scholarly journals IDENTIFYING OF HUMAN METAPNEUMOVIRUS AND ITS PHENOTYPE AS A CAUSATIVE AGENTS OF PNEUMONIA IN CHILDREN

Author(s):  
Abbas Mohammed Hussein Al-shebani ◽  
Adnan Hamad Aubaid

Objectives: The present investigational study was aimed to detect and identify the genotypes of Human metapneumovirus (hMPV) and its phylogeny with respiratory syncytial viruses (RSV) that cause pulmonary inflammation.Material and Methods: A total of 250 samples of patients who were clinically diagnosed respiratory tract illness were collected from Maternity and Children Hospital in Al Diwaniyah city, Iraq. The clinical samples were nasopharyngeal, nasal and throat swabs. The current study screened the presence of hMPV and RSV (A and B) genotypes from nasopharyngeal specimens of children aged from several days to 10 years old.Results: The results revealed that 6% were infected with hMPV, 8% of respiratory syncytial viruses type A (RSV-A) and 14% of respiratory syncytial virus’s type B (RSV-B) from children who are suffering from respiratory illness. Phylogenetic tree analysis of hMPV based on the partial sequences of the fusion protein (F) gene was used for genotyping and detection. The phylogenetic tree was constructed using maximum likelihood tree method in MEGA 6.0 version. The local hMPV isolates (S1) were closely related to NCBI-Blast hMPV genotype A1 (KM408076.1), the local hMPV isolates (S2, S3, and S5) were closely related to NCBI-Blast hMPV genotype B1 (KJ196323.1), and the local hMPV isolates (S4) were closely related to NCBI-Blast hMPV genotype B2 (JQ041689.1).Conclusions: The prevalence rate of hMPV is less than RSV, and both subtypes of hMPV, A and B may exist and circulate in one season, and the predominant sublineage of hMPV shifts in progressive season. 

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Everlyn Kamau ◽  
John W. Oketch ◽  
Zaydah R. de Laurent ◽  
My V. T. Phan ◽  
Charles N. Agoti ◽  
...  

Abstract Background Human metapneumovirus (HMPV) is an important cause of acute respiratory illness in young children. Whole genome sequencing enables better identification of transmission events and outbreaks, which is not always possible with sub-genomic sequences. Results We report a 2-reaction amplicon-based next generation sequencing method to determine the complete genome sequences of five HMPV strains, representing three subgroups (A2, B1 and B2), directly from clinical samples. In addition to reporting five novel HMPV genomes from Africa we examined genetic diversity and sequence patterns of publicly available HMPV genomes. We found that the overall nucleotide sequence identity was 71.3 and 80% for HMPV group A and B, respectively, the diversity between HMPV groups was greater at amino acid level for SH and G surface protein genes, and multiple subgroups co-circulated in various countries. Comparison of sequences between HMPV groups revealed variability in G protein length (219 to 241 amino acids) due to changes in the stop codon position. Genome-wide phylogenetic analysis showed congruence with the individual gene sequence sets except for F and M2 genes. Conclusion This is the first genomic characterization of HMPV genomes from African patients.


Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 3910-3910
Author(s):  
Muhammad Ali ◽  
Jillian Baker ◽  
Susan Elaine Richardson ◽  
Upton Allen ◽  
Oussama Abla

