2023 Vol.38(6)

In recent decades, bats have been identified as natural hosts of various zoonotic viruses. Bat-borne viruses, directly or indirectly spilling into human society, have caused numerous devastating outbreaks. To prevent future pandemics, it is crucial to conduct long-term epidemiological surveys on natural reservoirs that have close interactions with humans and livestock. In this issue, Guo et al. investigated the molecular characteristics and genetic diversity of coronaviruses discovered in different bat species from southern China. Two representative full-length genomes of bat CoVs were obtained, which share the highest identity with pangolin HKU4-related coronaviruses. One of the strains has a putative furin protease cleavage site in its S protein and is likely to utilize human dipeptidyl peptidase-4 as a cell-entry receptor. This is the first report of a bat HKU4-related-CoV strain containing a furin protease cleavage site. The cover image depicts the greater bamboo bat sharing its habitat with other wild animals that live near human villages and have frequent interactions with humans, livestock, and poultry. (Kindly designed and provided by Prof. Libiao Zhang). See page 868–876 for details.

Review Articles

Reverse genetics systems for SARS-CoV-2: Development and applications

Hou-Li Cai, Yao-Wei Huang

2023, 38(6): 837 doi: 10.1016/j.virs.2023.10.001

Received: 09 July 2023 Accepted: 07 October 2023
Abstract [PDF 1843 KB] ScienceDirect
The recent emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused serious harm to human health and struck a blow to global economic development. Research on SARS-CoV-2 has greatly benefited from the use of reverse genetics systems, which have been established to artificially manipulate the viral genome, generating recombinant and reporter infectious viruses or biosafety level 2 (BSL-2)-adapted non-infectious replicons with desired modifications. These tools have been instrumental in studying the molecular biological characteristics of the virus, investigating antiviral therapeutics, and facilitating the development of attenuated vaccine candidates. Here, we review the construction strategies, development, and applications of reverse genetics systems for SARS-CoV-2, which may be applied to other CoVs as well.

Recent advances in understanding T cell activation and exhaustion during HBV infection

Lu Wang, Xiaoqing Zeng, Zida Wang, Ling Fang, Jia Liu

2023, 38(6): 851 doi: 10.1016/j.virs.2023.10.007

Received: 04 July 2023 Accepted: 18 October 2023
Abstract [PDF 617 KB] ScienceDirect
Chronic hepatitis B virus (HBV) infection remains a major public health concern globally, and T cell responses are widely believed to play a pivotal role in mediating HBV clearance. Accordingly, research on the characteristics of HBV-specific T cell responses, from activation to exhaustion, has advanced rapidly. Here, we summarize recent developments in characterizing T cell immunity in HBV infection by reviewing basic and clinical research published in the last five years. We provide a comprehensive summary of the mechanisms that induce effective anti-HBV T cell immunity, as well as the latest developments in understanding T cell dysfunction in chronic HBV infection. Furthermore, we briefly discuss current novel treatment strategies aimed at restoring anti-HBV T cell responses.
Research Articles

First detection of cutavirus DNA in stools of patients with rheumatic diseases in Guangzhou, China

Yongzhi Li, Liting Zheng, Huan He, Husheng Xiong, Jiaqi Chen, Hengbiao Sun, Caiyun Chen, Qiushuang Li, Jiaqi Fu, Fei Wu, Yuhan Gao, Juxian Xian, Minyi Liang, Gang Xiao, Qing Chen

