Human Infection with Avian Influenza A(H9N2) Virus, Cambodia, February 2021

Um, Samnang; Siegers, Jurre Y.; Sar, Borann; Chin, Savuth; Patel, Sarika; Bunnary, Seng; Hak, Makara; Sor, Sothy; Sokhen, Oum; Heng, Seng; Chau, Damon; Tum, Sothyra; Khalakdina, Asheena; Mott, Joshua A.; Olsen, Sonja J.; Claes, Filip; Ly, Sovann; Karlsson, Erik A.

doi:10.3201/eid2710.211039

Cited by 19 publications

(12 citation statements)

References 8 publications

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“…The IAV subtypes are potential causal agents of pandemic in the human population in the future. However, (Gao et al 2013 ; Koopmans et al 2004 ; Marinova-Petkova et al 2017 ; Meineke et al 2019 ; Skowronski et al 2006 ; Song and Qin 2020 ; Terebuh et al 2018 ; Tong et al 2018 ; Tweed et al 2004 ; Um et al 2021 ; Westenius et al 2018 ) current management of human influenza A is limited to vaccines and antiviral treatments targeting viral proteins (Uyeki et al 2019 ). Due to their rapid mutation capacity, IAVs have a strong evasion mechanism to the host immune system (Chang et al 2020 ; Huang et al 2021 ; Li et al 2012 ; Peacock et al 2017 ; Peng et al 2014 ; Sitaras et al 2014 ), thus reducing the effectiveness of antivirals targeting viral proteins.…”

Section: Introductionmentioning

confidence: 99%

Human genes with codon usage bias similar to that of the nonstructural protein 1 gene of influenza A viruses are conjointly involved in the infectious pathogenesis of influenza A viruses

2022

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Molecular mechanisms of the non-structural protein 1 (NS1) in influenza A-induced pathological changes remain ambiguous. This study explored the pathogenesis of human infection by influenza A viruses (IAVs) through identifying human genes with codon usage bias (CUB) similar to NS1 gene of these viruses based on the relative synonymous codon usage (RSCU). CUB of the IAV subtypes H1N1, H3N2, H3N8, H5N1, H5N2, H5N8, H7N9 and H9N2 was analyzed and the correlation of RSCU values of NS1 sequences with those of the human genes was calculated. The CUB of NS1 was uneven and codons ending with A/U were preferred. The ENC-GC3 and neutrality plots suggested natural selection as the main determinant for CUB. The RCDI, CAI and SiD values showed that the viruses had a high degree of adaptability to human. A total of 2155 human genes showed significant RSCU-based correlation (p < 0.05 and r > 0.5) with NS1 coding sequences and was considered as human genes with CUB similar to NS1 gene of IAV subtypes. Differences and similarities in the subtype-specific human protein–protein interaction (PPI) networks and their functions were recorded among IAVs subtypes, indicating that NS1 of each IAV subtype has a specific pathogenic mechanism. Processes and pathways involved in influenza, transcription, immune response and cell cycle were enriched in human gene sets retrieved based on the CUB of NS1 gene of IAV subtypes. The present work may advance our understanding on the mechanism of NS1 in human infections of IAV subtypes and shed light on the therapeutic options. Supplementary Information The online version contains supplementary material available at 10.1007/s10709-022-00155-9.

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Section: Introductionmentioning

confidence: 99%

Human genes with codon usage bias similar to that of the nonstructural protein 1 gene of influenza A viruses are conjointly involved in the infectious pathogenesis of influenza A viruses

2022

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“…Human infections by A(H9N2) viruses have been sporadically reported mainly from both G1-like and Y280-like lineages [ 11 ], with most infections leading to mild clinical signs in children [ 13 ]. In addition to directly causing new infections in humans [ 14 , 15 ], A(H9N2) viruses have contributed to the internal genes of multiple avian influenza strains that have caused lethal human infections in China [ 16 ]. The internal genes of the G1-like lineage A(H9N2) viruses are genetically related to those of the 1997 A(H5N1) viruses [ 17 ].…”

Section: Introductionmentioning

confidence: 99%

Limited onward transmission potential of reassortment genotypes from chickens co-infected with H9N2 and H7N9 avian influenza viruses

