Wednesday, December 14, 2016

Korea H5N6: New Genetic Analysis & Investigating Its Rapid Spread


Three Korean H5N6 stories of note this morning. 

First, from MAFRA, a second (partial) genetic analysis of the H5N6 virus, which compares 106 recent samples and finds they fall into 5 different genotypes, with type C4 making up just over half of all isolates tested. 
You may recall that 10 days ago, in Cell Host Microbe: Genesis, Evolution and Prevalence of HPAI H5N6 In China, we looked at a report that had identified 34 different genotypes of the virus in China. 

Clade viruses (which include both H5N8 and H5N6) have demonstrated an enhanced ability to reassort with other - mostly LPAI - viruses, and continue to evolve into new genotypes and occasionally churn out viable novel subtypes.

Translation software for Korean produces somewhat cryptic results, but the gist (bolding mine) is fairly easy to follow:

H5N6 type AI virus gene analysis 2nd intermediate result

Entry date 2016-12-14 11:00:00

The H5N6 virus has been identified as a genetically susceptible strain of the H5N6 virus in Korea, and the H5N6 virus has been isolated from the Korean population. Belonged to
○ This is the same result without adding any of the five genotypes published by the Epidemiological Investigation Committee on November 29 (C1-C5 type)

- C1 type 2 cases, C2 type 20 cases, C3 type 9 cases, C4 type 59 cases, C5 type 16 cases

* Based on the three PA genes (91.49 to 94.14% among the groups) and the two NS genes (96.72 to 97.33% among the groups), theoretically there are five possible genotypes

The H5N6 virus was similar to the H5N6 virus in China,

- Estimated influx of wild birds infected with H5N6 in Guangdong province, China in spring of 2016, migrated to breeding sites in Siberia and northeastern China, where cross-contaminated wild birds arrived in Korea
Of the H5N6 viruses in Korea, C1 and C2 were 98.42 ~ 99.93% homologous with the Chinese H5N6 virus

- The C3 to C5 type showed some differences (91.82 to 92.79% homology) from the PA gene to the Chinese H5N6 virus, and the PA gene was presumed to be derived from a low-pathogenic AI virus in wild birds

According to the data released recently in China, there are at least 34 H5N6 viruses that are prevalent in China, among which G1.1.9 is most similar to the H5N6 virus in Korea

* A paper published in China (Cell Host Microbe, December 16, 2004)

○ Type G1.1.9 is the genotype of the virus isolated in January 2016 in the duck of the Guangdong Provincial Livestock Market
□ The full-length gene analysis data analyzed so far (8 cases) were published on December 13 in the influenza gene database (GISAID, global initiative on sharing all influenza data, accession no. EPI866074-EPI866137)

□ In the future, we plan to utilize genetic analysis information and field dynamics analysis data for epidemiological investigation

A second MAFRA report looks at the epidemiology of the virus, its introduction into the country by wild birds, and the likely ways it has entered poultry farms.

The epidemiologic investigation of this highly pathogenic AI (H5N6) occurred mid-term

