RNA viromes of Dermacentor nuttalli ticks reveal a novel uukuvirus in Qinghǎi Province, China.

Ticks are a major parasite on the Qinghǎi-Tibet Plateau, western China, and represent an economic burden to agriculture and animal husbandry. Despite research on tick-borne pathogens that threaten humans and animals, the viromes of dominant tick species in this area remain unknown. In this study, we collected Dermacentor nuttalli ticks near Qinghǎi Lake and identified 13 viruses belonging to at least six families through metagenomic sequencing. Four viruses were of high abundance in pools, including Xinjiang tick-associated virus 1 (XJTAV1), and three novel viruses: Qinghǎi Lake virus 1, Qinghǎi Lake virus 2 (QHLV1, and QHLV2, unclassified), and Qinghǎi Lake virus 3 (QHLV3, genus Uukuvirus of family Phenuiviridae in order Bunyavirales), which lacks the M segment. The minimum infection rates of the four viruses in the tick groups were 8.2%, 49.5%, 6.2%, and 24.7%, respectively, suggesting the prevalence of these viruses in D. nuttalli ticks. A putative M segment of QHLV3 was identified from the next-generation sequencing data and further characterized for its signal peptide cleavage site, N-glycosylation, and transmembrane region. Furthermore, we probed the L, M, and S segments of other viruses from sequencing data of other tick pools by â€‹using the putative M segment sequence of QHLV3. By revealing the viromes of D. nuttalli ticks, this study enhances our understanding of tick-borne viral communities in highland regions. The putative M segment identified in a novel uukuvirus suggests that previously identified uukuviruses without M segments should have had the same genome organization as typical bunyaviruses. These findings will facilitate virus discovery and our understanding of the phylogeny of tick-borne uukuviruses.

Cladophora reblooming after half a century: effect of climate change-induced increases in the water level of the largest lake in Tibetan Plateau.

Massive Cladophora growth was reported half a century ago around Birds Island in Qinghai Lake, and in 2015, Cladophora populations have rebloomed and have formed green "meadows," with areas up to thousands of hectares. The present study investigated the distribution and biomass of Cladophora in Qinghai Lake and found that two key factors contribute to Cladophora blooming. First, recent climate change, especially increased precipitation, has induced the expansion of the lake's area, and the submerged grassland around Birds Island has provided a plethora of grass stems on which Cladophora can attach and twine. In addition, the submerged grasslands are covered with less than 1 m of water, which allows enough sunlight to support the growth of Cladophora on available substrates. Second, the submerged grassland may function as a key source of nutrients, especially phosphate. A large number of migratory birds live in these area for very long times, which lead to higher phosphorus content due to the accumulated birds dropping. Thus, the high phosphate level further exacerbates the massive growth. Future studies should investigate the functions of Cladophora in the nutrient cycling of submerged areas, and the improvement of methods for removing Cladophora biomass.

Circulation, Evolution and Transmission of H5N8 virus, 2016-2018.

OBJECTIVES: A second wave of highly pathogenic avian influenza A virus (HPAIV) H5N8 clade 2.3.4.4 has spread globally, causing outbreaks among wild birds and domestic poultry since autumn 2016. The circulation and evolutionary dynamics of the virus remain largely unknown. METHODS: We performed surveillance for H5N8 in Qinghai Lake in China since the emergence of the virus (from 2016 to 2018). By analyzing recovered viruses in Qinghai Lake and all related viruses worldwide (449 strains), we identified the genotypes, estimated their genesis and reassortment, and evaluated their global distribution and transmission. RESULTS: Through surveillance of wild migratory birds around Qinghai Lake between 2016 and 2018, we revealed that the H5N8 was introduced into Qinghai Lake bird populations (QH-H5N8), with distinct gene constellations in 2016 and 2017. A global analysis of QH-H5N8-related viruses showed that avian influenza viruses with low pathogenicity in wild birds contributed to the high diversity of genotypes; the major reassortment events possibly occurred during the 2016 breeding season and the following winters. CONCLUSIONS: Continued circulation of QH-H5N8-related viruses among wild birds has resulted in the global distribution of high genotypic diversity. Thus, these viruses pose an ongoing threat to wild and domestic bird populations and warrant continuous surveillance.

Highly Pathogenic Avian Influenza A(H5N8) Virus in Wild Migratory Birds, Qinghai Lake, China.

In May 2016, a highly pathogenic avian influenza A(H5N8) virus strain caused deaths among 3 species of wild migratory birds in Qinghai Lake, China. Genetic analysis showed that the novel reassortant virus belongs to group B H5N8 viruses and that the reassortment events likely occurred in early 2016.

Highly pathogenic avian influenza H5N1 Clade 2.3.2.1c virus in migratory birds, 2014-2015.

A novel Clade 2.3.2.1c H5N1 reassortant virus caused several outbreaks in wild birds in some regions of China from late 2014 to 2015. Based on the genetic and phylogenetic analyses, the viruses possess a stable gene constellation with a Clade 2.3.2.1c HA, a H9N2-derived PB2 gene and the other six genes of Asian H5N1-origin. The Clade 2.3.2.1c H5N1 reassortants displayed a high genetic relationship to a human H5N1 strain (A/Alberta/01/2014). Further analysis showed that similar viruses have been circulating in wild birds in China, Russia, Dubai (Western Asia), Bulgaria and Romania (Europe), as well as domestic poultry in some regions of Africa. The affected areas include the Central Asian, East Asian-Australasian, West Asian-East African, and Black Sea/Mediterranean flyways. These results show that the novel Clade 2.3.2.1c reassortant viruses are circulating worldwide and may have gained a selective advantage in migratory birds, thus posing a serious threat to wild birds and potentially humans.