2023, 38(6): 860 doi: 10.1016/j.virs.2023.10.006

Received: 13 February 2023 Accepted: 08 October 2023
Abstract [PDF 1332 KB] ScienceDirectESM
Cutavirus (CuV) is a novel protoparvovirus possibly associated with diarrhea and cutaneous T-cell lymphomas. Patients with rheumatic disease are immunosuppressed and may be more vulnerable to pathogenic viruses. A descriptive study was conducted among hospitalized patients with rheumatic diseases and individuals undergoing medical health check-ups between June 2019 and June 2022 in Guangzhou, China. Stool samples of subjects were tested for CuV DNA. Demographic and fecal examination data of patients were obtained from electronic medical records. A total of 505 patients with rheumatic diseases and 244 individuals who underwent medical health check-ups were included in the study. Of the patients with rheumatic disease, 5.74% [95% confidence interval (CI): 4.03%–8.12%] were positive for CuV DNA, while no individual in the medical health check-up group was positive, indicating a close correlation between CuV and rheumatic disease. Men and patients with rheumatoid arthritis or ankylosing spondylitis, according to the disease classification, were more susceptible to being infected with CuV (P < 0.01). After adjustments, being male remained the only significant factor, with an adjusted odd ratio (OR) of 4.4 (95% CI: 1.7–11.4, P = 0.002). Phylogenetic analysis of the CuV VP2 sequences showed three diverse clades, one of which was segregated to be a single branching independent of previously known sequences, which is possible a new genotype.

Pangolin HKU4-related coronaviruses found in greater bamboo bats from southern China

Min Guo, Kai Zhao, Xingwen Peng, Xiangyang He, Jin Deng, Bo Wang, Xinglou Yang, Libiao Zhang

2023, 38(6): 868 doi: 10.1016/j.virs.2023.11.003

Received: 10 April 2023 Accepted: 10 November 2023
Abstract [PDF 2903 KB] ScienceDirectESM
Coronavirus (CoV) spillover originating from game animals, particularly pangolins, is currently a significant concern. Meanwhile, vigilance is urgently needed for coronaviruses carried by bats, which are known as natural reservoirs of many coronaviruses. In this study, we collected 729 anal swabs of 20 different bat species from nine locations in Yunnan and Guangdong provinces, southern China, in 2016 and 2017, and described the molecular characteristics and genetic diversity of alphacoronaviruses (αCoVs) and betacoronaviruses (βCoVs) found in these bats. Using RT-PCR, we identified 58 (8.0%) bat CoVs in nine bat species from six locations. Furthermore, using the Illumina platform, we obtained two representative full-length genomes of the bat CoVs, namely TyRo-CoV-162275 and TyRo-CoV-162269. Sequence analysis showed that TyRo-CoV-162275 shared the highest identity with Malayan pangolin (Manis javanica) HKU4-related coronaviruses (MjHKU4r-CoVs) from Guangxi Province, whereas TyRo-CoV-162269 was closely related to HKU33-CoV discovered in a greater bamboo bat (Tylonycteris robustula) from Guizhou Province. Notably, TyRo-CoV-162275 has a putative furin protease cleavage site in its S protein and is likely to utilize human dipeptidyl peptidase-4 (hDPP4) as a cell-entry receptor, similar to MERS-CoV. To the best of our knowledge, this is the first report of a bat HKU4r-CoV strain containing a furin protease cleavage site. These findings expand our understanding of coronavirus geographic and host distributions.

The genomic characteristics and pathogenicity of a mammalian orthoreovirus within a new lineage from wild pika in plateau

Kexin Zong, Yuanyuan Guo, Jingdong Song, Maoshun Liu, Junfeng Hao, Jie Zhang, Xin Li, Shiyan Zhu, Shuting Huo, Ziqian Xu, Peipei Liu, Yingze Zhao, Yuhai Bi, Jiapeng Qu, George F. Gao, Jun Liu

