SARS-CoV-2, the causative agent of COVID-19, emerged in December 2019. Its origins remain uncertain. It has been reported that a number of the early human cases had a history of contact with the Huanan Seafood Market. Here we present the results of surveillance for SARS-CoV-2 within the market. From January 1^st 2020, after closure of the market, 923 samples were collected from the environment. From 18^th January, 457 samples were collected from 18 species of animals, comprising of unsold contents of refrigerators and freezers, swabs from stray animals, and the contents of a fish tank. Using RT-qPCR, SARS-CoV-2 was detected in 73 environmental samples, but none of the animal samples. Three live viruses were successfully isolated. The viruses from the market shared nucleotide identity of 99.99% to 100% with the human isolate HCoV-19/Wuhan/IVDC-HB-01/2019. SARS-CoV-2 lineage A (8782T and 28144C) was found in an environmental sample. RNA-seq analysis of SARS-CoV-2 positive and negative environmental samples showed an abundance of different vertebrate genera at the market. In summary, this study provides information about the distribution and prevalence of SARS-CoV-2 in the Huanan Seafood Market during the early stages of the COVID-19 outbreak.

Background: Mosquitoes host and transmit numerous arthropod-borne viruses (arboviruses) that cause disease in both humans and animals. Effective surveillance of virome profiles in mosquitoes is vital to the prevention and control of mosquito-borne diseases in northwestern China, where epidemics occur frequently. Methods: Mosquitoes were collected in the Shaanxi-Gansu-Ningxia region (Shaanxi Province, Gansu Province, and Ningxia Hui Autonomous Region) of China from June to August 2019. Morphological methods were used for taxonomic identification of mosquito species. High-throughput sequencing and metagenomic analysis were used to characterize mosquito viromes. Results: A total of 22,959 mosquitoes were collected, including Culex pipiens (45.7%), Culex tritaeniorhynchus (40.6%), Anopheles sinensis (8.4%), Aedes (5.2%), and Armigeres subalbatus (0.1%). In total, 3,014,183 (0.95% of clean reads) viral sequences were identified and assigned to 116 viral species (including pathogens such as Japanese encephalitis virus and Getah virus) in 31 viral families, including Flaviviridae, Togaviridae, Phasmaviridae, Phenuiviridae, and some unclassified viruses. Mosquitoes collected in July (86 species in 26 families) showed greater viral diversity than those from June and August. Culex pipiens (69 species in 25 families) and Culex tritaeniorhynchus (73 species in 24 families) carried more viral species than Anopheles sinensis (50 species in 19 families) or Aedes (38 species in 20 families) mosquitoes. Conclusion: Viral diversity and abundance were affected by mosquito species and collection time. The present study elucidates the virome compositions of various mosquito species in northwestern China, improving the understanding of virus transmission dynamics for comparison with those of disease outbreaks.

Rodents are natural reservoirs of diverse zoonotic viruses and widely distributed on the Tibetan Plateau. A comprehensive understanding of the virome in local rodent species could provide baseline of viral content and assist in efforts to reduce the risk for future emergence of rodent related zoonotic diseases. A total of 205 tissue and fecal samples from 41 wild Qinghai voles were collected. Metagenomic analyses were performed to outline the characteristics of the viromes, and phylogenetic analyses were used to identify the novel viral genomes. The virome distribution among five tissues (liver, lung, spleen, small intestine with content and feces) was also compared. We identified sequences related to 46 viral families. Novel viral genomes from distinct evolutionary lineages with known viruses were characterized for their genomic and evolutionary characteristics, including Hepatovirus, Hepacivirus, Rotavirus, and Picobirnavirus. Further analyses revealed that the core virome harbored by rodent internal tissues were quite different from the virome found in intestine and fecal samples. These findings provide an overview of the viromes in wild Qinghai voles, which are unique and the most common rodent species in the eastern Tibetan Plateau. A high diversity of viruses is likely present in rodent species in this area.

