Emer. Microb. & Inf.: Avian Flu Co-Infection in Poultry - Cambodia, 2017–2018

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Over the past 5 weeks two previously unreported avian flu subtypes -  HPAI H5N6 and LPAI H7N4 - have been detected and reported from Cambodia.

OIE: 1st occurrence of HPAI H5N6 in Cambodia

OIE: Multiple Outbreaks Of LPAI H7N4 In Cambodian Poultry

While surveillance and reporting from Cambodia is often - to put it kindly, suboptimal - in 2017 and 2018 multiple outbreaks of HPAI H5N1 were reported (see OIE Final Report) in poultry.

Cambodia hasn't reported a human avian flu case since 2014, but six years ago they saw a flurry of HPAI H5N1 human infections (see Cambodia’s H5N1 Surge & the `M’ Word).

In 2016, we looked at a seroprevalence study (see Sci Rpts: Intense Circulation Of A/H5N1 In Cambodian LBMs & Evidence Of Subclinical Human Infection) conducted during the height of the H5N1 human outbreaks in 2013 at four live bird markets in Cambodia.

Researchers not only found an incredibly high incidence of H5N1 infected poultry (35%), they found a plethora of other LPAI subtypes (HA1, HA2, HA3, HA4, HA6, HA7, HA9, HA10 and HA11) as well.

Seroprevalence studies also found evidence of sub-clinical H5N1 and H9N2 infection in LMB workers, and additional seroconversions were documented during the course of the 11 month study. 

The obvious concern with multiple co-circulating subtypes of avian flu is the potential for reassortment, and the generation of new, potentially dangerous, hybrid viruses.

While the avian flu world remained relatively stable from 1996 to 2013 - with HPAI H5N1 being our primary concern - over the past 6 years we've seen a spate of new reassortant viruses (H7N9, H5N6, H6N8, H10N8, H7N4, etc.) emerge - mostly from China or Southeast Asia.

All of which brings us to a research letter, published last week in Emerging Microbes & Infections, which describes recent AI surveillance results, and quantifies the level and types of co-infections, found in Cambodian poultry.

I've only included some excerpts from a much longer, more detailed letter. So follow the link to read it in its entirety. 

Avian influenza virus detection, temporality and co-infection in poultry in Cambodian border provinces, 2017–2018

Erik A. Karlsson , Srey Viseth Horm, Songha Tok, Sothyra Tum, Wantanee Kalpravidh, Filip Claes, show all

Pages 637-639 | Received 03 Feb 2019, Accepted 01 Apr 2019, Published online: 19 Apr 2019

Highly pathogenic avian influenza virus (AIV) has been endemic in Cambodia since 2004, and is a major agricultural and public health concern. Cambodia is a tropical, resource poor, lower-middle income country in Southeast Asia with a large socio-economic dependence on agriculture.

In 2015, 87% of Cambodian households with agricultural holdings raised poultry mainly on small, backyard farms with minimal biosafety and/or biosecurity. In conjunction with the National Animal Health and Production Institute (NaHPRI), Institut Pasteur du Cambodge (IPC) has maintained active longitudinal surveillance at key live bird markets (LBMs) in the heavily populated, southern part of the country.

Cambodian LBMs have high levels of AIV circulation, with 30–50% of ducks and 20–40% of chickens testing positive. Intense circulation of A/H5N1 and other avian influenza viruses in Cambodian live-bird markets with serological evidence of sub-clinical human infections.

Concerningly, a multitude of high and low pathogenic AIVs circulate concurrently. Previous studies suggest peak AIV circulation corresponds to the dry season (November to May) especially around Lunar New Year (LNY) celebrations when poultry consumption is highest.

        (SNIP)

Overall, 23.3% of the poultry samples screened were positive for AIV by RT-qPCR with 20.0% and 32.6% positivity in chickens and ducks, respectively. Percentages were similar for individual provinces (Supplemental Table 1). Longitudinally, total AIV detection fluctuated between 4.0% and 48.3%, with highest levels the week before or the week of festivals with increased poultry consumption.