2023, 38(6): 877 doi: 10.1016/j.virs.2023.11.001

Received: 08 June 2023 Accepted: 03 November 2023
Abstract [PDF 13094 KB] ScienceDirectESM
Emerging and re-emerging viruses from wild animals have seriously threatened the health of humans and domesticated animals in recent years. Herein, we isolated a new mammalian orthoreovirus (MRV), Pika/MRV/GCCDC7/2019 (PMRV-GCCDC7), in the Qinghai-Tibet Plateau wild pika (Ochotona curzoniae). Though the PMRV-GCCDC7 shows features of a typical reovirus with ten gene segments arranged in 3:3:4 in length, the virus belongs to an independent evolutionary branch compared to other MRVs based on phylogenetic tree analysis. The results of cellular susceptibility, species tropism, and replication kinetics of PMRV-GCCDC7 indicated the virus could infect four human cell lines (A549, Huh7, HCT, and LoVo) and six non-human cell lines, including Vero-E6, LLC-MK2, BHK-21, N2a, MDCK, and RfKT cell, derived from diverse mammals, i.e. monkey, mice, canine and bat, which revealed the potential of PMRV-GCCDC7 to infect a variety of hosts. Infection of BALB/c mice with PMRV-GCCDC7 via intranasal inoculation led to relative weight loss, lung tissue damage and inflammation with the increase of virus titer, but no serious respiratory symptoms and death occurred. The characterization of the new reovirus from a plateau-based wild animal has expanded our knowledge of the host range of MRV and provided insight into its risk of trans-species transmission and zoonotic diseases.

Genotype analysis of rotaviruses isolated from children during a phase III clinical trial with the hexavalent rotavirus vaccine in China

Wenqi Zou, Qingchuan Yu, Yan Liu, Qingliang Li, Hong Chen, Jiamei Gao, Chen Shi, Ying Wang, Wei Chen, Xuan Bai, Biao Yang, Jiuwei Zhang, Ben Dong, Bo Ruan, Liuyifan Zhou, Gelin Xu, Zhongyu Hu, Xiaoming Yang

2023, 38(6): 889 doi: 10.1016/j.virs.2023.11.002

Received: 02 February 2023 Accepted: 09 November 2023
Abstract [PDF 4594 KB] ScienceDirect ESM
The oral hexavalent live human-bovine reassortant rotavirus vaccine (RV6) developed by Wuhan Institute of Biological Products Co., Ltd (WIBP) has finished a randomized, placebo-controlled phase III clinical trial in four provinces of China in 2021. The trail demonstrated that RV6 has a high vaccine efficacy against the prevalent strains and is safe for use in infants. During the phase III clinical trial (2019–2021), 200 rotavirus-positive fecal samples from children with RV gastroenteritis (RVGE) were further studied. Using reverse transcription-polymerase chain reaction and high-throughput sequencing, VP7 and VP4 sequences were obtained and their genetic characteristics, as well as the differences in antigenic epitopes of VP7, were analyzed in detail. Seven rotavirus genotypes were identified. The predominant rotavirus genotype was G9P [8] (77.0%), followed by prevalent strains G8P [8] (8.0%), G3P [8] (3.5%), G3P [9] (1.5%), G1P [8] (1.0%), G2P [4] (1.0%), and G4P [6] (1.0%). The amino acid sequence identities of G1, G2, G3, G4, G8, and G9 genotypes of isolates compared to the vaccine strains were 98.8%, 98.2%–99.7%, 88.4%–99.4%, 98.2%, 94.2%–100%, and 93.9%–100%, respectively. Notably, the vaccine strains exhibited high similarity in amino acid sequence, with only minor differences in antigenic epitopes compared to the Chinese endemic strains. This supports the potential application of the vaccine in preventing diseases caused by rotaviruses.

Classical swine fever virus NS5A protein antagonizes innate immune response by inhibiting the NF-κB signaling

Jinfu Sun, Jiaying Li, Liming Li, Haixiao Yu, Ping Ma, Yingnan Wang, Jinqi Zhu, Zezhong Feng, Changchun Tu

2023, 38(6): 900 doi: 10.1016/j.virs.2023.09.002

Received: 11 February 2023 Accepted: 08 September 2023
Abstract [PDF 2517 KB] ScienceDirectESM
The NS5A non-structural protein of classical swine fever virus (CSFV) is a multifunctional protein involved in viral genomic replication, protein translation, assembly of infectious virus particles, and regulation of cellular signaling pathways. Previous report showed that NS5A inhibited nuclear factor kappa B (NF-κB) signaling induced by poly(I:C); however, the mechanism involved has not been elucidated. Here, we reported that NS5A directly interacted with NF-κB essential modulator (NEMO), a regulatory subunit of the IκB kinase (IKK) complex, to inhibit the NF-κB signaling pathway. Further investigations showed that the zinc finger domain of NEMO and the aa 126–250 segment of NS5A are essential for the interaction between NEMO and NS5A. Mechanistic analysis revealed that NS5A mediated the proteasomal degradation of NEMO. Ubiquitination assay showed that NS5A induced the K27-linked but not the K48-linked polyubiquitination of NEMO for proteasomal degradation. In addition, NS5A blocked the K63-linked polyubiquitination of NEMO, thus inhibiting IKK phosphorylation, IκBα degradation, and NF-κB activation. These findings revealed a novel mechanism by which CSFV inhibits host innate immunity, which might guide the drug design against CSFV in the future.

