Extensive Genetic Diversity and Epidemiological Patterns of Factor H-Binding Protein Variants among Neisseria meningitidis in China.

Factor H-binding protein (fHbp) is a virulence factor expressed by Neisseria meningitidis (N. meningitidis), the primary causative agent of invasive meningococcal disease (IMD) in humans. fHbp is utilized as the main component in vaccines to provide protection against IMD caused by serogroup B N. meningitidis. In order to comprehensively investigate the genetic diversity and epidemiological patterns of fHbp variants within isolates of Chinese N. meningitidis, we utilized the NEIS0349 locus, which encompasses the complete coding sequences of fHbp. This enabled us to identify allelic variants of fHbp with enhanced resolution. A total of 109 fHbp variants were identified in 1013 Chinese N. meningitidis isolates. We reconstructed a phylogenetic tree and analyzed the epidemiological characteristics of each variant. Considering both temporal and geographical distribution patterns, only four fHbp variants (v2.16, v2.18, v2.404, and v2.21) exhibited persistent nationwide prevalence during the previous decade (2011-2021). These variants were highly prevalent in both serogroup B strains from patients and healthy individuals, suggesting their potential as suitable vaccine candidates for nationwide implementation against IMD caused by serogroup B strains. Our study emphasizes the significance of conducting continuous surveillance of meningococcal strains to monitor the genetic diversity of fHbp for the purpose of vaccine development.

Epidemiological Investigation of Hospital Transmission of Corynebacterium striatum Infection by Core Genome Multilocus Sequence Typing Approach.

Corynebacterium striatum has recently received increasing attention due to its multiple antimicrobial resistances and its role as an invasive infection/outbreak agent. Recently, whole-genome sequencing (WGS)-based core genome multilocus sequence typing (cgMLST) has been used in epidemiological studies of specific human pathogens. However, this method has not been reported in studies of C. striatum. In this work, we aim to propose a cgMLST scheme for C. striatum. All publicly available C. striatum genomes, 30 C. striatum strains isolated from the same hospital, and 1 epidemiologically unrelated outgroup C. striatum strain were used to establish a cgMLST scheme targeting 1,795 genes (hereinafter referred to as 1,795-cgMLST). The genotyping results of cgMLST showed good congruence with core genome-based single-nucleotide polymorphism typing in terms of tree topology. In addition, the cgMLST provided a greater discrimination than the MLST method based on 6 housekeeping genes (gyrA, gyrB, hsp65, rpoB, secA1, and sodA). We established a clonal group (CG) threshold based on 104 allelic differences; a total of 56 CGs were identified from among 263 C. striatum strains. We also defined an outbreak threshold based on seven allelic differences that is capable of identifying closely related isolates that could give clues on hospital transmission. According to the results of analysis of drug-resistant genes and virulence genes, we identified CG4, CG5, CG26, CG28, and CG55 as potentially hypervirulent and multidrug-resistant CGs of C. striatum. This study provides valuable genomic epidemiological data on the diversity, resistance, and virulence profiles of this potentially pathogenic microorganism. IMPORTANCE Recently, WGS of many human and animal pathogens has been successfully used to investigate microbial outbreaks. The cgMLST schema are powerful genotyping tools that can be used to investigate potential epidemics and provide classification of the strains precise and reliable. In this study, we proposed the development of a cgMLST typing scheme for C. striatum, and then we evaluated this scheme for its applicability to hospital transmission investigations. This report describes the first cgMLST schema for C. striatum. The analysis of hospital transmission of C. striatum based on cgMLST methods has important clinical epidemiological significance for improving nosocomial infection monitoring of C. striatum and in-depth understanding of its nosocomial transmission routes.

Viral Metagenome-Based Precision Surveillance of Pig Population at Large Scale Reveals Viromic Signatures of Sample Types and Influence of Farming Management on Pig Virome.