Highest detection was associated with LNY followed closely by KNY (Figure 1(A)). Similar patterns were observed in individual provinces (Figure 1(B–D)). By subtype, 25.2%, 7.4%, 52.3%, 18.1% of AIV positive poultry samples were subtyped as A/H5, A/H7, A/H9, and “unknown,” respectively (Supplemental Table 1). 

        (SNIP)

Co-infections comprised 3.2% of all AIV positive samples (Figure 1(I)). The majority (86.7%) of co-infections were classified as A/H5 + A/H9; however, co-infections between A/H5 + A/H7 and A/H7 + A/H9 were also detected in 6.7% and 13.3% of total co-infections, respectively.

Prevalence of co-infection was similar between chickens (3.2%) and ducks (3.3%); however, co-infections in chickens were exclusively the A/H5 + A/H9 combination whereas ducks had a higher diversity with 50%, 16.7% and 33.3% of co-infections identified as A/H5 + A/H9, A/H5 + A/H7, and A/H7 + A/H9, respectively (Supplemental Figure 4(A,E)).

Co-infections were detected in both chickens (2.8%) and ducks (13.6%) in Kandal, but only in chickens (4.8%) in BM and only in ducks (2.7%) in Takeo (Supplemental Figure 4(B–D,F–H)). The greatest prevalence of co-infections were detected at week 11 of 2018 at 5.7% of total AIV positive samples (Supplemental Figure 4(I)).

As observed previously, A/H5 isolates that could be subtyped were also positive for neuraminidase (NA) subtype N1 by RT-qPCR. No novel H5Nx viruses were detected. A/H9 isolates were subtyped with N2 and A/H7 samples were identified with the N7 and N4 NA subtype by conventional PCR. All A/H7 samples are of the Eurasian lineage, and, to date, AIV similar to the A/Anhui/1/2013-lineage have not been detected in Cambodia. While some samples could not be typed due to low viral load, no positive samples were subtyped for N3, N6, N8 or N9 by RT-qPCR or conventional methods.

Overall, AIV continues to circulate within Cambodia at high levels as previously described, correlating to festival periods when poultry production and consumption is increased

However, a human infection has not been detected since 2014. Border regions display variable AIV prevalence and diversity, possibly due to poultry movement across borders. While A/H7 was detected previously in Cambodia, subtype A/H7N4 presents concern due to the human case in nearby China at a similar time period.

In addition, detection of co-infections in 3.2% of AIV positive poultry, especially with A/H9, raises concerns about reassortment and emergence of novel viruses with epizootic or pandemic potential.

Isolation, Whole Genome Sequencing, and unknown subtype determination is on-going to further characterize these viruses on a molecular and phylogenetic level. Continued, active, vigilant surveillance is vital and interventions to decrease the prevalence of AIVs in LBMs should be considered, especially during festival periods.

        (Continue . . . )

   
Note: The author's concerns about A/H7N4 in Cambodia were confirmed a month ago (see OIE announcement). 

Not unexpectedly, over 90% of the co-infections reported involved the highly promiscuous H9N2 virus, which - while it has some pandemic potential on its own (see CDC IRAT Score) - is more infamous for lending its internal genes to many of the HPAI viruses of greatest concern today (see The Lancet's Poultry carrying H9N2 act as incubators for novel human avian influenza viruses).

While reassortments can occur anytime and anywhere - in any host (avian, swine, human, etc.) able to be co-infected with influenza A viruses - we normally look to China as being the most likely region to produce new HPAI viruses (see Viral Reassortants: Rocking The Cradle Of Influenza). 

That changed - at least temporarily - 18 months ago following their highly successful H5+H7 Nationwide poultry vaccination campaign, which has greatly suppressed avian flu activity across China for more than a year. 

Which makes increased surveillance in other locations - particularly in Southeast Asia - a high priority.