African swine fever virus S273R protein antagonizes type I interferon production by interfering with TBK1 and IRF3 interaction

Hui Li, Xiaojie Zheng, You Li, Yingqi Zhu, Yangyang Xu, Zilong Yu, Wen-Hai Feng

2023, 38(6): 911 doi: 10.1016/j.virs.2023.08.009

Received: 09 March 2023 Accepted: 28 August 2023
Abstract [PDF 3445 KB] ScienceDirectESM
African swine fever (ASF) is originally reported in East Africa as an acute hemorrhagic fever. African swine fever virus (ASFV) is a giant and complex DNA virus with icosahedral structure and encodes a variety of virulence factors to resist host innate immune response. S273R protein (pS273R), as a SUMO-1 specific cysteine protease, can affect viral packaging by cutting polymeric proteins. In this study, we found that pS273R was an important antagonistic viral factor that suppressed cGAS-STING-mediated type I interferon (IFN-I) production. A detailed analysis showed that pS273R inhibited IFN-I production by interacting with interferon regulatory factor 3 (IRF3). Subsequently, we showed that pS273R disrupted the association between TBK1 and IRF3, leading to the repressed IRF3 phosphorylation and dimerization. Deletion and point mutation analysis verified that pS273R impaired IFN-I production independent of its cysteine protease activity. These findings will help us further understand ASFV pathogenesis.

Ebola virus VP35 perturbs type I interferon signaling to facilitate viral replication

Zengguo Cao, Chenchen Liu, Cheng Peng, Yong Ran, Yulin Yao, Gengfu Xiao, Entao Li, Zixi Chen, Xia Chuai, Sandra Chiu

2023, 38(6): 922 doi: 10.1016/j.virs.2023.10.004

Received: 13 June 2023 Accepted: 08 October 2023
Abstract [PDF 2385 KB] ScienceDirectESM
As one of the deadliest viruses, Ebola virus (EBOV) causes lethal hemorrhagic fevers in humans and nonhuman primates. The suppression of innate immunity leads to robust systemic virus replication of EBOV, leading to enhanced transmission. However, the mechanism of EBOV-host interaction is not fully understood. Here, we identified multiple dysregulated genes in early stage of EBOV infection through transcriptomic analysis, which are highly clustered to Jak-STAT signaling. EBOV VP35 and VP30 were found to inhibit type I interferon (IFN) signaling. Moreover, exogenous expression of VP35 blocks the phosphorylation of endogenous STAT1, and suppresses nuclear translocation of STAT1. Using serial truncated mutations of VP35, N-terminal 1–220 amino acid residues of VP35 were identified to be essential for blocking on type I IFN signaling. Remarkably, VP35 of EBOV suppresses type I IFN signaling more efficiently than those of Bundibugyo virus (BDBV) and Marburg virus (MARV), resulting in stable replication to facilitate the pathogenesis. Altogether, this study enriches understanding on EBOV evasion of innate immune response, and provides insights into the interplay between filoviruses and host.

