Recent #advances in the #detection of #respiratory virus #infection in #humans (J Med Virol., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

J Med Virol. 2020 Jan 15. doi: 10.1002/jmv.25674. [Epub ahead of print]

Recent advances in the detection of respiratory virus infection in humans.

Zhang N1, Wang L2, Deng X3, Liang R3, Su M3, He C3, Hu L3, Su Y3, Ren J3, Yu F3, Du L4, Jiang S4,5.

Author information: 1 Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, China. 2 State Key Laboratory of North China Crop Improvement and Regulation, Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China. 3 State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China. 4 Lindsley F. Kimball Research Institute, New York Blood Center, New York, USA. 5 Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.

 

Abstract

Respiratory tract viral infection caused by viruses or bacteria is one of the most common diseases in human worldwide, while those caused by emerging viruses, such as the novel coronavirus, 2019-nCoV that caused the pneumonia outbreak in Wuhan, China most recently, have posed great threats to global public health. Identification of the causative viral pathogens of respiratory tract viral infections is important to select an appropriate treatment, save people’s lives, stop the epidemics, and avoid unnecessary use of antibiotics. Conventional diagnostic tests, such as the assays for rapid detection of antiviral antibodies or viral antigens, are widely used in many clinical laboratories. With the development of modern technologies, new diagnostic strategies, including multiplex nucleic acid amplification and microarray-based assays, are emerging. This review summarizes currently available and novel emerging diagnostic methods for the detection of common respiratory viruses, such as influenza virus, human respiratory syncytial virus (RSV), coronavirus, human adenovirus (hAdV), and human rhinovirus (hRV). Multiplex assays for simultaneous detection of multiple respiratory viruses are also described. It is anticipated that such data will assist researchers and clinicians to develop appropriate diagnostic strategies for timely and effective detection of respiratory virus infections.

This article is protected by copyright. All rights reserved.

KEYWORDS: Respiratory viral infection; adenovirus; coronavirus; diagnostic methods; influenza virus; respiratory syncytial virus; rhinovirus

PMID: 31944312 DOI: 10.1002/jmv.25674

Keywords: Infectious Diseases; Diagnostic tests; 2019-nCoV.

——

#Reassortment and #adaptive #mutations of an emerging #avian #influenza virus #H7N4 subtype in #China (PLOS One, abstract)

[Source: PLOS One, full page: (LINK). Abstract, edited.]

OPEN ACCESS /  PEER-REVIEWED / RESEARCH ARTICLE

Reassortment and adaptive mutations of an emerging avian influenza virus H7N4 subtype in China

Bingqian Qu , Xue Li , Carol J. Cardona, Zheng Xing

___

Published: January 17, 2020 / DOI: https://doi.org/10.1371/journal.pone.0227597

 

Abstract

Human infections with avian influenza viruses including H5, H7 and H9 hemagglutinin subtypes occur at a low rate. Among human infections with H7 viruses, regional outbreaks with H7N2, H7N3, H7N7 and H7N9 have been documented. Early in 2018, a human infection with a novel H7N4 avian influenza virus was reported in Jiangsu, China. This study is aimed at understanding the probable origin and molecular features of this emerging H7N4 virus. Genomic segments encoding hemagglutinin (HA) and neuraminidase (NA) of H7Nx and HxN4 viruses were compared with this H7N4 strain by alignment and phylogenetic tree analysis. Phylogenetic analysis indicated that the human H7N4 virus probably originated from multiple reassortments of avian H7N7 and H8N4 viruses for its HA and NA, respectively, and likely a regional uncharacterized virus for its internal segments. Our data excluded that circulating avian H9N2 viruses were the origin of the H7N4 internal segments, unlike the human H5N1 and H7N9 viruses that both had H9N2 backbones. This index case provided a unique opportunity to examine viral mutations by directly comparing the human isolate with its closest viral relatives isolated from avian species from the patient’s farm, which may suggest critical mutations required for viral adaptation in humans. Whole-genome scanning was performed and the sequences of the human and related avian H7N4 isolates were compared. Mutations in PB2 (E627K), PB2 (K683T), PB1-F2 (N47S), HA (N283D), HA(K321E), NA(A137V), NA(K296R) and M2 (C19Y) were identified in the human isolate while no mutations were found in PB1, NP, NS1, and NS2 of the human H7N4 compared to the avian H7N4 viruses. Our data in this report provide further evidence for the genesis of this novel H7N4 virus with a multi-reassortment model and show molecular changes that might be responsible for the transmission of this virus from chickens or ducks to and subsequent replication in humans.

___

Citation: Qu B, Li X, Cardona CJ, Xing Z (2020) Reassortment and adaptive mutations of an emerging avian influenza virus H7N4 subtype in China. PLoS ONE 15(1): e0227597. https://doi.org/10.1371/journal.pone.0227597

Editor: Florian Krammer, Icahn School of Medicine at Mount Sinai, UNITED STATES

Received: August 26, 2019; Accepted: December 23, 2019; Published: January 17, 2020

Copyright: © 2020 Qu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: All relevant data are within the manuscript

Funding: ZX; National Natural Science Foundation of China; Grant No. 81571993; www.nsfc.gov.cn/; The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

Keywords: Avian Influenza; H7N4; H7N7; H8N4; Reassortant strain; Human; China.