Abstract Abstract 3910 The human metapneumovirus (HMPV) is a paramyxovirus that has been recently associated with respiratory tract infections in children. HMPV was first described in 2001 by researchers in the Netherlands. Since this initial report, HMPV has been reported from many other countries across the world. HMPV was found to be the second most frequent cause, after RSV, of viral respiratory infections in children less than 1 year of age. In hospitalized children, the most frequent clinical manifestations associated with HMPV are pneumonitis, bronchiolitis and asthma. Severe HMPV infection can also occur in the elderly and in immunocompromised patients. We carried out a retrospective study to describe the clinical features and severity of HMPV in pediatric oncology patients at The Hospital for Sick Children. Thirty one children with cancer found to have HMPV infection during the study period from January 2005 till December 2010. HMPV was isolated by nasopharyngeal (NP) swab in 30/31 patients while one patient had bronchalveolar lavage (BAL). Direct fluorescent-antibody (DFA) was positive in all 31 patients while 13 patients also had viral culture positive. Eight patients had culture negative while this test was not done in 10 patients (after December 2008). The majority of HMPV infection was diagnosed in the winter months from November to March and also in the spring till May. Of 31 patients, 13 were male and 18 were female. The most common underlying diagnosis was leukemia 14/31 (45.1%). Nine patients had different types of solid tumours including 3 with neuroblastoma, 2 with rhabdomyosarcoma, 1 with hepatoblastoma, 1 with nasopharyngeal sarcoma, and 1 with undifferentiated sarcoma. Twenty-nine of thirty-one (93.5%) of the patients presented with cough, 24/31 (77.4%) with fever, 16/31 (51.6%) with rhinorrhea. Vomiting was noticed in 25.8% of the patients and diarrhea in 32.2%. Sixteen of thirty-one (51.6%) patients were diagnosed with upper respiratory tract infection (URTI), 7/31 (22.5%) patients were diagnosed as bronchiolitis and 8/31 (25.8%) diagnosed to have pneumonia. 19.3% (6/31) patients had co-infection with different organisms including coagulase negative Staphylococcus and Streptococcus pneumoniae requiring antibiotic treatment. The average duration of symptoms on presentation was 7 days (1-90 days). One patient with average risk acute lymphoblastic leukemia on maintenance treatment presented with 3 months history of cough and subsequently NP swab and BAL were positive for HMPV. He required prolonged therapy with inhaled bronchodilator and steroid. Twenty of thirty-one (64.5%) patients were admitted. The average duration of admission was 18.3 days and average duration of respiratory illness was 13.5 days. None of the patient required mechanical ventilation because of HMPV infection. Twenty-one of thirty-one patients were treated with antibiotics for duration of 3 to 14 days. One patient was empirically treated with oseltamivir (Tamiflu). All of the patients recovered from their viral illness completely, only one patient had prolonged respiratory symptoms for six months. Conclusion: Our study showed HMPV is an important respiratory virus causing both upper respiratory tract illness (URTI) and lower respiratory tract illness (LRTI) in children with cancer. Although the majority of the children recovered from HMPV infection without clinically significant illness, a minority had prolonged respiratory illness requiring supportive treatment. Disclosures: No relevant conflicts of interest to declare.


Science ◽  
2021 ◽  
Vol 372 (6539) ◽  
pp. eabg0821 ◽  
Author(s):  
Katrina A. Lythgoe ◽  
Matthew Hall ◽  
Luca Ferretti ◽  
Mariateresa de Cesare ◽  
George MacIntyre-Cockett ◽  
...  

Extensive global sampling and sequencing of the pandemic virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have enabled researchers to monitor its spread and to identify concerning new variants. Two important determinants of variant spread are how frequently they arise within individuals and how likely they are to be transmitted. To characterize within-host diversity and transmission, we deep-sequenced 1313 clinical samples from the United Kingdom. SARS-CoV-2 infections are characterized by low levels of within-host diversity when viral loads are high and by a narrow bottleneck at transmission. Most variants are either lost or occasionally fixed at the point of transmission, with minimal persistence of shared diversity, patterns that are readily observable on the phylogenetic tree. Our results suggest that transmission-enhancing and/or immune-escape SARS-CoV-2 variants are likely to arise infrequently but could spread rapidly if successfully transmitted.


2021 ◽  
Author(s):  
Jihye Shin ◽  
SeEun Choe ◽  
Bang-Hun Hyun ◽  
Dong-Jun An

Abstract The prevalence of porcine kobuvirus (PKoV) and porcine astrovirus (PAstV) in 845 Korean wild boars (KWB) during 2016-2018 were 28.0% and 10.6%, respectively, and co-infection of two viruses showed 5.1%. Phylogenetic tree analysis also revealed that 236 PKoVs from KWB were divided to diverse lineages within Aichivirus C group but the one strain (WKoV16CN-8627) was included the same cluster with bovine kobuvirus (Achivirus B). Eighty-nine PAstVs from KWB was belonged predominantly to lineage PAstV4 and only one strain (WAst17JN-10931) included novel to lineage PAstV2. Two viruses are epidemic more in young (≤ 12 months) than in old pigs (> 12 months).


2021 ◽  
Vol 8 (4) ◽  
pp. 260-265
Author(s):  
Meryem Colak ◽  
Selin Yigit ◽  
Anil Tapisiz ◽  
Hager Muftah ◽  
Kenan Yuce ◽  
...  