Allopregnanolone targets nucleoprotein as a novel influenza virus inhibitor

Meiyue Dong, Yanyan Wang, Ping Li, Zinuo Chen, Varada Anirudhan, Qinghua Cui, Lijun Rong, Ruikun Du

2023, 38(6): 931 doi: 10.1016/j.virs.2023.09.003

Received: 11 June 2023 Accepted: 19 September 2023
Abstract [PDF 2555 KB] ScienceDirectESM
Influenza A virus (IAV) poses a global public health concern and remains an imminent threat to human health. Emerging antiviral resistance to the currently approved influenza drugs emphasizes the urgent need for new therapeutic entities against IAV. Allopregnanolone (ALLO) is a natural product that has been approved as an antidepressant drug. In the present study, we repurposed ALLO as a novel inhibitor against IAVs. Mechanistic studies demonstrated that ALLO inhibited virus replication by interfering with the nucleus translocation of viral nucleoprotein (NP). In addition, ALLO showed significant synergistic activity with compound 16, a hemagglutinin inhibitor of IAVs. In summary, we have identified ALLO as a novel influenza virus inhibitor targeting NP, providing a promising candidate that deserves further investigation as a useful anti-influenza strategy in the future.

Myocardial injury and related mortality in hospitalized patients with COVID-19 during the Omicron pandemic: new perspectives and insights

Wu He, Ke Xu, Li Ni, Junfang Wu, Yuxuan Zhang, Kun Miao, Luyun Wang, Dao Wen Wang

2023, 38(6): 940 doi: 10.1016/j.virs.2023.10.005

Received: 04 July 2023 Accepted: 09 October 2023
Abstract [PDF 2266 KB] ScienceDirectESM
Myocardial injury is one of the most common comorbidity in SARS-CoV-2 infected patients, and has poor prognosis. However, the incidence of myocardial injury in patients with SARS-CoV-2 infection has not been sufficiently investigated during the Omicron wave. We conducted a retrospective study of 2690 patients with confirmed SARS-CoV-2 Omicron infection from Tongji Hospital. The results indicated that the myocardial injury accounted for 30.8% of the total patients with SARS-CoV-2 infection and was associated with higher in-hospital mortality than those without injury before and after propensity score matching (PSM) [adjusted hazard ratio (HR), 10.61; 95% confidence interval (CI), 7.76–14.51; P < 0.001; adjusted HR, 2.70; 95% CI, 1.86–3.93; P < 0.001; respectively]. Further, the levels of cytokines (IL-1β, IL-6, IL-10, and TNF-α) in patients with myocardial injury were higher than those without injury, and the higher levels of cytokines in the myocardial injury group were associated with increased mortality. Administration of angiotensin-converting enzyme inhibitors or angiotensin receptor blockers (ACEI/ARB) could significantly reduce the mortality in patients with myocardial injury (adjusted HR, 0.52; 95% CI, 0.38–0.71; P < 0.001). Additionally, the level of angiotensin II increased in patients with SARS-CoV-2 infection was even higher in myocardial injury group compared to those without injury. Collectively, the study summarized the clinical characteristic and outcome of SARS-CoV-2 infected patients with myocardial injury during the Omicron wave in China, and validated the protective role of ACEI/ARB in improving the survival of those with myocardial injury.

Equine ANP32 proteins support influenza A virus RNA polymerase activity

Yuan Zhang, Xing Guo, Mengmeng Yu, Liuke Sun, Yuxing Qu, Kui Guo, Zhe Hu, Diqiu Liu, Haili Zhang, Xiaojun Wang

2023, 38(6): 951 doi: 10.1016/j.virs.2023.10.009

Received: 14 May 2023 Accepted: 23 October 2023
Abstract [PDF 2346 KB] ScienceDirectESM
Host ANP32 family proteins are crucial for maintaining the activity of influenza RNA polymerase and play an important role in the cross-species transmission of influenza viruses. To date, the molecular properties of equine ANP32 (eqANP32) protein are poorly understood, particularly the mechanisms that affect equine influenza virus (EIV) RNA polymerase activity. Here, we found that there are six alternative splicing variants of equine ANP32A (eqANP32A) with different levels of expression. Further studies showed that these six splicing variants of eqANP32A supported the activity of EIV RNA polymerase to varying degrees, with the variant eqANP32A_X2 having the highest expression abundance and exhibiting the highest support of polymerase activity. Sequence analysis demonstrated that the differences in the N-Cap regions of the six splicing variants significantly affected their N-terminal conformation, but did not affect their ability to bind RNA polymerase. We also demonstrated that there is only one transcript of eqANP32B, and that this transcript showed only very low support to the EIV RNA polymerase. This functional defect in eqANP32B is caused by the sequence of the 110–259 amino acids at its C-terminus. Our results indicated that it is the eqANP32A_X2 protein that mainly determines the efficiency of the EIV replication in horses. In conclusion, our study parsed the molecular properties of eqANP32 family proteins and revealed the sequence features of eqANP32A and eqANP32B, suggesting for the first time that the N-Cap region of ANP32A protein also plays an important role in supporting the activity of the influenza virus polymerase.

