenicity, binding affinity and other parameters. Molecular docking analysis confirmed that these T-cell epitopes developed strong structural associations with HLA allele(s). By integrating these prioritized epitopes with linkers and a cholera toxin-derived adjuvant, a multi-epitope vaccine was designed. The developed vaccine was found to be stable, non-allergenic, flexible and antigenic. Molecular docking analysis revealed a striking mean HADDOCK score (-143.3) of top-ranked vaccine-TLR cluster and a Gibbs free energy change (ΔG) value of -11.3 kcal mol-1. As per computational immune simulation results, the vaccine generated a high titer of antibodies (especially IgM) and effector T-cells. Also, codon optimization and in silico cloning ensured the increased expression of vaccine in Escherichia coli. Altogether, we anticipate that the multi-epitope vaccine reported in this study will stimulate humoral and cellular responses against RSV infection, subject to follow-up experimental validation.

Molecular typing and epidemiologic profiles of human metapneumovirus infection among children with severe acute respiratory infection in Huzhou, China

Background

Human metapneumovirus (hMPV) is one of the important pathogens in infant respiratory tract infection. However, the molecular epidemiology of hMPV among children < 14 years of age hospitalized with severe acute respiratory infection (SARI) is unclear. We investigated the hMPV infection status and genotypes of children hospitalized with SARI from January 2016 to December 2020 in Huzhou, China.

Methods

A nasopharyngeal flocked swab, nasal wash, or nasopharyngeal swab/or opharyngeal swab combination sample was collected from children with SARI in Huzhou from January 2016 to December 2020. Quantitative reverse transcription-polymerase chain reaction was performed to detect hMPV RNA. The hMPV F gene was amplified and sequenced, followed by analysis using MEGA software (ver. 7.0). Epidemiological data were analyzed using Microsoft Excel 2010 and SPSS (ver. 22.0) software.

Results

A total of 1133 children with SARI were recruited from 2016 to 2020. Among them, 56 (4.94%) were positive for hMPV-RNA. Children < 5 years of age accounted for 85.71% of the positive cases. The hMPV incidence was high in spring and winter, especially in December and January to March. Phylogenetic analysis of the F-gene sequences of 28 hMPV strains showed that the A1, B1, and B2 genotypes were prevalent in Huzhou, and the dominant hMPV genotype varied according to surveillance year.

Conclusions

HMPV is an important respiratory pathogen in children in Huzhou, with a high incidence in winter and spring in children < 5 years of age. In this study, genotypes A1, B1, and B2 were the most prevalent.

Vaccination against Paediatric Respiratory Pathogens

Acute respiratory infections (ARIs) are extremely common in children, especially those under 5 years old. They can lead to complications, super-infection, respiratory failure, and even compromised respiratory function in adulthood. For some of the responsible pathogens, vaccines are available. This review reports current issues about vaccines against the main respiratory pathogens to highlight the available strategies to reduce the burden of paediatric respiratory disease. The optimal use of influenza, pneumococcal, pertussis and measles vaccines is required in order to reduce ARI burden. Vaccination coverage rates must be improved to achieve the full benefits of these vaccines. Recently, advances in the knowledge of respiratory syncytial virus structural biology and immunology as well as the development of new techniques to generate vaccine candidates have increased the number of promising vaccines even against this harmful pathogen.

Epidemiology, evolution and transmission of human metapneumovirus in Guangzhou China, 2013-2017

Human metapneumovirus (hMPV), first identified in 2001, is a major viral respiratory pathogen that worldwide reported. Fundamental questions concerning the dynamics of viral evolution and transmission at both regional and global scales remain unanswered. In this study, we obtained 32 G gene and 51 F gene sequences of hMPV in Guangzhou, China in 2013–2017. Temporal and spatial phylogenetic analyses were undertaken by incorporating publicly available hMPV G gene (978) and F gene (767) sequences. The phylogenetic results show different global distribution patterns of hMPV before 1990, 1990–2005, and 2006–2017. A sharply increasing hMPV positive rate (11%) was detected in Guangzhou 2017, mainly caused by the B1 lineage of hMPV. A close phylogenetic relation was observed between hMPV strains from China and Japan, suggesting frequent hMPV transmissions between these regions. These results provide new insights into hMPV evolution, transmission, and spatial distribution and highlight Asia as a new epicenter for viral transmission and novel variant seeding after the year 2005. Conducting molecular surveillance of hMPV in Asian countries is critical for understanding the global circulation of hMPV and future vaccine design.

Etiology of acute viral respiratory infections common in Pakistan: A review

Respiratory infections, especially those of the lower respiratory tract, remain a foremost cause of mortality and morbidity of children greater than 5 years in developing countries including Pakistan. Ignoring these acute-level infections may lead to complications. Particularly in Pakistan, respiratory infections account for 20% to 30% of all deaths of children. Even though these infections are common, insufficiency of accessible data hinders development of a comprehensive summary of the problem. The purpose of this study was to determine the prevalence rate in various regions of Pakistan and also to recognize the existing viral strains responsible for viral respiratory infections through published data. Respiratory viruses are detected more frequently among rural dwellers in Pakistan. Lower tract infections are found to be more lethal. The associated pathogens comprise respiratory syncytial virus (RSV), human metapneumovirus (HMPV), coronavirus, enterovirus/rhinovirus, influenza virus, parainfluenza virus, adenovirus, and human bocavirus. RSV is more dominant and can be subtyped as RSV-A and RSV-B (BA-9, BA-10, and BA-13). Influenza A (H1N1, H5N1, H3N2, and H1N1pdm09) and Influenza B are common among the Pakistani population. Generally, these strains are detected in a seasonal pattern with a high incidence during spring and winter time. The data presented include pneumonia, bronchiolitis, and influenza. This paper aims to emphasise the need for standard methods to record the incidence and etiology of associated pathogens in order to provide effective treatment against viral infections of the respiratory tract and to reduce death rates.