#Biodiversity and emerging infectious #threats: the microbial dark matter of Southwest #China

 

Abstract

Southwest China is a global biodiversity hotspot, and its complex and diverse ecosystems harbor vast amounts of “microbial dark matter.” This paper systematically examines the distribution characteristics of microbial dark matter in hosts such as arthropods, mammals, and birds, as well as in environments including soil, hot springs, and high-altitude lakes, with a particular focus on the cross-species transmissibility and pathogenic potential of emerging pathogens. Research indicates that new microbial species in the Southwest exhibit significant geographic concentration and host specificity: Yunnan Province is a core hotspot, while the Tibet Autonomous Region contributes a wealth of microbial resources due to its extreme environments, with arthropods and mammals accounting for the highest proportion of novel species. Regarding public health risks, eight novel pathogens with evidence of human infection have been identified, spanning the three major groups of viruses, bacteria, and parasites. The cross-species transmission potential of some pathogens (such as DPRV rhabdovirus, PPV arenaviridae, Luxi hantavirus, Banna virus and a novel Babesia species) has been confirmed through serological surveys or molecular testing. Deepening the exploration of microbial dark matter and risk early warning in this region will provide critical scientific support for public health safety monitoring.

Source: 

Link: https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2026.1846062/full

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Avian #Influenza #Report - May 31 – June 6 '26 (Wk 23) (#HK CHP, June 9 '26): 2 new human #H5N1 virus cases in #Bangladesh, #India; 1 new case of H9N2 virus in #China

(...)

    -- Bangladesh

        ° Avian influenza A(H5N1) 

            ° Sylhet Division: 

                - The case involved a child with symptom onset on March 27, 2026.  

                - The patient was admitted to a hospital on March 28 for treatment of measles with bronchopneumonia, and was discharged on March 30. 

                - Epidemiological investigations revealed the case had exposure to household poultry.   

                - No additional cases were reported among the identified contacts.  

    -- India

        ° Avian influenza A(H5N1)

            - The case involved a child who developed symptoms and was admitted to a hospital on March 19, 2026. 

            - The patient was discharged on March 23.  

            - Epidemiological investigations revealed the case likely had indirect exposure to poultry. 

            - No additional cases were reported among the identified contacts. 

        -- China

            ° Avian influenza A(H9N2): 

                ° Yunnan Province: 

                    - A 4-year-old boy with onset on May 17, 2026. 

(...)

Link: https://www.chp.gov.hk/files/pdf/2026_avian_influenza_report_vol22_wk23.pdf

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Avian #Influenza #Report. May 17 - 23 '26 (Wk 21) (HK CHP, May 26, 2026): one new #human case of #H9N2 virus infection in #China

 

{Excerpt}

(...)

    ° Avian influenza A(H9N2): 

        -- Yunnan Province: 

            * A three-year-old boy with onset on April 28, 2026. 

(...)

Source: 

Link: https://www.chp.gov.hk/files/pdf/2026_avian_influenza_report_vol22_wk21.pdf

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Avian #Influenza #Report - Reporting period: April 12 - 18 '26 (Wk 16) (HK CHP, April 21 '26): 3 new #human cases of #H9N2 virus in #China

 

{Excerpt}

(...)

Avian influenza A(H9N2): 

-- Guangdong Province: 

1) A five-year-old boy with onset on February 23, 2026.

-- Jiangxi Province: 

2) A two-year-old boy with onset on March 20, 2026. 

-- Yunnan Province:

3) A two-year-old girl with onset on March 3, 2026. 

(...)

Source: 

Link: https://www.chp.gov.hk/files/pdf/2026_avian_influenza_report_vol22_wk16.pdf

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Infectome analysis of #bat #kidneys from #Yunnan province, #China, reveals novel #henipaviruses related to #Hendra and #Nipah viruses and prevalent bacterial and eukaryotic microbes

Abstract

Bats are natural reservoirs for a wide range of microorganisms, including many notable zoonotic pathogens. However, the composition of the infectome (i.e., the collection of viral, bacterial and eukaryotic microorganisms) within bat kidneys remains poorly understood. To address this gap, we performed meta-transcriptomic sequencing on kidney tissues from 142 bats, spanning ten species sampled at five locations in Yunnan province, China. This analysis identified 22 viral species, including 20 novel viruses, two of which represented newly discovered henipaviruses closely related to the highly pathogenic Hendra and Nipah viruses. These henipaviruses were found in the kidneys of bats inhabiting an orchard near villages, raising concerns about potential fruit contamination via bat urine and transmission risks to livestock or humans. Additionally, we identified a novel protozoan parasite, tentatively named Klossiella yunnanensis, along with two highly abundant bacterial species, one of which is a newly discovered species—Flavobacterium yunnanensis. These findings broaden our understanding of the bat kidney infectome, underscore critical zoonotic threats, and highlight the need for comprehensive, full-spectrum microbial analyses of previously understudied organs to better assess spillover risks from bat populations.

Author summary

Although extensive investigations have been conducted on the bat virome, most studies have focused on fecal samples, leaving other tissues, such as the kidney, largely unexplored. However, the kidney can harbor important zoonotic pathogens, including the highly pathogenic Hendra and Nipah viruses, and genomic evidence of henipaviruses in bats from China has remained undocumented. In this study, we report the first detection of two novel henipavirus genomes from bat kidneys in China, one of which is the closest known relative of pathogenic henipaviruses identified to date. Beyond virome analysis, our study also examined highly prevalent bacteria and eukaryotic microbes, identifying those potentially relevant to bat infections. Overall, these findings provide valuable insights into the infectome of the bat kidney, highlighting the need for broader microbial surveillance beyond the gastrointestinal tract.

Source: PLoS Pathogens, https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1013235

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Sustained cross-species #transmission of #gammacoronavirus in wild #birds reveled by viral characterization in #China

Abstract

Gammacoronavirus (γ-CoV) primarily infects poultry, wild birds, and marine mammals. The widespread distribution and circulation of γ-CoV in the ecological environment may lead to sustained transmission and economic loss. To better understand the diversity of γ-CoV in wild birds, we collect 482 wild-bird fecal samples from Yunnan, encompassing fourteen bird species. We detected twelve γ-CoV positive samples in five bird species, with the characterization of five complete genomes - HNU5-1, HNU5-2, HNU5-3, HNU6-1, and HNU6-2-indicating that these genomes represent two viral species. The HNU5 strains were derived from Black-headed gull (Chroicocephalus ridibundus), while the HNU6 strains were came from Mallard (Anas platyrhynchos), and both of those were recombinant. The HNU5 strain exhibited the highest sequence identity (95.45%) with a γ-CoV strain isolated from Numenius phaeopus (GenBank accession: PP845452). Similarly, the HNU6 strain showed 95.18% nucleotide identity with a γ-CoV strain (GenBank accession: PP845437) derived from Anas platyrhynchos. Taxonomic analysis confirmed that HNU6s belong to the Gammacoronavirus anatis species, while HNU5s attributed to a new species. Cross-species analysis revealed active host-switching events among γ-CoVs, indicating potential transmission of γ-CoVs from marine mammals to wild bird, from wild bird to poultry, and inter-wild bird and inter-poultry transmission. In summary, we report five new γ-CoV strains in wild birds and outline the cross-species transmission of γ-CoVs. Our findings link γ-CoV hosts across different natural environments and provide new insights for exploring γ-CoVs.

Source: BioRxIV, https://www.biorxiv.org/content/10.1101/2025.04.17.648926v1

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