The difference of detection rate of avian influenza virus in the wild bird surveillance using various methods

Abstract

Korea is located within the East Asian-Australian flyway of wild migratory birds during the fall and winter seasons. Consequently, the likelihood of introduction of numerous subtypes and pathotypes of the Avian influenza (AI) virus to Korea has been thought to be very high. In the current study, we surveyed wild bird feces for the presence of AI virus that had been introduced to Korea between September 2017 and February 2018. To identify and characterize the AI virus, we employed commonly used methods, namely, virus isolation (VI) via egg inoculation, real-time reverse transcription-polymerase chain reaction (rRT-PCR), conventional RT-PCR (cRT-PCR) and a newly developed next generation sequencing (NGS) approach. In this study, 124 out of 11,145 fresh samples of wild migratory birds tested were rRT-PCR positive; only 52.0% of VI positive samples were determined as positive by rRT-PCR from fecal supernatant. Fifty AI virus specimens were isolated from fresh fecal samples and typed. The cRT-PCR subtyping results mostly coincided with the NGS results, although NGS detected the presence of 11 HA genes and four NA genes that were not detected by cRT-PCR. NGS analysis confirmed that 12% of the identified viruses were mixed-subtypes which were not detected by cRT-PCR. Prevention of the occurrence of AI virus requires a workflow for rapid and accurate virus detection and verification. However, conventional methods of detection have some limitations. Therefore, different methods should be combined for optimal surveillance, and further studies are needed in aspect of the introduction and application of new methods such as NGS.

Characterization of Avian Influenza Virus H10–H12 Subtypes Isolated from Wild Birds in Shanghai, China from 2016 to 2019

“…The positive samples were transcribed into cDNA using the Uni12 primer (5ʹ-AGC AAA AGC AGG-3ʹ) and PrimeScript™ II 1st Strand cDNA synthesis kit (Takara, Japan). AIV subtypes were determined using primers specific to HA and NA genes [ 19 , 22 ], and the eight segments of the H10–H12 AIV isolates were amplified using universal primers [ 23 ]. The PCR reactions consisted of 1 μL of cDNA, 1 μL each of forward and reverse primers, 12.5 μL of Taq HS Perfect Mix (Takara, Shiga, Japan) and 10.5 μL of RNAse-free water, with a final volume of 25 μL.…”

Genetic Characteristics of Avian Influenza Virus Isolated from Wild Birds in South Korea, 2019–2020

“…The East Asian-Australian flyway, which supports the greatest populations and diversity of migratory birds [9], includes territories of 22 countries. South Korea is located within this flyway [10]. There is a high possibility that AIVs in domestic chickens were introduced to South Korea through wild birds.…”

Prevalence, Seroprevalence and Risk Factors of Avian Influenza in Wild Bird Populations in Korea: A Systematic Review and Meta-Analysis

“…Studies that reported both prevalence and seroprevalence had a risk of bias, assessed by sorting each result. Prevalence studies that used samples from the entire nation [ 8 , 17 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 ] or major migratory bird habitats [ 2 , 57 , 58 , 59 , 60 , 61 , 62 , 63 ] determined that the sampling frame was properly chosen, as samples were taken from within the pertinent regions to calculate the prevalence therein. The sampling frame made for the studies whose primary goal was to identify the characteristics of isolated AIVs [ 64 , 65 , 66 , 67 ] was judged to be at a high risk of bias because the isolation rate reported in the studies was constrained to a particular region.…”

“…Seven primary studies that evaluated the prevalence of AIVs were judged to have a low bias in the sampling method, owing to proper capture methods from randomized wild birds [ 2 , 41 , 42 , 43 , 48 , 50 , 57 ]. All studies, except for two [ 59 , 66 ] that did not describe the isolation method in detail, recorded the condition of the samples by examining them with the proper techniques, such as RT-PCR [ 2 , 8 , 17 , 41 , 42 , 43 , 44 , 48 , 49 , 50 , 51 , 52 , 54 , 55 , 56 , 58 , 60 , 61 , 62 , 65 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 ], rRT-PCR [ 53 , 63 , 64 , 75 , 76 ], or HA tests [ 41 , 42 , 46 , 47 , 57 , 77 ]. All investigations, except for 12 studies [ 8 , 46 ,…”