Encephalitis and meningitis are notable global public health concerns, especially among infants or children. Metagenomic next-generation sequencing (mNGS) has greatly advanced our understanding of the viruses responsible for these diseases. However, the detection rate of the aetiology remains low. We conducted RNA sequencing and virome analysis on cerebrospinal fluid (CSF) and serum samples commonly used in the clinical diagnosis to detect viral pathogens. In total, 226 paired CSF and serum samples from 113 children with encephalitis and meningitis were enrolled. The results showed that the diversity of viruses was higher in CSF, with a total of 12 viral taxa detected, including one case each of herpesvirus, coronavirus and enterovirus, and six cases of adenovirus related to human diseases. In contrast, the Anelloviridae was the most abundant viral family detected in serum, and only a few samples contained human viral pathogens, including one case of enterovirus and two cases of adenovirus. The detection rate for human viral pathogens increases to 10.6 %(12/113) when both types of samples are used simultaneously, compared to CSF along 7.9 % (9/113) or serum alone 2.6 % (3/113). However, we did not detect these viruses simultaneously in paired samples from the same case. These results suggest that CSF samples still have irreplaceable advantages for using mNGS to detect viruses in patients with meningitis and encephalitis, and serum can supplement to improve the detection rate of viral encephalitis and meningitis. The findings of this study could help improve the etiological diagnosis, clinical management and prognosis of patients with meningitis and encephalitis in children.

• Scientific questions: While controlling imported infectious diseases is critical, conventional traveler screening overlooks environmental microbial threats at international ports. Assessing microbial risks and sources in high-risk customs environments remains an unresolved challenge. • Evidence before this study: Metagenomic sequencing has enabled analysis of complex microbial communities, yet microbial risk assessment in high-risk customs settings requires deeper investigation. • New findings: We identified a deoxyribonucleic acid (DNA) virus-dominated pathogen profile and detected cross-border contaminants including pigeon circovirus (Columbid circovirus, Belgian strain) and Influenza A virus (Asian avian-origin H4N2). Four disinfection zones were delineated by microbial load, enabling targeted infection control in high-risk port environments. • Significance of the study: Environmental metagenomics complements traveler screening. We propose an evidence-based four-tier disinfection strategy aligned with microbial distribution to mitigate cross-border biosecurity risks.

Bundibugyo ebolavirus (BDBV), a member of the genus Orthoebolavirus, family Filoviridae, is hereafter referred to as Bundibugyo virus, with the associated illness termed Bundibugyo virus disease (BVD). First identified in Uganda in 2007, the virus has received far less scientific attention than the highly pathogenic Zaire ebolavirus. In April 2026, a cluster of unexplained deaths emerged in the mining-intensive Mongbwalu Health Zone of Ituri Province in the Democratic Republic of the Congo (DRC), and the causative agent was confirmed by whole-genome sequencing on 14 May 2026 as Bundibugyo virus. This is the DRC’s 17th Ebola outbreak and only the third BVD epidemic globally. As of 10 June 2026, the DRC has reported 662 confirmed cases and 124 confirmed deaths, with the outbreak expanding across 25 health zones in Ituri, North Kivu, and South Kivu provinces; Uganda has reported 19 confirmed cases and 2 deaths. Unlike Zaire ebolavirus outbreaks, no licensed vaccine or specific therapeutic exists for BVD, and the response is further complicated by armed conflict, population mobility through mining corridors, fragile health systems, and community mistrust that has occasionally erupted into violence against responders. The World Health Organization (WHO) declared a Public Health Emergency of International Concern (PHEIC) on 17 May 2026, and the Africa Centres for Disease Control and Prevention (Africa CDC) declared a Public Health Emergency of Continental Security (PHECS) on 18 May 2026. Under a unified “One Team, One Plan, One Budget, and One M&E Framework” architecture, the Africa Centres for Disease Control and Prevention and World Health Organization jointly issued the Bundibugyo Virus Disease Continental Preparedness and Response Plan, with a budget of $517.7 million over six months and structured around 14 technical pillars. This review provides a comprehensive synthesis of the virology, epidemiology, critical research gaps, and international response strategy, aiming to inform both ongoing outbreak operations and future scientific efforts.