——-

Quantifying within-host #diversity of #H5N1 #influenza viruses in #humans and #poultry in #Cambodia (PLOS Pathog., abstract)

[Source: PLOS Pathogens, full page: (LINK). Abstract, edited.]

OPEN ACCESS /  PEER-REVIEWED / RESEARCH ARTICLE

Quantifying within-host diversity of H5N1 influenza viruses in humans and poultry in Cambodia

Louise H. Moncla , Trevor Bedford, Philippe Dussart, Srey Viseth Horm, Sareth Rith, Philippe Buchy, Erik A. Karlsson, Lifeng Li, Yongmei Liu, Huachen Zhu, Yi Guan, Thomas C. Friedrich, Paul F. Horwood

___

Published: January 17, 2020 / DOI: https://doi.org/10.1371/journal.ppat.1008191 / This is an uncorrected proof.

 

Abstract

Avian influenza viruses (AIVs) periodically cross species barriers and infect humans. The likelihood that an AIV will evolve mammalian transmissibility depends on acquiring and selecting mutations during spillover, but data from natural infection is limited. We analyze deep sequencing data from infected humans and domestic ducks in Cambodia to examine how H5N1 viruses evolve during spillover. Overall, viral populations in both species are predominated by low-frequency (<10%) variation shaped by purifying selection and genetic drift, and half of the variants detected within-host are never detected on the H5N1 virus phylogeny. However, we do detect a subset of mutations linked to human receptor binding and replication (PB2 E627K, HA A150V, and HA Q238L) that arose in multiple, independent humans. PB2 E627K and HA A150V were also enriched along phylogenetic branches leading to human infections, suggesting that they are likely human-adaptive. Our data show that H5N1 viruses generate putative human-adapting mutations during natural spillover infection, many of which are detected at >5% frequency within-host. However, short infection times, genetic drift, and purifying selection likely restrict their ability to evolve extensively during a single infection. Applying evolutionary methods to sequence data, we reveal a detailed view of H5N1 virus adaptive potential, and develop a foundation for studying host-adaptation in other zoonotic viruses.

 

Author summary

H5N1 avian influenza viruses can cross species barriers and cause severe disease in humans. H5N1 viruses currently cannot replicate and transmit efficiently among humans, but animal infection studies and modeling experiments have suggested that human adaptation may require only a few mutations. However, data from natural spillover infection has been limited, posing a challenge for risk assessment. Here, we analyze a unique dataset of deep sequence data from H5N1 virus-infected humans and domestic ducks in Cambodia. We find that well-known markers of human receptor binding and replication arise in multiple, independent humans. We also find that 3 mutations detected within-host are enriched along phylogenetic branches leading to human infections, suggesting that they are likely human-adapting. However, we also show that within-host evolution in both humans and ducks are shaped heavily by purifying selection and genetic drift, and that a large fraction of within-host variation is never detected on the H5N1 phylogeny. Taken together, our data show that H5N1 viruses do generate human-adapting mutations during natural infection. However, short infection times, purifying selection, and genetic drift may severely limit how much H5N1 viruses can evolve during the course of a single infection.

___

Citation: Moncla LH, Bedford T, Dussart P, Horm SV, Rith S, Buchy P, et al. (2020) Quantifying within-host diversity of H5N1 influenza viruses in humans and poultry in Cambodia. PLoS Pathog 16(1): e1008191. https://doi.org/10.1371/journal.ppat.1008191

Editor: Wendy S. Barclay, Imperial College London, UNITED KINGDOM

Received: July 8, 2019; Accepted: November 4, 2019; Published: January 17, 2020

Copyright: © 2020 Moncla et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: All raw sequence data are available in the SRA under accession number PRJNA547644 (https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA547644). All code used to analyze the data, as well as data files with within-host variant calls and phylogenetic trees are available at https://github.com/blab/h5n1-cambodia.

Funding: The study was funded by the US Agency for International Development (grant No. AID-442-G-14-00005). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: Dr. Philippe Buchy is a former Head of Virology at Institut Pasteur du Cambodge and is currently an employee of GSK Vaccines, Singapore. The other authors declare no conflict of interest.

Keywords: Avian Influenza, H5N1, Human, Poultry, Cambodia.

——-

Detection of a #Reassortant #H9N2 #Avian #Influenza Virus with #Intercontinental Gene Segments in a Resident #Australian Chestnut #Teal (Viruses, abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Viruses. 2020 Jan 13;12(1). pii: E88. doi: 10.3390/v12010088.

Detection of a Reassortant H9N2 Avian Influenza Virus with Intercontinental Gene Segments in a Resident Australian Chestnut Teal.

Bhatta TR1,2, Chamings A1,2, Vibin J1,2, Klaassen M1,3, Alexandersen S1,2,4.