registration date 2016-12-13 11:30:00

The quarantine headquarters explained the intermediate situation of epidemiological investigation of the incidence of highly pathogenic AI (H5N6).
Regarding the cause of domestic inflow, it was judged that migratory birds migrated to the domestic area in the northern part of China, breeding area * of winter birds,
* New breeding grounds for winter: Jilin province in China, Hayrong province, eastern Mongolia, Vladivostok in Russia, etc.
* The genetic analysis of H5N6 (HPAI) virus in Korea is similar to that of H5N6, which is prevalent in Guangdong Province and Hong Kong, China. Domestic AI is classified into 5 types according to internal genetic recombination
As for the causes of farms, infected migratory birds, along the migratory birds route, mainly polluted the western coasts,
  • * A total of 24 wild bird antigens were detected in 8 cities and 12 cities (as of 12.11)
  • * Sejong 1 (1), Gyeonggi 1 (Icheon 1), Gangwon 2 (Wonju 1, Cheolwon 1), Chungbuk 2 (Cheongpyeong 2), Chungnam 11 (Bye 1, Asan 6, Cheonan 4) ), Jeonnam 5 (Gangjin 3, Haenam 2), Gyeongnam 1 (Changyeong 1)
It was estimated that the virus was introduced into farms through people, vehicles (small apparatus), small wild birds (resident birds, etc.) in contaminated areas.
- In a polluted environment around the farm, the visitor or farm visitor visits the farm without proper disinfection procedures,
- Feed Churns Contaminants may enter the process of bringing in products such as drugs or carrying out eggs,
* There are 102 (73.9%) farms where reservoir rivers are located near the outbreak farms (138 farms out of H5N6 confirmed farms, as of December 12)
- It is presumed that the wild birds such as the resident birds from the farm invaded into the farm or housing,
* The number of farms where wild birds are observed is 113 cases (81.9%), which is the largest number (138 farms out of H5N6 confirmed farms, as of 12.12)
According to the main items of each type,
To date, there have been 42 positive farms (15 occurrences, precautionary killings 27) in the laying hens farm, and the total incidence tends to increase when farms in dense areas occur
* This year, there are a lot of scattered areas: Pocheon (12 cases), Asan (6 cases), Icheon (5 cases), etc.
* 64% (27/42 cases) of laying hens were found within 3km, especially 75% (9/12 cases) in Pocheon within 3km
- In the farm situation, the frequency of accessing the facility in the farm is higher than that of other species,
* Egg transport (5 tons) 4, feed (32 tons) 2, etc.
In the case of laying hens (200 thousand raising), entrance into the vehicle twice a day (egg transport (5 tons) 1, feed (15 tons) 1)
* For broiler farms, once every three days, vehicle access (feed vehicle)
Egg transport vehicles entered the farm directly and carried eggs (34 out of 38 cases, 42 out of 42 cases, 89.4%)
Eggs were shipped from the entrance of the egg chamber (36 out of 38, 94%)
Egg transporters did not use any apparel during the egg laying process (28 out of 38, 73.6%)
Farm workers managed egg laying and egg laying (28 out of 38, 73.6%)
There are many cases where the system is located in the farm (25 out of 38 cases, 65.7%)
* In the area where weaves and rice husks are mixed, we have a facility where the stray vehicles frequently enter and exit, and wild birds such as resident birds are easily attracted to the facility.
There are 16 positive cases (10 cases, prevention of sickness dismissal 6) in Jongli Duck Farm. However, this year, the most frequent vehicle movement factor (35%) is not confirmed in the past, Naju (3 cases) And Jincheon (4 cases).
- In the case of farms, plastic is used in farms (6 out of the 12 cases, 50 out of 16 surveyed)
* Possibility of cross contamination due to mixed use in hatcheries when plastics are recycled
- Workers were asked to carry out tasks such as duck management, confinement, and bombardment, and did not take disinfection measures (12 out of 12, 100%).
There have been 59 positive cases (13 cases, 46 cases of preventive slaughter) and 6 cases have been found in duck farms with densely populated voices and Jincheon.
* 92% of the voice (26/28 cases) and 93% (14/15 cases) of Jincheon are within 3km due to the prophesied killings
- In view of the farm situation, most farms are greenhouses,
* 41 out of 59 duck farms (69.5%) are housed in plastic houses
- Most farm houses have disinfection facilities (51 cases, 86.4%), but farm boundaries (fences) are unclear (40 cases, 67.8%), )
- In particular, 26 out of 59 cultivars (44%) were found to have been farmed more than 2 times.
So far, the occurrence pattern has occurred at the same time, and a lot of positive farms are appearing in the contaminated area of ​​the area in some areas (Voice, Jincheon, Pocheon, etc.)
Therefore, the quarantine headquarters is carrying out an epidemiological survey focusing on prevention of spreading due to mechanical propagation and prevention of farm shutdown.

And lastly, an English language report from the Korean Times indicates a farm in Sejong may have sold infected poultry and eggs prior to reporting suspected AI to authorities, which may have contributed to the rapid spread of the virus.

By Jung Min-ho
The government is looking into a chicken farm in Sejong over allegations that it sold chickens and eggs possibly infected with avian influenza to other parts of Korea.

According to the Ministry of Agriculture, Food and Rural Affairs, Wednesday, the owner of the farm sent at least 100,000 chickens to Paju in Gyeonggi Province and Yeosu in South Jeolla Province two days before reporting suspected bird flu cases to health authorities, Nov. 26.

About 700,000 chickens were slaughtered later on the farm after many of them were confirmed to have been infected with the H5N6 avian influenza virus.

The ministry has confirmed that some 2 million eggs were also delivered to markets across the country just before the report.

It suspects the delivery of the chickens and eggs may be part of the reason for the rapid spread of the virus across the country. 

(Continue .  .  .)

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