Co-circulation of Influenza A H5, H7, and H9 Viruses and Co-infected Poultry in Live Bird Markets, Cambodia

Horwood, Paul F.; Horm, Srey Viseth; Suttie, Annika; Thet, Sopheak; Phalla, Y; Rith, Sareth; Sorn, San; Holl, Davun; Tum, Sothyra; Ly, Sowath; Karlsson, Erik A.; Tarantola, Arnaud; Dussart, Philippe

doi:10.3201/eid2402.171360

Cited by 42 publications

(55 citation statements)

References 12 publications

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“…RNA was extracted from swab samples using the QIAmp Viral RNA Mini Kit (Qiagen, Valencia, CA, USA), following manufacturer’s guidelines and eluted in buffer AVE. Extracts were tested for influenza A virus (M-gene)[24] and subtypes H5 (primer sets H5a and H5b), N1, H7, and H9 by using quantitative RT-PCR (qRT-PCR) using assays sourced from the International Reagent Resource (https://www.internationalreagentresource.org/Home.aspx), as previously outlined[25]. Only samples with high viral load (≥10 3 copies/μl of extracted viral RNA in buffer AVE), as assessed by RT-qPCR, were selected for sequence analysis.…”

Section: Methodsmentioning

confidence: 99%

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

Moncla

Bedford

Dussart

et al. 2019

Preprint

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25leading to human infections, suggesting that they are likely human-adapting. However, we also 51 show that within-host evolution in both humans and ducks are shaped heavily by purifying 52 selection and genetic drift, and that a large fraction of within-host variation is never detected on 53 the H5N1 phylogeny. Taken together, our data show that H5N1 viruses do generate human-54 adapting mutations during natural infection. However, short infection times, purifying selection, 55 and genetic drift may severely limit how much H5N1 viruses can evolve during the course of a 56 single infection. 57 58 Introduction 59Influenza virus cross-species transmission poses a continual threat to human health. Since 60 emerging in 1997, H5N1 avian influenza viruses (AIVs) have caused 860 confirmed infections 61 and 454 deaths in humans [1]. H5N1 viruses naturally circulate in aquatic birds, but some 62 lineages have integrated into poultry populations. H5N1 viruses are now endemic in domestic 63 birds in some countries [2][3][4], and concern remains that continued human infection may one day 64 facilitate human adaptation. 65 66The likelihood that an AIV will adapt to replicate and transmit among humans depends on 67 generating and selecting human-adaptive mutations during spillover. Influenza viruses have 68 high mutation rates[5-8], short generation times [9], and large populations, and rapidly generate 69 diversity within-host. Laboratory studies using animal models [10][11][12] show that only 3-5 amino 70 acid substitutions may be required to render H5N1 viruses mammalian-transmissible [10][11][12], 71and that viral variants present at frequencies as low as 5% may be transmitted by respiratory 72 droplets [13]. Subsequent modeling studies suggest that within-host dynamics are conducive to 73 generating human-transmissible viruses, but that these viruses may remain at frequencies too 74 low for transmission [14,15]. Although these studies offer critical insight for H5N1 virus risk 75 4 assessment, it is unclear whether they adequately describe how cross-species transmission 76 proceeds in nature. 77 78 H5N1 virus outbreaks offer rare opportunities to study natural cross-species transmission, but 79 data are limited. One study of H5N1 virus-infected humans in Vietnam identified mutations 80 affecting receptor binding, polymerase activity, and interferon antagonism; however, they 81 remained at low frequencies throughout infection [16]. Recent characterization of H5N1 virus-82 infected humans in Indonesia identified novel mutations within-host that enhance polymerase 83 activity in human cells [17]. Unfortunately, neither of these studies include data from naturally 84 infected poultry, which would provide a critical comparison for assessing whether infected 85 humans exhibit signs of adaptive evolution. A small number of studies have examined within-86 host diversity in experimentally infected poultry [18][19][20], but these may not recapitulate the 87 dynamics of natural infection. 88 89As part of ongoing diagnostic and surv...