Author information: 1 Geelong Centre for Emerging Infectious Diseases, Geelong, Victoria 3220, Australia. 2 School of Medicine, Deakin University, Geelong, Victoria 3220, Australia. 3 Centre for Integrative Ecology, Deakin University, Victoria 3220, Australia. 4 Barwon Health, University Hospital Geelong, Geelong, Victoria 3220, Australia.

 

Abstract

The present study reports the genetic characterization of a low-pathogenicity H9N2 avian influenza virus, initially from a pool and subsequently from individual faecal samples collected from Chestnut teals (Anas castanea) in southeastern Australia. Phylogenetic analyses of six full gene segments and two partial gene segments obtained from next-generation sequencing showed that this avian influenza virus, A/Chestnut teal/Australia/CT08.18/12952/2018 (H9N2), was a typical, low-pathogenicity, Eurasian aquatic bird lineage H9N2 virus, albeit containing the North American lineage nucleoprotein (NP) gene segment detected previously in Australian wild birds. This is the first report of a H9N2 avian influenza virus in resident wild birds in Australia, and although not in itself a cause of concern, is a clear indication of spillover and likely reassortment of influenza viruses between migratory and resident birds, and an indication that any lineage could potentially be introduced in this way.

KEYWORDS: Chestnut teal; Eurasian lineage; H9N2; avian influenza virus; low pathogenicity; phylogenetic analysis; reassortant

PMID: 31940999 DOI: 10.3390/v12010088

Keywords: Avian Influenza; H9N2; Wild Birds; Reassortant strain; Australia.

——

#EVD68 #outbreak #detection through a syndromic disease #epidemiology #network (J Clin Virol., abstract)

[Source: Journal of Clinical Virology, full page: (LINK). Abstract, edited.]

Journal of Clinical Virology / Available online 16 January 2020, 104262 / In Press, Journal Pre-proof

Enterovirus D68 outbreak detection through a syndromic disease epidemiology network

Authors: Lindsay Meyers a, Jennifer Dien Bard bc, Ben Galvin a, Jeff Nawrocki a, Hubert G.M. Niesters d, Kathleen A. Stellrecht e, Kirsten St. George f, Judy A. Daly gh, Anne J. Blaschke i, Christine Robinson j, Huanyu Wang k, Camille V. Cook a, Ferdaus Hassan l, Sam R. Dominguez j, Kristin Pretty j, Samia Naccache b, Katherine E. Olin a, Benjamin M. Althousem n, Jay D. Jones a, Christine C. Ginocchioao p, Mark A. Poritz q2, Amy Leber k1, Rangaraj Selvarangan l1

{a} BioFire Diagnostics, Salt Lake City, UT, 84103, United States; {b} Department of Pathology and Laboratory Medicine, Children’s Hospital of Los Angeles, Los Angeles, CA 90027, United States; {c} Keck School of Medicine, University of Southern California, Los Angeles, CA 90039, United States; {d} The University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Division of Clinical Virology, Groningen, The Netherlands; {e} Department of Pathology and Laboratory Medicine, Albany Medical Center, Albany, NY 12208, United States; {f} New York State Department of Health, Albany, NY, 12202, United States; {g} Department of Pathology, University of Utah, Salt Lake City, UT 84132, United States; {h} Division of Inpatient Medicine, Primary Children’s Hospital, Salt Lake City, UT 84132, United States; {i} Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT 84132, United States; {j} Department of Pathology and Laboratory Medicine, Children’s Colorado, Aurora, CO 80045, United States; {k} Department of Laboratory Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, United States; {l} Department of Pathology and Laboratory Medicine, Children’s Mercy Hospital, Kansas City, MO 64108, United States; {m} Information School, University of Washington, Seattle, WA, 98105, United States; {n} Department of Biology, New Mexico State University, Las Cruces, NM, 88003, United States; {o} Global Medical Affairs, bioMérieux, Durham, NC 27712, United States; {p}
Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, United States; {q} BioFire Defense, Salt Lake City, UT 84107, United States

Received 3 June 2019, Revised 8 January 2020, Accepted 14 January 2020, Available online 16 January 2020. DOI: https://doi.org/10.1016/j.jcv.2020.104262

 

Highlights

  • An algorithm to predict the presence enterovirus D68 among hinovirus/Enterovirus results obtained from a commercial respiratory disease diagnostic test was developed
  • The algorithm was used in conjunction with test results exported to a cloud-based epidemiology network for use in real-time monitoring and historical outbreak prediction
  • Historical outbreak predictions coincide with known periods of high EV-D68 circulation in 2014 and 2016
  • The algorithm alerted participating clinical laboratories of the potential circulation of EV-D68 in 2018, prompting clinical testing for EV-D68 at one site

Keywords: EV-D68; USA.

——

The Beach at Villerville, Eugene Boudin (1864)

Annotazione 2020-01-16 184111

___

The Beach at Villerville
Eugene Boudin
Date: 1864; France
Style: Realism
Genre: genre painting
Media: oil
Tag: walking, leisure-and-sleep

___

Permissions: Public Domain.

Source: WikiArt, full page: https://www.wikiart.org/en/eugene-boudin/the-beach-at-villerville-1864

 

—–