A Unique Protease Cleavage Site Predicted in the Spike Protein of the Novel Pneumonia Coronavirus(2019-nCoV) Potentially Related to Viral Transmissibility

Dear Editor,In December 2019,a novel human coronavirus caused an epidemic of severe pneumonia(Coronavirus Disease 2019,COVID-19)in Wuhan,Hubei,China(Wu et al.2020;Zhu et al.2020).So far,this virus has spread to all areas of China and even to other countries.The epidemic has caused 67,102 confirmed infections with 1526 fatal cases worldwide by February 14th,2020.

Coexistence of multiple genotypes of porcine epidemic diarrhea virus with novel mutant S genes in the Hubei Province of Chinain 2016

The emergence of highly virulent porcine epidemic diarrhea virus(PEDV) variants in China caused huge economic losses in 2010. Since then, large-scale sporadic outbreaks of PED caused by PEDV variants have occasionally occurred in China. However, the molecular diversity and epidemiology of PEDV in different provinces has not been completely understood. To determine the molecular diversity of PEDV in the Hubei Province of China, we collected 172 PED samples from 34 farms across the province in 2016 and performed reverse transcription polymerase chain reaction(RTPCR)by targeting the nucleocapsid(N) gene. Seventy-four samples were found to be PEDVpositive.We further characterized the complete spike(S) glycoprotein genes from the positive samples and found 21 different S genes with amino acid mutations. The PEDV isolates here presented most of the genotypes which were found previously in field isolates in East and SouthEast Asia, North America, and Europe. Besides the typical Genotypes Ⅰ and Ⅱ, the INDEX groups were also found. Importantly, 58 new amino acids mutant sites in the S genes, including 44 sites in S1 and 14 sites in S2, were first described. Our results revealed that the S genes of PEDV showed variation and that diverse genotypes of PEDV coexisted and were responsible for the PED outbreaks in Hubei in 2016. This work highlighted the complexity of the epidemiology of PEDV and emphasized the need for reassessing the efficacy of classic PEDV vaccines against emerging variant strains and developing new vaccines to facilitate the prevention and control of PEDV in fields.

Genetic diversity and temporal dynamics of phytoplankton viruses in East Lake, China

Phytoplankton viruses are important components of aquatic ecosystems. However, their prevalence and genetic diversity in marine and freshwater systems are largely under estimated owing to the immense size of water bodies and limitations in virus discovery techniques. In this study, we conducted a 1-year survey of phytoplankton virus communities by collecting surface water monthly from an inland lake(East Lake) in China between May 2012 and April 2013. We examined four phytoplankton viruses, i.e., myoviruses, podoviruses, siphoviruses, and phycodnaviruses, and seven sets of primers were used to target conserved genes within these four species. In this year-long investigation, a total of 358 different virus-related sequences from four virus families were obtained. All virus families were detected in all months, except for cyanopodoviruses, which were only identified during eight of the 12 months surveyed. Moreover, virus abundance and diversity changed dynamically over time. Phylogenetic analysis revealed that the majority of viral sequences from East Lake, China displayed distinct clustering patterns compared with published sequences. These results supported the existence of a highly diverse and unique phytoplankton virus community in East Lake, China.

Genetic Evidence of Middle East Respiratory Syndrome Coronavirus(MERS-Cov) and Widespread Seroprevalence among Camels in Kenya

We describe the first genome isolation of Middle East respiratory syndrome coronavirus(MERS-CoV) in Kenya. This fatal zoonotic pathogen was first described in the Kingdom of Saudi Arabia in 2012. Epidemiological and molecular evidence revealed zoonotic transmission from camels to humans and between humans. Currently, MERS-CoV is classified by the WHO as having high pandemic potential requiring greater surveillance. Previous studies of MERS-CoV in Kenya mainly focused on site-specific and archived camel and human serum samples for antibodies. We conducted active nationwide cross-sectional surveillance of camels and humans in Kenya, targeting both nasal swabs and plasma samples from 1,163 camels and 486 humans collected from January 2016 to June 2018. A total of 792 camel plasma samples were positive by ELISA. Seroprevalence increased with age, and the highest prevalence was observed in adult camels(82.37%, 95%confidence interval(CI) 79.50–84.91). More female camels were significantly seropositive(74.28%, 95% CI 71.14–77.19)than male camels(P \ 0.001)(53.74%, 95% CI 48.48–58.90). Only 11 camel nasal swabs were positive for MERS-CoV by reverse transcription-quantitative PCR. Phylogenetic analysis of whole genome sequences showed that Kenyan MERSCoV clustered within sub-clade C2, which is associated with the African clade, but did not contain signature deletions of orf4 b in African viruses. None of the human plasma screened contained neutralizing antibodies against MERS-CoV. This study confirms the geographically widespread occurrence of MERS-CoV in Kenyan camels. Further one-health surveillance approaches in camels, wildlife, and human populations are needed.