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Section: Methodsmentioning

confidence: 99%

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

Moncla

Bedford

Dussart

et al. 2019

Preprint

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“…The H7 subtype AIV has spread worldwide and has been detected in China (Wu et al, ), the United States (Olsen et al, ), Korea (Lee et al, ), Bangladesh (El‐Shesheny et al, ), Australia (Scott et al, ), Cambodia (Horwood et al, ) and Belgium (Van Borm et al, ). The pathogenic H7 subtype AIV changed from low pathogenicity in birds to high pathogenicity in both humans and birds (Dhingra et al, ).…”

Section: Discussionmentioning

confidence: 99%

“…Rapid detection of the H7 subtype AIV in the field, especially in live-bird markets, is crucial to the effective control of this subtype (Biswas et al, 2018;Horwood et al, 2018). H7 subtype AIV is currently diagnosed by RT-PCR (Chaharaein, Omar, Aini, Yusoff, & Hassan, 2009;Xie et al, 2006) and real-time RT-PCR (Jia et al, 2017;Liu et al, 2018;Sidoti et al, 2010).…”

Section: Discussionmentioning

confidence: 99%

Reverse‐transcription recombinase‐aided amplification assay for H7 subtype avian influenza virus

Wang

Huang

Liu

et al. 2019

Transbound Emerg Dis

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H7 subtype avian influenza virus infection is an emerging zoonosis in some Asian countries and an important avian disease worldwide. A rapid and simple test is needed to confirm infection in suspected cases during disease outbreaks. In this study, we developed a reverse‐transcription recombinase‐aided amplification assay for the detection of H7 subtype avian influenza virus. Assays were performed at a single temperature (39°C), and the results were obtained within 20 min. The assay showed no cross‐detection with Newcastle disease virus or infectious bronchitis virus, which are the other main respiratory viruses affecting birds. The analytical sensitivity was 102 RNA copies per reaction at a 95% probability level according to probit regression analysis, with 100% specificity. Compared with published reverse‐transcription quantitative real‐time polymerase chain reaction assays, the κ value of the reverse‐transcription recombinase‐aided amplification assay in 342 avian clinical samples was 0.988 (p < .001). The sensitivity for avian clinical sample detection was 100% (95%CI, 90.40%–100%), and the specificity was 99.96% (95%CI, 97.83%–99.98%). These results indicated that our reverse‐transcription recombinase‐aided amplification assay may be a valuable tool for detecting avian influenza H7 subtype virus.

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“…Identification of H7 is not novel in Cambodia. Prior studies in 2013 and 2015 in live bird markets have identified low pathogenicity AIV (LPAIV) subtype H7 circulating in chickens and ducks ( 6 , 7 ). Phylogenetic analyses indicated that all of the gene segments from both H7N3 isolates from Cambodia showed the highest degree sequence similarity to each other and fell into the Eurasian lineage of H7 viruses circulating in Asia, predominantly during 2012–2015.…”

Section: The Studymentioning

confidence: 99%

“…Although control measures for HPAI in Cambodia include culling of poultry that is infected, suspected to be infected, or in contact with infected/suspected poultry, reporting is minimal, and no compensation mechanism exists. Since 2004, a total of 58 reported AIV outbreaks (mostly HPAI) have occurred in poultry and wild birds (as of April 2018), and 56 human influenza A(H5N1) cases (37 fatalities [case-fatality rate 66%]) have been reported in Cambodia ( 6 ). …”

mentioning

confidence: 99%

Detection of Low Pathogenicity Influenza A(H7N3) Virus during Duck Mortality Event, Cambodia, 2017

Suttie¹,

Yann²,

Phalla³

et al. 2018

Emerg. Infect. Dis.

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Co-circulation of Influenza A H5, H7, and H9 Viruses and Co-infected Poultry in Live Bird Markets, Cambodia

Cited by 42 publications

References 12 publications

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

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

Reverse‐transcription recombinase‐aided amplification assay for H7 subtype avian influenza virus

Detection of Low Pathogenicity Influenza A(H7N3) Virus during Duck Mortality Event, Cambodia, 2017

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