Wild bird migration across the Qinghai-Tibetan plateau: a transmission route for highly pathogenic H5N1.

BACKGROUND: Qinghai Lake in central China has been at the center of debate on whether wild birds play a role in circulation of highly pathogenic avian influenza virus H5N1. In 2005, an unprecedented epizootic at Qinghai Lake killed more than 6000 migratory birds including over 3000 bar-headed geese (Anser indicus). H5N1 subsequently spread to Europe and Africa, and in following years has re-emerged in wild birds along the Central Asia flyway several times. METHODOLOGY/PRINCIPAL FINDINGS: To better understand the potential involvement of wild birds in the spread of H5N1, we studied the movements of bar-headed geese marked with GPS satellite transmitters at Qinghai Lake in relation to virus outbreaks and disease risk factors. We discovered a previously undocumented migratory pathway between Qinghai Lake and the Lhasa Valley of Tibet where 93% of the 29 marked geese overwintered. From 2003-2009, sixteen outbreaks in poultry or wild birds were confirmed on the Qinghai-Tibet Plateau, and the majority were located within the migratory pathway of the geese. Spatial and temporal concordance between goose movements and three potential H5N1 virus sources (poultry farms, a captive bar-headed goose facility, and H5N1 outbreak locations) indicated ample opportunities existed for virus spillover and infection of migratory geese on the wintering grounds. Their potential as a vector of H5N1 was supported by rapid migration movements of some geese and genetic relatedness of H5N1 virus isolated from geese in Tibet and Qinghai Lake. CONCLUSIONS/SIGNIFICANCE: This is the first study to compare phylogenetics of the virus with spatial ecology of its host, and the combined results suggest that wild birds play a role in the spread of H5N1 in this region. However, the strength of the evidence would be improved with additional sequences from both poultry and wild birds on the Qinghai-Tibet Plateau where H5N1 has a clear stronghold.

Bird migration and risk for H5N1 transmission into Qinghai Lake, China.

The highly pathogenic avian influenza H5N1 virus still cause devastating effects to humans, agricultural poultry flocks, and wild birds. Wild birds are also detected to carry H5N1 over long distances and are able to introduce it into new areas during migration. In this article, our objective is to provide lists of bird species potentially involved in the introduction of highly pathogenic avian influenza H5N1 in Qinghai Lake, which is an important breeding and stopover site for aquatic birds along the Central Asian Flyway. Bird species were classified according to the following behavioral and ecological factors: migratory status, abundance, degree of mixing species and gregariousness, and the prevalence rate of H5N1 virus. Most of the high-risk species were from the family Anatidae, order Anseriformes (9/14 in spring, 11/15 in fall). We also estimated the relative risk of bird species involved by using a semi-quantitative method; species from family Anatidae accounted for over 39% and over 91% of the total risk at spring and fall migration periods, respectively. Results also show the relative risk for each bird aggregating site in helping to identify high-risk areas. This work may also be instructive and meaningful to the avian influenza surveillance in the breeding, stopover, and wintering sites besides Qinghai Lake along the Central Asian Flyway.

Persistent circulation of highly pathogenic influenza H5N1 virus in Lake Qinghai area of China.

To trace the endemic situation of highly pathogenic influenza H5N1 virus in wildlife in the Lake Qinghai area of northwest China, a continuous surveillance program was implemented from September 2005 to September 2007. A total of 2699 field samples were collected, and 95 of the samples were positive by a reverse transcription-polymerase chain reaction (RT-PCR) test of subtype H5 influenza virus. To some extent, the detection rate correlated with the species, the location, and the seasons of collection. In 2007, two H5N1 isolates were identified from two species of migratory birds. The two 2007 isolates showed high similarities of the hemagglutinin and neuraminidase genes with those of the 2005 and 2006 Qinghai isolates (98.6-99.8% for HA and 98.7-98.9% for NA at the nucleotide level). Both isolates fell into clade 2.2.2 and were experimentally highly pathogenic to chickens and mice. According to our surveillance results, HPAI H5N1 viruses still exist in this region.

The survey of H5N1 flu virus in wild birds in 14 Provinces of China from 2004 to 2007.

BACKGROUND: The highly pathogenic H5N1 avian influenza emerged in the year 1996 in Asia, and has spread to Europe and Africa recently. At present, effective monitoring and data analysis of H5N1 are not sufficient in Chinese mainland. METHODOLOGY/PRINCIPAL FINDINGS: During the period from April of 2004 to August of 2007, we collected 14,472 wild bird samples covering 56 species of 10 orders in 14 provinces of China and monitored the prevalence of flu virus based on RT-PCR specific for H5N1 subtype. The 149 positive samples involved six orders. Anseriformes had the highest prevalence while Passeriformes had the lowest prevalence (2.70% versus 0.36%). Among the 24 positive species, mallard (Anas platyrhynchos) had the highest prevalence (4.37%). A difference of prevalence was found among 14 provinces. Qinghai had a higher prevalence than the other 13 provinces combined (3.88% versus 0.43%). The prevalence in three species in Qinghai province (Pintail (Anas acuta), Mallard (Anas platyrhynchos) and Tufted Duck (Aythya fuligula)) were obviously higher than those in other 13 provinces. The results of sequence analysis indicated that the 17 strains isolated from wild birds were distributed in five clades (2.3.1, 2.2, 2.5, 6, and 7), which suggested that genetic diversity existed among H5N1 viruses isolated from wild birds. The five isolates from Qinghai came from one clade (2.2) and had a short evolutionary distance with the isolates obtained from Qinghai in the year 2005. CONCLUSIONS/SIGNIFICANCE: We have measured the prevalence of H5N1 virus in 56 species of wild birds in 14 provinces of China. Continuous monitoring in the field should be carried out to know whether H5N1 virus can be maintained by wild birds.