Sia

Choy

et al. 2021

Emerging Microbes & Infections

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The segmented genome of influenza A virus has conferred significant evolutionary advantages to this virus through genetic reassortment, a mechanism that facilitates the rapid expansion of viral genetic diversity upon influenza co-infections. Therefore, co-infection of genetically diverse avian influenza viruses in poultry may pose a significant public health risk in generating novel reassortants with increased zoonotic potential. This study investigated the reassortment patterns of a Pearl River Delta-lineage avian influenza A(H7N9) virus and four genetically divergent avian influenza A(H9N2) viruses upon co-infection in embryonated chicken eggs and chickens. To characterize “within-host” and “between-host” genetic diversity, we further monitored the viral genotypes that were subsequently transmitted to contact chickens in serial transmission experiments. We observed that co-infection with A(H7N9) and A(H9N2) viruses may lead to the emergence of novel reassortant viruses in ovo and in chickens, albeit with different reassortment patterns. Novel reassortants detected in donor chickens co-infected with different combinations of the same A(H7N9) virus and different A(H9N2) viruses showed distinct onward transmission potential to contact chickens. Sequential transmission of novel reassortant viruses was only observed in one out of four co-infection combinations. Our results demonstrated different patterns by which influenza viruses may acquire genetic diversity through co-infection in ovo , in vivo , and under sequential transmission conditions.

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“…Most commercial tests are not specifically designed to identify/distinguish AIV or novel IAV. However, detection of zoonotic AIV infection is paramount, especially in endemic countries such as Cambodia [29], and for pandemic prevention and preparedness globally. GX package insert does assert the test adequately detects AIV [21]; however, PC and TP have no previous data available.…”

Section: Discussionmentioning

confidence: 99%

One Assay to Test Them All: Comparing Multiplex Assays for Expansion of Respiratory Virus Surveillance

Boukli

Flammand

Chea

et al. 2023

Preprint

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Background: Molecular multiplex assays (MPAs) for simultaneous detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza and respiratory syncytial virus (RSV) in a single RT-PCR reaction reduce time and increase efficiency to identify multiple pathogens with overlapping clinical presentation but different treatments or public health implications. Methods: Clinical performance of XpertXpress SARS-CoV-2/Flu/RSV (Cepheid, GX), TaqPathTM COVID-19, FluA/B, RSV Combo kit (Thermo Fisher Scientific, TP), and PowerChekTM SARS-CoV-2/Influenza A&B/RSV Multiplex RT-PCR kit II (KogeneBiotech, PC) was compared to individual Standards of Care (SoC). Thirteen isolates of SARS-CoV-2, human seasonal influenza, and avian influenza served to assess limit of detection (LoD). Then, positive and negative residual nasopharyngeal specimens, collected under public health surveillance and pandemic response served for evaluation. Subsequently, comparison of effectiveness was assessed. Results: The three MPAs confidently detect all lineages of SARS-CoV-2 and influenza viruses. MPA-LoDs vary from 1-2 Log10 differences from SoC depending on assay and strain. Clinical evaluation resulted in overall agreement between 97% and 100%, demonstrating a high accuracy to detect all targets. Existing differences in costs, testing burden and implementation constraints influence the choice in primary or community settings. Conclusion: TP, PC and GX, reliably detect SARS-CoV-2, influenza and RSV simultaneously, with reduced time-to-results and simplified workflows. MPAs have the potential to enhancediagnostics, surveillance system, and epidemic response to drive policy on prevention and control of viral respiratory infections.

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Human Infection with Avian Influenza A(H9N2) Virus, Cambodia, February 2021

Cited by 19 publications

References 8 publications

Human genes with codon usage bias similar to that of the nonstructural protein 1 gene of influenza A viruses are conjointly involved in the infectious pathogenesis of influenza A viruses

Human genes with codon usage bias similar to that of the nonstructural protein 1 gene of influenza A viruses are conjointly involved in the infectious pathogenesis of influenza A viruses

Limited onward transmission potential of reassortment genotypes from chickens co-infected with H9N2 and H7N9 avian influenza viruses

One Assay to Test Them All: Comparing Multiplex Assays for Expansion of Respiratory Virus Surveillance

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