Pigs are a major meat source worldwide and a pillar of Chinese animal husbandry; hence, their health and safety are a prioritized concern of the national economy. Although pig viruses have been continuously investigated, the full extent of the pig virome has remained unknown and emerging viruses are still a major threat to the pig industry. Here, we report a comprehensive study to delineate the pig virome of 1,841 healthy weaned pigs from 45 commercial farms collected from 25 major pig-producing regions across China. A viromic sequence data set, named Pigs_VIRES, which matched 96,586 viral genes from at least 249 genera within 66 families and which almost tripled the number of previously published pig viromic genes, was established. The majority of the mammalian viruses were closely related to currently known ones. A comparison with previously published viromes of bovines, avians, and humans has revealed the distinct composition of Pigs_VIRES, which has provided characteristic viromic signatures of serum, pharyngeal, and anal samples that were significantly influenced by farming management and disease control measures. Taken together, Pigs_VIRES has revealed the most complete viromic data set of healthy pigs to date. The compiled data also provide useful guidance to pig viral disease control and prevention and the biosafety management of pig farms. Especially, the established viromic protocol has created a precision surveillance strategy to potentially innovate currently used surveillance methods of animal infectious diseases, particularly by making precision surveillance available to other animal species on a large scale or even during a nationwide surveillance campaign. IMPORTANCE Pigs are deeply involved in human lives; hence, their viruses are associated with public health. Here, we established the most comprehensive virome of healthy piglets to date, which provides a viromic baseline of weaned pigs for disease prevention and control, highlighting that longitudinal viromic monitoring is needed to better understand the dynamics of the virome in pig development and disease occurrence. The present study also shows how high standards of animal farm management with strict biosafety measures can significantly minimize the risk of introduction of pathogenic viruses into pig farms. Particularly, the viromic strategy established, i.e., high-throughput detection and analyses of various known and unknown pathogenic viruses in a single test at large scale, has completely innovated current surveillance measures in provision of timely and precise detection of all potentially existing pathogenic viruses and can be widely applied in other animal species.

Bat-borne polyomaviruses in Europe reveal an evolutionary history of intrahost divergence with horseshoe bats distributed across the African and Eurasian continents.

Polyomaviruses (PyVs) are small, circular dsDNA viruses carried by diverse vertebrates, including bats. Although previous studies have reported several horseshoe bat PyVs collected in Zambia and China, it is still unclear how PyVs evolved in this group of widely dispersed mammals. Horseshoe bats (genus Rhinolophus) are distributed across the Old World and are natural reservoirs of numerous pathogenic viruses. Herein, non-invasive bat samples from European horseshoe bat species were collected in Hungary for PyV identification and novel PyVs with complete genomes were successfully recovered from two different European horseshoe bat species. Genomic and phylogenetic analysis of the Hungarian horseshoe bat PyVs supported their classification into the genera Alphapolyomavirus and Betapolyomavirus. Notably, despite the significant geographical distances between the corresponding sampling locations, Hungarian PyVs exhibited high genetic relatedness with previously described Zambian and Chinese horseshoe bat PyVs, and phylogenetically clustered with these viruses in each PyV genus. Correlation and virus-host relationship analysis suggested that these PyVs co-diverged with their European, African and Asian horseshoe bat hosts distributed on different continents during their evolutionary history. Additionally, assessment of selective pressures over the major capsid protein (VP1) of horseshoe bat PyVs showed sites under positive selection located in motifs exposed to the exterior of the capsid. In summary, our findings revealed a pattern of stable intrahost divergence of horseshoe bat PyVs with their mammalian hosts on the African and Eurasian continents over evolutionary time.

Newly identified viral genomes in pangolins with fatal disease.

