scholarly journals Genetic Characteristics of Human Parainfluenza Virus Types 1–4 From Patients With Clinical Respiratory Tract Infection in China

2021 ◽  
Vol 12 ◽  
Author(s):  
Nan Shao ◽  
Bo Liu ◽  
Yan Xiao ◽  
Xinming Wang ◽  
Lili Ren ◽  
...  
Keyword(s):  
Amino Acid ◽  
Respiratory Tract ◽  
Amino Acid Substitution ◽  
Negative Selection ◽  
Amino Acid Position ◽  
F Protein ◽  
Parainfluenza Viruses ◽  
Substitution Site ◽  
Hn Gene ◽  
Human Parainfluenza Viruses

Human parainfluenza viruses (HPIV1–4) cause acute respiratory tract infections, thereby impacting human health worldwide. However, there are no current effective antivirals or licensed vaccines for infection prevention. Moreover, sequence information for human parainfluenza viruses (HPIVs) circulating in China is inadequate. Therefore, to shed light on viral genetic diversity and evolution, we collected samples from patients infected with HPIV1–4 in China from 2012 to 2018 to sequence the viruses. We obtained 24 consensus sequences, comprising 1 for HPIV1, 2 for HPIV2, 19 for HPIV3, and 2 for HPIV4A. Phylogenetic analyses classified the 1 HPIV1 into clade 2, and the 2 HPIV4 sequences into cluster 4A. Based on the hemagglutinin-neuraminidase (HN) gene, a new sub-cluster was identified in one of the HPIV2, namely G1c, and the 19 HPIV3 sequences were classified into the genetic lineages of C3f and C3a. The results indicated that HPIV1–4 were co-circulated in China. Further, the lineages of sub-cluster C3 of HPIV3 were co-circulated in China. A recombination analysis indicated that a putative recombination event may have occurred in the HN gene of HPIV3. In the obtained sequences of HPIV3, we found that two amino acid substitution sites (R73K in the F protein of PUMCH14028/2014 and A281V in the HN protein of PUMCH13961/2014) and a negative selection site (amino acid position 398 in the F protein) corresponded to the previously reported neutralization-related sites. Moreover, amino acid substitution site (K108E) corresponded to the negative selection site (amino acid position 108) in the 10 F proteins of HPIV3. However, no amino acid substitution site corresponded to the glycosylation site in the obtained HPIV3 sequences. These results might help in studying virus evolution, developing vaccines, and monitoring HPIV-related respiratory diseases.

Upper respiratory tract infections, including influenza

2018 ◽  
Author(s):  
Pippa Newton
Keyword(s):  
Natural History ◽  
Respiratory Tract ◽  
Respiratory Tract Infections ◽  
Upper Respiratory Tract Infections ◽  
Upper Respiratory Tract ◽  
Type B ◽  
Parainfluenza Viruses ◽  
Upper Respiratory ◽  
Tract Infections ◽  
Human Parainfluenza Viruses

Infections of the nasal cavity, sinuses, pharynx, epiglottis, and larynx are termed upper respiratory tracts infections. These include acute coryza, pertussis, sinusitis, pharyngitis, tonsillitis, epiglottitis, laryngitis, laryngotracheobronchitis, and influenza. Rhinoviruses and coronaviruses account for the majority of acute coryzal illnesses. Acute sinusitis (<4 weeks duration) is also usually viral in origin. About 70% of pharyngitis and tonsillitis cases are viral in etiology. Haemophilus influenzae (Type B) is responsible for most cases of epiglottitis. Acute laryngitis and laryngotracheobronchitis are usually caused by human parainfluenza viruses. This chapter focuses on upper respiratory tract infections, including their etiology, symptoms, demographics, natural history, complications, diagnosis, prognosis, and treatment.

scholarly journals An S101P Substitution in the Putative Cleavage Motif of the Human Metapneumovirus Fusion Protein Is a Major Determinant for Trypsin-Independent Growth in Vero Cells and Does Not Alter Tissue Tropism in Hamsters

2005 ◽  
Vol 79 (16) ◽  
pp. 10678-10689 ◽  
Author(s):  
Jeanne H. Schickli ◽  
Jasmine Kaur ◽  
Nancy Ulbrandt ◽  
Richard R. Spaete ◽  
Roderick S. Tang
Keyword(s):  
Amino Acid ◽  
Respiratory Tract ◽  
Amino Acid Substitution ◽  
Cleavage Site ◽  
Vero Cells ◽  
Human Metapneumovirus ◽  
Single Amino Acid ◽  
Putative Cleavage Site ◽  
Single Amino Acid Change ◽  
Fusion Glycoprotein

ABSTRACT Human metapneumovirus (hMPV), a recently described paramyxovirus, is a major etiological agent for lower respiratory tract disease in young children that can manifest with severe cough, bronchiolitis, and pneumonia. The hMPV fusion glycoprotein (F) shares conserved functional domains with other paramyxovirus F proteins that are important for virus entry and spread. For other paramyxovirus F proteins, cleavage of a precursor protein (F0) into F1 and F2 exposes a fusion peptide at the N terminus of the F1 fragment, a likely prerequisite for fusion activity. Many hMPV strains have been reported to require trypsin for growth in tissue culture. The majority of these strains contain RQSR at the putative cleavage site. However, strains hMPV/NL/1/00 and hMPV/NL/1/99 expanded in our laboratory contain the sequence RQPR and do not require trypsin for growth in Vero cells. The contribution of this single amino acid change was verified directly by generating recombinant virus (rhMPV/NL/1/00) with either proline or serine at position 101 in F. These results suggested that cleavage of F protein in Vero cells could be achieved by trypsin or S101P amino acid substitution in the putative cleavage site motif. Moreover, trypsin-independent cleavage of hMPV F containing 101P was enhanced by the amino acid substitution E93K. In hamsters, rhMPV/93K/101S and rhMPV/93K/101P grew to equivalent titers in the respiratory tract and replication was restricted to respiratory tissues. The ability of these hMPV strains to replicate efficiently in the absence of trypsin should greatly facilitate the generation, preclinical testing, and manufacturing of attenuated hMPV vaccine candidates.

Hubsm: A Novel Amino Acid Substitution Matrix for Comparing Hub Proteins

2017 ◽  
Vol 7 (8) ◽  
pp. 212
Author(s):  
Renganayaki G. ◽  
Achuthsankar S. Nair
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
Low Complexity ◽  
Database Search ◽  
Substitution Matrix ◽  
Compositional Bias ◽  
Sequence Alignments ◽  
Amino Acid Substitution Matrix ◽  
Alignment Algorithms ◽  
Hub Proteins

Sequence alignment algorithms and  database search methods use BLOSUM and PAM substitution matrices constructed from general proteins. These de facto matrices are not optimal to align sequences accurately, for the proteins with markedly different compositional bias in the amino acid.   In this work, a new amino acid substitution matrix is calculated for the disorder and low complexity rich region of Hub proteins, based on residue characteristics. Insights into the amino acid background frequencies and the substitution scores obtained from the Hubsm unveils the  residue substitution patterns which differs from commonly used scoring matrices .When comparing the Hub protein sequences for detecting homologs,  the use of this Hubsm matrix yields better results than PAM and BLOSUM matrices. Usage of Hubsm matrix can be optimal in database search and for the construction of more accurate sequence alignments of Hub proteins.

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