Characterization of the First Genome of Porcine mastadenovirus B(HNU1 Strain) and Implications on Its Lymphoid and Special Origin

Porcine adenoviruses(PAdVs)are classified into three species,PAdV-A,PAdV-B,and PAdV-C.The genomes of PAdV-A and PAdV-C have been well characterized.However,the genome of PAdV-B has never been completely sequenced,and the epidemiology of PAdV-B remains unclear.In our study,we have identified a novel strain of PAdV-B,named PAdV-BHNU1,in porcine samples collected in China by viral metagenomic assay and general PCR.The genome of PAdV-BHNU1 is 31,743 bp in length and highly similar to that of California sea lion adenovirus 1(C.sea lion AdV-1),which contains typical mastadenoviral structures and some unique regions at the carboxy-terminal end.Especially,PAdV-BHNU1 harbors a dUTPase coding region not clustering with other mastadenoviruses except for C.sea lion AdV-1 and afiber coding region homologous with galectin 4 and 9 of animals.However,the variance of GC contents between PAdV-BHNU1(55%)and C.sea lion AdV-1(36%)indicates their differential evolutionary paths.Further epidemiologic study revealed a high positive rate(51.7%)of PAdV-B-HNU1 in porcine lymph samples,but low positive rates of 10.2%and16.1%in oral swabs and rectal swabs,respectively.In conclusion,this study characterized a novel representative genome of a lymphotropic PAdV-B with unique evolutionary origin,which contributes to the taxonomical and pathogenic studies of PAdVs.

Coexistence of multiple coronaviruses in several bat colonies in an abandoned mineshaft

Since the 2002–2003 severe acute respiratory syndrome(SARS) outbreak prompted a search for the natural reservoir of the SARS coronavirus, numerous alpha- and betacoronaviruses have been discovered in bats around the world. Bats are likely the natural reservoir of alpha- and betacoronaviruses, and due to the rich diversity and global distribution of bats, the number of bat coronaviruses will likely increase. We conducted a surveillance of coronaviruses in bats in an abandoned mineshaft in Mojiang County, Yunnan Province, China, from 2012–2013. Six bat species were frequently detected in the cave: Rhinolophus sinicus, Rhinolophus affinis, Hipposideros pomona, Miniopterus schreibersii, Miniopterus fuliginosus, and Miniopterus fuscus. By sequencing PCR products of the coronavirus RNA-dependent RNA polymerase gene(Rd Rp), we found a high frequency of infection by a diverse group of coronaviruses in different bat species in the mineshaft. Sequenced partial Rd Rp fragments had 80%–99% nucleic acid sequence identity with well-characterized Alphacoronavirus species, including Bt CoV HKU2, Bt CoV HKU8, and Bt CoV1,and unassigned species Bt CoV HKU7 and Bt CoV HKU10. Additionally, the surveillance identified two unclassified betacoronaviruses, one new strain of SARS-like coronavirus, and one potentially new betacoronavirus species. Furthermore, coronavirus co-infection was detected in all six bat species, a phenomenon that fosters recombination and promotes the emergence of novel virus strains. Our findings highlight the importance of bats as natural reservoirs of coronaviruses and the potentially zoonotic source of viral pathogens.

Cross-neutralization of SARS coronavirus-specific antibodies against bat SARS-like coronaviruses

Dear Editor,The 2002–2003 global pandemic caused by severe acute respiratory syndrome coronavirus(SARS-CoV)infected around 8,000 people with 10%mortality(http://www.who.int/csr/sars/en/).The virus has a positivestranded RNA genome that encodes a large polyprotein(1a and 1ab),four structural proteins,including spike(S),

Longitudinal surveillance of SARS-like coronaviruses in bats by quantitative real-time PCR

Dear Editor,The 2002–2003 severe acute respiratory syndrome coronavirus(SARS-CoV)(Drosten et al.,2003)caused human pandemics that began in China and spread globally.Subsequently,diverse SARS-like

Identification of a novel strain of influenza A (H9N2) virus in chicken

Dear Editor,Avian Influenza virus(AIV)H9N2 subtype viruses circulate widely in domestic fowl,and usually cause mild clinical signs in poultry(Li et al.,2005).Occasionally,avian H9N2 can infect humans and cause mild clinical symptoms(Peiris et al.,1999;Lin et al.,2000).Genetic analysis indicates that the H9N2 genotype viruses exist in major poultry species(such as duck and chicken)and in minor poultry species(such as quail,partridge,chukar,pheasant,and guinea fowl)(Guan et al.,2000;Li et al.,2005).Meanwhile,frequent reassortment events