Epizootic pathogens pose a major threat to many wildlife species, particularly in the context of rapidly changing environments. Pangolins (order Pholidota) are highly threatened mammals, in large part due to the trade in illegal wildlife. During July to August 2018 four sick wild pangolins (three Manis javanica and one Manis pentadactyla) exhibiting a variety of clinical symptoms were rescued by the Jinhua Wildlife Protection Station in Zhejiang province, China. Although three of these animals died, fortunately one recovered after 2 weeks of symptomatic treatment. Using meta-transcriptomics combined with reverse transcription polymerase chain reaction (RT-PCR), we identified two novel RNA viruses in two of the dead pangolins. Genomic analysis revealed that these viruses were most closely related to pestiviruses and coltiviruses, although still highly genetically distinct, with more than 48 and 25 per cent sequence divergence at the amino acid level, respectively. We named these Dongyang pangolin virus (DYPV) and Lishui pangolin virus (LSPV) based on the sampling site and hosts. Although coltiviruses (LSPV) are known to be transmitted by ticks, we found no evidence of LSPV in ticks sampled close to where the pangolins were collected. In addition, although DYPV was present in nymph ticks (Amblyomma javanense) collected from a diseased pangolin, they were not found in the local tick population. Epidemiological investigation revealed that both novel viruses might have been imported following the illegal international trade of pangolins. Hence, these data indicate that illegal wildlife trafficking not only threatens the status of pangolin populations, but may also spread epizootic pathogens.

Extensive Genetic Diversity of Polyomaviruses in Sympatric Bat Communities: Host Switching versus Coevolution.

Polyomaviruses (PyVs) are small DNA viruses carried by diverse vertebrates. The evolutionary relationships of viruses and hosts remain largely unclear due to very limited surveillance in sympatric communities. In order to investigate whether PyVs can transmit among different mammalian species and to identify host-switching events in the field, we conducted a systematic study of a large collection of bats (n = 1,083) from 29 sympatric communities across China which contained multiple species with frequent contact. PyVs were detected in 21 bat communities, with 192 PyVs identified in 186 bats from 15 species within 6 families representing at least 28 newly described PyVs. Surveillance results and phylogenetic analyses surprisingly revealed three interfamily PyV host-switching events in these sympatric bat communities: two distinct PyVs were identified in two bat species in restricted geographical locations, while another PyV clustered phylogenetically with PyVs carried by bats from a different host family. Virus-host relationships of all discovered PyVs were also evaluated, and no additional host-switching events were found. PyVs were identified in different horseshoe bat species in sympatric communities without observation of host-switching events, showed high genomic identities, and clustered with each other. This suggested that even for PyVs with high genomic identities in closely related host species, the potential for host switching is low. In summary, our findings revealed that PyV host switching in sympatric bat communities can occur but is limited and that host switching of bat-borne PyVs is relatively rare on the predominantly evolutionary background of codivergence with their hosts.IMPORTANCE Since the discovery of murine polyomavirus in the 1950s, polyomaviruses (PyVs) have been considered highly host restricted in mammals. Sympatric bat communities commonly contain several different bat species in an ecological niche facilitating viral transmission, and they therefore represent a model to identify host-switching events of PyVs. In this study, we screened PyVs in a large number of bats in sympatric communities from diverse habitats across China. We provide evidence that cross-species bat-borne PyV transmission exists, though is limited, and that host-switching events appear relatively rare during the evolutionary history of these viruses. PyVs with close genomic identities were also identified in different bat species without host-switching events. Based on these findings, we propose an evolutionary scheme for bat-borne PyVs in which limited host-switching events occur on the background of codivergence and lineage duplication, generating the viral genetic diversity in bats.

Genomes and seroprevalence of severe fever with thrombocytopenia syndrome virus and Nairobi sheep disease virus in Haemaphysalis longicornis ticks and goats in Hubei, China.

Ticks are medically-important arthropods that maintain and transmit numerous emerging viruses. China suffers severely from tick-borne viral diseases such as tick-borne encephalitis and severe fever with thrombocytopenia syndrome (SFTS), but the background of tick-borne viruses is very limited. Here we report the virome profiling of ticks and goat sera from SFTS-epidemic areas, and serological investigation of SFTS virus (SFTSV) and Nairobi sheep disease virus (NSDV). Results revealed divergent viruses in ticks and goat sera, including SFTSV and NSDV. Sequence and phylogenetic analyses showed that the SFTSV identified here was most closely related to human SFTSV in sampling and surrounding areas, and the NSDV to the previously identified NSDV from northeast China. Serological investigation of SFTSV infection in goats revealed intensive activity in those areas. Surprisingly, two different methods of NSDV serological investigation showed no sera positive for this virus.

