Molecular Evolution of Human Parainfluenza Virus Type 2 Based on Hemagglutinin-Neuraminidase Gene

Feng, Yi; Zhu, Zhen; Xu, Jianping; Sun, Liwei; Zhang, Hui; Xu, Hongmei; Zhang, Feng; Wang, Qianqian; Han, Guangyue; Jiang, Jie; Liu, Ying; Zhou, Shihao; Zhang, Yan; Ji, Yixin; Mao, Naiying; Xu, Wenbo

doi:10.1128/spectrum.04537-22

Cited by 4 publications

(2 citation statements)

References 47 publications

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“…The N-glycosylation sites at the HN gene of four Riyadh isolates revealed only eight conserved N-glycosylation sites at amino acids 6 (NLS), 286 (NTT), 335 (NIT), 388 (NNS), 498 (NES), 504 (NPT), 517 (NTT), and 539 (NGT). These ndings are consistent with a recent work that found four N-glycosylation sites (N6, N115, N142, and N272) to be substantially conserved in all HN sequences of Chinese HPIV2 strains [21].…”

Section: Discussionsupporting

confidence: 93%

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Genetic Analysis of Human Parainfluenza Type 2 Virus in Riyadh, Saudi Arabia

Alsaleh

Aziz

Alkubaisi

et al. 2023

Preprint

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The extensive mass gathering of pilgrims from all over the world, as well as the constant flow of foreign workers via country entry crossings, raises the likelihood of respiratory virus outbreaks spreading and evolving in Saudi Arabia. Here, we report the sequence and phylogenetic analysis of the human parainfluenza type-2 (HPIV-2) in nasopharyngeal aspirates (NPAs) collected from Riyadh, Saudi Arabia, from 2020/21 and 2021/22 seasons. RNA was extracted from the clinical samples and subjected to RT-PCR analysis for the detection of IAV and IBV. The full-length HN gene of HPIV-2 was amplified and sequenced. Multiple sequence alignments (both nucleotides and deduced amino acids) were aligned using Clustal W, MegAlign program of Lasergene software, and MEGA 7.0. HPIV-2 was found in (4; 2% of 200) NPAs. Sequence and phylogenetic analysis results showed that indicated a genotype shifting from G3 to G4a with 83% sequence homology 62-M786 from Japan, which was prominent throughout the winter seasons of 2008/09. Multiple amino acid sequence alignment revealed 25 sites of possible difference between G3 genotypes and G4a. A total of twenty- two of these locations were shared by the other G4a genotypes, whereas three positions, 67V, 175S, and 377Q, were exclusively shared by G3. Only eight conserved N-glycosylation sites were found at amino acids 6(NLS), 286(NTT), 335(NIT), 388(NNS), 498(NES), 504(NPT), 517(NTT), and 539(NGT) in four Riyadh isolates. Our findings also revealed that the G4a genotype of HPIV-2 predominated in Riyadh during the winter seasons of 2020/21 and 2021/22. Further research with a large sample size covering numerous regions of Saudi Arabia throughout different epidemic seasons is needed to achieve an improved knowledge of HPIV-2 circulation.

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Section: Discussionsupporting

confidence: 93%

“…In a recent study, 21 HPIV-2 HN sequences were acquired from LRTI pediatric cases in seven Chinese provinces (Henan, Jilin, Gansu, Chongqing, Shandong, Anhui, and Hebei) in children aged 1 to 12 years between 2011 and 2017 to 2021. [21].…”