Objective: Human Parainfluenza viruses (HPIVs) cause respiratory tract infections, and the second most common cause of acute respiratory illness-related hospitalizations after the respiratory syncytial virus in children <5 years of age. The aim of the study; determination of HPIVs positivity and common types in pediatric patients with respiratory tract infection; investigation the distribution of HPIV positivity by age groups, months and seasons, respectively. Material and Method: HPIV results of 1613 pediatric patients who were sent to the molecular virology laboratory from various pediatric clinics of Gazi Hospital between March 2016 and February 2021 (five years period) were investigated. Nucleic acid isolation was performed on the EZ1 Advanced (Qiagen, Germany) device using the EZ1 Virus Mini Kit by the manufacturer's protocol. Results: HPIV positivity was detected as 4.1% in clinical samples and, the most common HPIV type was found to be HPIV-3 (55%). The distribution of other HPIV types were; HPIV-2, HPIV-4 and HPIV-1 with 26%, 23% and 14%, respectively. HPIV-3 is the most common type in 2016, 2017, 2018 and 2019; however, HPIV-1 is the most common type in 2020. HPIVs co-infection was detected with other respiratory tract viruses in 51% of samples. The highest HPIV co-infection was detected in Rhinovirus. The highest HPIV positivity rate (45%) were determined in the 0-2 age group compared to other age groups (p<0.05). The highest positivity rate was in October in the autumn season (p<0.05), the lowest was in January and February in winter. The highest rate (8.1%) of HPIV positivity was found in 2016 and the lowest rate (0.7%) was in 2020. Conclusions: Since it is not possible to diagnose viral etiology of respiratory tract infections based on clinical findings, viral respiratory tract panel and Multiplex real-time PCR test are a fast and useful method in early diagnosis, treatment decision and prevention of unnecessary antibiotic use. HPIVs positivity is seen at higher rates in children aged 0-2 and in autumn months with seasonal differences.


2018 ◽  
Vol 15 (1) ◽  
pp. 37-42
Author(s):  
Baghdad Science Journal

This study aims at detecting the differences in genotyping of coding region fusA gene in clinical isolates of Acinetobacter baumannii from Baghdad, Iraq. Collected two hundred clinical samples (50 samples from urine, 50 samples from wound, 50 samples from sputum and 50 samples from otitis infections). Laboratory diagnosis for bacterial isolates carried out by some biochemical tests and confirmed by using VITEK- 2 compact system. The results appeared that twenty isolates of Acinetobacter baumannii in all these samples. Genotyping study was performed of coding region fusA gene of the extracted genome of all bacterial isolates and used specific primers in achieved amplification process of this target gene. DNA sequencing of this gene and alignment of sequencing in NCBI was achieved and drew phylogenetic tree by using Geneious 9 software among locally isolates alone and then among locally isolates and high identity global isolates in GenBank. The results in phylogenetic tree of fusA gene in locally isolates showed 4 groups of isolates included more than one source of isolation. The results in phylogenetic tree of the locally and global isolates showed that are four different groups and each group included some locally isolates and global isolates except group A (AE_22, AE_26) and group E (AE_35, AE_32, AE_33) that not identity with global isolates. The nucleotides sequence of fusA gene from localized isolate (AE_35) was registered in national GenBank under accession number (LOCUS KY818057) and protein ID "ARV90995.1.


Author(s):  
Chatzidaki V ◽  
◽  
Perdikogianni C ◽  
Galanakis E ◽  
Paraskevis D ◽  
...  

ackground: Vertical transmission of Hepatitis B Virus (HBV) is the primary infection source for infants, but little is known on the proportion of children that have acquired HBV from their mothers. Objective: We investigated the relationship of HBV sequencing in HBVpositive children and their mothers and explored the HBV phylogenetic tree. Methods: Serum-extracted HBV-DNA from 38 individuals (13 children paired to nine mothers, 16 unpaired infected children) was amplified by polymerase chain reaction and the target region HBV surface glycoprotein (amino acids 40-171) was directly sequenced. Following editing and alignment of these sequences, phylogenetic tree analysis was performed using the neighbourjoining and maximum-likelihood methods. Results: Analysis was successfully performed in 29 subjects (23 children and six mothers), including six mother-child pairs. All individuals were infected by genotype D. Subgenotype adw3 prevailed (21, 72.4%), followed by ayw2 (4, 13.8%) and ayw3 (4, 13.8%). Among six mother-child pairs, three had identical and three had different subgenotypes. Phylogenetic analysis revealed that HBV sequences from three children did not cluster with their siblings suggesting a different source of infection. Conclusion: Our findings suggest that HBV subgenotypes in infected children may not be identical to their mothers’ and point to non-vertical HBV transmission in childhood.


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