Diversity analysis of tick-associated viruses in northeast China

Yang Li, Yu Bai, Wenli Liu, Jing Li, Fengjuan Tian, Xiaohu Han, Lei Liu, Yigang Tong

2023, 38(6): 961 doi: 10.1016/j.virs.2023.10.003

Received: 13 May 2023 Accepted: 08 October 2023
Abstract [PDF 1489 KB] ScienceDirect ESM
1. This study identified eleven tick-borne viruses in Liaoning Province and Inner Mongolia, China, which greatly enrich the diversity of tick-borne virus.
2. Tacheng tick virus 2 is for the first time detected outside Xinjiang and in a novel tick species D. niveus.
3. The Alongshan virus and Tacheng tick virus 2 identified in this study can be considered as novel species.

Isolation and characterization of Akabane virus Ib substrain and its pathogenesis in sulking mice

Xiaohui Zan, Shirong Wang, Tianqi Zhang, Ying Li, Chunge Zhang, Cun Fu, Jialei Wang, Youzhi Wu, Yanhua Ma, Zhifei Li, Yan Wang, Hao Wang, Yuhai Bi, Wei Wang

2023, 38(6): 966 doi: 10.1016/j.virs.2023.09.006

Received: 15 October 2022 Accepted: 28 September 2023
Abstract [PDF 2926 KB] ScienceDirectESM
1. A novel Akabane virus strain LK07 was isolated from cattle.
2. Here, we firstly reported the identification and isolation of the Akabane virus sub-lineage genogroup Ib in China.
3. The suckling mice showed clinical symptoms after intracerebrally infected with LK07 strain.
4. Viral antigen was detected in brain of mice infected with LK07 strain via IC, IP and SC routes.

Direct infection of SARS-CoV-2 in human iPSC-derived 3D cardiac organoids recapitulates COVID-19 myocarditis

Weijie Wang, Jinxuan Yang, Pinfang Kang, Jinsong Bai, Xiaoli Feng, Liuqi Huang, Yiming Zhang, Yuechun Wu, Bi Tang, Hongju Wang, JianJie Jiang, Minghua Li, Bing Zhao, Xinglou Yang

2023, 38(6): 971 doi: 10.1016/j.virs.2023.09.005

Received: 07 July 2023 Accepted: 27 September 2023
Abstract [PDF 2972 KB] ScienceDirect ESM
1. Establishment of 3D cardiac organoids composed of cardiomyocyte and endothelial layers.
2. SARS-CoV-2 infection causes multi-lineage cardiac injuries.
3. Cardiovascular health should be greatly concerned in COVID-19 patients.

Structural insight into EV-A71 3A protein and its interaction with a peptide inhibitor

Yahui Liu, Panjing Lv, Wei Wang, Jiahai Zhang, Xi Zhou, Yang Qiu, Kun Cai, Haoran Zhang, Yuan Fang, Yan Li

2023, 38(6): 975 doi: 10.1016/j.virs.2023.09.004

Received: 07 July 2023 Accepted: 22 September 2023
Abstract [PDF 1298 KB] ScienceDirectESM
1. Our results disclosed a dihelical structure of Enterovirus A71 3A1-57 protein in apo form.
2. We depicted rigid helices and a unique flexible C-terminus for apo-form 3A1-57.
3. This study revealed a competitive binding-based molecular mechanism underlying inhibition of dimeric 3A by ER-DRI.