Section: Discussionmentioning

confidence: 99%

Genetic Analysis of Human Parainfluenza Type 2 Virus in Riyadh, Saudi Arabia

Alsaleh

Aziz

Alkubaisi

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

Genetic analysis of human parainfluenza type 2 virus in Riyadh, Saudi Arabia

Alsaleh,

Aziz,

Alkubaisi

et al. 2023

Virus Genes

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The extensive mass gathering of pilgrims from all over the world, as well as the constant ow of foreign workers via country entry crossings, raises the likelihood of respiratory virus outbreaks spreading and evolving in Saudi Arabia. Here, we report the sequence and phylogenetic analysis of the human parain uenza type-2 (HPIV-2) in nasopharyngeal aspirates (NPAs) collected from Riyadh, Saudi Arabia, from 2020/21 and 2021/22 seasons. RNA was extracted from the clinical samples and subjected to RT-PCR analysis for the detection of IAV and IBV. The full-length HN gene of HPIV-2 was ampli ed and sequenced. Multiple sequence alignments (both nucleotides and deduced amino acids) were aligned using Clustal W, MegAlign program of Lasergene software, and MEGA 7.0. HPIV-2 was found in (4; 2% of 200) NPAs. Sequence and phylogenetic analysis results showed that indicated a genotype shifting from G3 to G4a with 83% sequence homology 62-M786 from Japan, which was prominent throughout the winter seasons of 2008/09. Multiple amino acid sequence alignment revealed 25 sites of possible difference between G3 genotypes and G4a. A total of twenty-two of these locations were shared by the other G4a genotypes, whereas three positions, 67V, 175S, and 377Q, were exclusively shared by G3. Only eight conserved N-glycosylation sites were found at amino acids 6(NLS), 286(NTT), 335(NIT), 388(NNS), 498(NES), 504(NPT), 517(NTT), and 539(NGT) in four Riyadh isolates. Our ndings also revealed that the G4a genotype of HPIV-2 predominated in Riyadh during the winter seasons of 2020/21 and 2021/22. Further research with a large sample size covering numerous regions of Saudi Arabia throughout different epidemic seasons is needed to achieve an improved knowledge of HPIV-2 circulation.

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Genetic characteristics of human parainfluenza viruses 1–4 associated with acute lower respiratory tract infection in Chinese children, during 2015–2021

Zhu,

Sun,

et al. 2024

Microbiol Spectr

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Human parainfluenza viruses (HPIVs) are a significant cause of acute lower respiratory tract infections (ALRTIs) among young children and elderly individuals worldwide. The four types of HPIVs (HPIV1–4) can cause recurrent infections and pose a significant economic burden on health care systems globally. However, owing to the limited availability of complete genome sequences, the genetic evolution of these viruses and the development of vaccines and antiviral treatments are hampered. To address this issue, this study utilized next-generation sequencing to obtain 156 complete genome sequences of HPIV1–4, which were isolated from hospitalized children with ALRTIs in six regions of China between 2015 and 2021. This study revealed multiple clades, lineages, or sublineages of HPIVs circulating in mainland China, with a novel clade D of HPIV1 identified as geographically restricted to China. Moreover, this study identified the endemic dominant genotype of HPIV3, lineage C3, which has widely spread and continuously circulated in China. Bioinformatic analysis of the genome sequences revealed that the proteins of HPIV3 possessed the most variable sites, with the P protein showing more diversity than the other proteins among all types of HPIVs. The HN proteins of HPIV1–3 are all under negative/purifying selection, and two amino acid substitutions in the HN proteins correspond to known mAb neutralizing sites in the two HPIV3 strains. These findings provide crucial insights into the genetic diversity and evolutionary dynamics of HPIVs circulating among children in China and may facilitate research on the molecular diagnosis, vaccine development, and surveillance of HPIVs. IMPORTANCE Phylogenetic analysis revealed the prevalence of multiple clades, lineages, or sublineages of human parainfluenza viruses (HPIVs) circulating in mainland China. Notably, a unique evolutionary branch of HPIV1 containing only Chinese strains was identified and designated clade D. Furthermore, in 2023, HPIV3 strains from Pakistan and Russia formed a new lineage within clade C, named C6. The first HPIV4b sequence obtained in this study from China belongs to lineage C2. Evolutionary rate assessments revealed that both the HN and whole-genome sequences of HPIV3 presented the lowest evolutionary rates compared with those of the other HPIV types, with rates of 6.98E−04 substitutions/site/year (95% HPD: 5.87E−04 to 8.25E−03) and 5.85E−04 substitutions/site/year (95% HPD: 5.12E−04 to 6.62E−04), respectively. Recombination analysis revealed a potential recombination event in the F gene of an HPIV1 strain in this study. Additionally, all the newly obtained HPIV1–3 strains exhibited negative selection pressure, and two mutations were identified in the HN protein of two HPIV3 strains at monoclonal antibody-binding sites.

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Molecular Evolution of Human Parainfluenza Virus Type 2 Based on Hemagglutinin-Neuraminidase Gene

Cited by 4 publications

References 47 publications

Genetic Analysis of Human Parainfluenza Type 2 Virus in Riyadh, Saudi Arabia

Genetic Analysis of Human Parainfluenza Type 2 Virus in Riyadh, Saudi Arabia

Genetic analysis of human parainfluenza type 2 virus in Riyadh, Saudi Arabia

Genetic characteristics of human parainfluenza viruses 1–4 associated with acute lower respiratory tract infection in Chinese children, during 2015–2021

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