Cloning, expression, and antiviral activity of interferon β from the Chinese microbat, Myotis davidii

Bats are natural reservoir hosts for many viruses that produce no clinical symptoms in bats.Therefore, bats may have evolved effective mechanisms to control viral replication. However, little information is available on bat immune responses to viral infection. Type I interferon(IFN) plays a key role in controlling viral infections. In this study, we report the cloning, expression, and biological activity of interferon β(IFNβ) from the Chinese microbat species, Myotis davidii. We demonstrated the upregulation of IFNB and IFN-stimulated genes in a kidney cell line derived from M. davidii after treatment with poly I:C or infection with Sendai virus. Furthermore, the recombinant IFNβ inhibited vesicular stomatitis virus and bat adenovirus replication in cell lines from two bat species, M. davidii and Rhinolophus sinicus. We provide the first in vitro evidence of IFNβ antiviral activity in microbats, which has important implications for virus interactions with these hosts.

Molecular detection of viruses in Kenyan bats and discovery of novel astroviruses, caliciviruses and rotaviruses

This is the first country-wide surveillance of bat-borne viruses in Kenya spanning from 2012–2015covering sites perceived to have medium to high level bat-human interaction. The objective of this surveillance study was to apply a non-invasive approach using fresh feces to detect viruses circulating within the diverse species of Kenyan bats. We screened for both DNA and RNA viruses;specifically, astroviruses(AstVs), adenoviruses(ADVs), caliciviruses(CalVs), coronaviruses(CoVs), flaviviruses, filoviruses, paramyxoviruses(PMVs), polyomaviruses(PYVs) and rotaviruses.We used family-specific primers, amplicon sequencing and further characterization by phylogenetic analysis. Except for filoviruses, eight virus families were detected with varying distributions and positive rates across the five regions(former provinces) studied. AstVs(12.83%), CoVs(3.97%), PMV(2.4%), ADV(2.26%), PYV(1.65%), CalVs(0.29%), rotavirus(0.19%) and flavivirus(0.19%). Novel CalVs were detected in Rousettus aegyptiacus and Mops condylurus while novel Rotavirus-A-related viruses were detected in Taphozous bats and R. aegyptiacus. The two Rotavirus A(RVA) strains detected were highly related to human strains with VP6 genotypes I2 and I16. Genotype I16 has previously been assigned to human RVA-strain B10 from Kenya only, which raises public health concern, particularly considering increased human-bat interaction.Additionally, 229E-like bat CoVs were detected in samples originating from Hipposideros bats roosting in sites with high human activity. Our findings confirm the presence of diverse viruses in Kenyan bats while providing extended knowledge on bat virus distribution. The detection of viruses highly related to human strains and hence of public health concern, underscores the importance of continuous surveillance.

EVIHVR: A platform for analysis of expression, variation and identification of human virus receptors

Motivation:Virus receptors are presented on the cell surfaces of a host and are key for viral infection of host cells.However,no unified resource for the study of viral receptors is currently available.Results:To address this problem,we built EVIHVR,a platform for analyzing the expression and variation,and for the identification of human virus receptors.EVIHVR provides three functions:(1)Receptor expression function for browsing and analyzing the expression of human virus receptors in various human tissues/cells;(2)Receptor gene polymorphism function for analyzing the genetic polymorphism of human virus receptors in different human populations and human tissues;and(3)Predict receptor function for identifying potential virus receptors based on differential expression analysis.EVIHVR can become a useful tool for the analysis and identification of human virus receptors.

Cross-species transmission and host range genes in poxviruses

The persistent epidemic of human mpox, caused by mpox virus (MPXV), raises concerns about the future spread ofMPXV and other poxviruses. MPXV is a typical zoonotic virus which can infect human and cause smallpox-likesymptoms. MPXV belongs to the Poxviridae family, which has a relatively broad host range from arthropods tovertebrates. Cross-species transmission of poxviruses among different hosts has been frequently reported andresulted in numerous epidemics. Poxviruses have a complex linear double-strand DNA genome that encodeshundreds of proteins. Genes related to the host range of poxvirus are called host range genes (HRGs). This reviewbriefly introduces the taxonomy, phylogeny and hosts of poxviruses, and then comprehensively summarizes thecurrent knowledge about the cross-species transmission of poxviruses. In particular, the HRGs of poxvirus aredescribed and their impacts on viral host range are discussed in depth. We hope that this review will provide acomprehensive perspective about the current progress of researches on cross-species transmission and HRGvariation of poxviruses, serving as a valuable reference for academic studies and disease control in the future.