Seroprevalence, cross antigenicity and circulation sphere of bat-borne hantaviruses revealed by serological and antigenic analyses.

Bats are newly identified reservoirs of hantaviruses (HVs) among which very divergent HVs have been discovered in recent years. However, their significance for public health remains unclear since their seroprevalence as well as antigenic relationship with human-infecting HVs have not been investigated. In the present study archived tissues of 1,419 bats of 22 species from 6 families collected in 5 south and southwest provinces in China were screened by pan-HV RT-PCR following viral metagenomic analysis. As a result nine HVs have been identified in two bat species in two provinces and phylogenetically classified into two species, Laibin virus (LAIV, ICTV approved species, 1 strain) and Xuan son virus (XSV, proposed species, 8 strains). Additionally, 709 serum samples of these bats were also analyzed by ELISA to investigate the seroprevalence and cross-reactivity between different HVs using expressed recombinant nucleocapsid proteins (rNPs) of LAIV, XSV and Seoul virus (SEOV). The cross-reactivity of some bat sera were further confirmed by western blot (WB) using three rNPs followed by fluorescent antibody virus neutralization test (FAVNT) against live SEOV. Results showed that the total HV seropositive rate of bat sera was 18.5% (131/709) with many cross reacting with two or all three rNPs and several able to neutralize SEOV. WB analysis using the three rNPs and their specific hyperimmune sera demonstrated cross-reactivity between XSV/SEOV and LAIV/XSV, but not LAIV/SEOV, indicating that XSV is antigenically closer to human-infecting HVs. In addition a study of the distribution of the viruses identified an area covering the region between Chinese Guangxi and North Vietnam, in which XSV and LAIV circulate within different bat colonies with a high seroprevalence. A circulation sphere of bat-borne HVs has therefore been proposed.

Virome profiling of rodents in Xinjiang Uygur Autonomous Region, China: Isolation and characterization of a new strain of Wenzhou virus.

Rodents, as the most diverse and widest distributed mammals, are a natural reservoir of many zoonotic viruses. However, little is known about the viral diversity harbored by rodents in China. Here we performed viral metagenomic analyses of 314 wild rodents covering 7 species, sampled in North-western China. We also conducted a systematic virological characterization of a new Wenzhou virus (WENV) isolate, QARn1, from a brown rat (Rattus norvegicus). Full genomic and phylogenetic analyses showed that QARn1 is a previously unidentified strain of Wenzhou mammarenavirus and forms a new branch within the Asian clade. Experimental infection of Sprague-Dawley rats with QARn1 did not present overt pathology, but specific humoral immune responses developed and mild hemorrhage and immunocyte infiltration of the lungs and thymus were observed. These observations have expanded the geographic distribution of WENV to Central Asia, and further confirm that brown rats are natural hosts of Wenzhou virus.

Virome analysis of tick-borne viruses in Heilongjiang Province, China.

Ticks are implicated in the transmission of various human and livestock pathogens worldwide. This study aimed to understand the geographical distribution of tick species, along with tick-associated viruses, in Heilongjiang Province, northeast China. Molecular methods were used to classify tick species, with next-generation sequencing and polymerase chain reaction-based analyses used to assess the viromes of ticks from four representative sampling locations in the Greater Khingan Mountains. Five species of ixodid ticks were identified, including Ixodes persulcatus, Dermacentor nuttalli, Dermacentor silvarum, Haemaphysalis longicornis, and Haemaphysalis concinna. From the 1102 ticks, 3,568,561 high-quality reads were obtained by next-generation sequencing. Following trimming, 302,540 reads were obtained, of which 6577 (2.16%) reads were annotated to viruses. Phylogenetic analysis revealed that the viral sequences shared a close relationship with Orthonairovirus, Phlebovirus, deer tick Mononegavirales-like virus, and Jingmen tick virus sequences, but the significance of these newly-identified tick-borne viruses to human and animal health requires further investigation. The results of this study provide a basis not only for further studies on the relationship between ticks and tick-borne viruses, but also for preventing future tick-borne epidemic outbreaks by means of vector control.