virus evolution
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2022 ◽  
Author(s):  
Sonalika Mahajan ◽  
Karikalan Mathesh ◽  
Vishal Chander ◽  
Abhijit M Pawde ◽  
G Saikumar ◽  
...  

We report patho-morphological and virological characterization of SARS-CoV-2 in naturally infected, free ranging Indian Leopard (Panthera pardus fusca). Whole genome sequence analysis confirmed infection of Delta variant of SARS-CoV-2, possibly spill over from humans, but the case was detected when infection level had dropped significantly in human population. This report underlines the need for intensive screening of wild animals for keeping track of the virus evolution and development of carrier status of SARS-CoV-2 among wildlife species.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jiaan Yang ◽  
Peng Zhang ◽  
Wen Xiang Cheng ◽  
Youyong Lu ◽  
Wu Gang ◽  
...  

AbstractThe mutation of SARS-CoV-2 influences viral function as residue replacements affect both physiochemical properties and folding conformations. Although a large amount of data on SARS-CoV-2 is available, the investigation of how viral functions change in response to mutations is hampered by a lack of effective structural analysis. Here, we exploit the advances of protein structure fingerprint technology to study the folding conformational changes induced by mutations. With integration of both protein sequences and folding conformations, the structures are aligned for SARS-CoV to SARS-CoV-2, including Alpha variant (lineage B.1.1.7) and Delta variant (lineage B.1.617.2). The results showed that the virus evolution with change in mutational positions and physicochemical properties increased the affinity between spike protein and ACE2, which plays a critical role in coronavirus entry into human cells. Additionally, these structural variations impact vaccine effectiveness and drug function over the course of SARS-CoV-2 evolution. The analysis of structural variations revealed how the coronavirus has gradually evolved in both structure and function and how the SARS-CoV-2 variants have contributed to more severe acute disease worldwide.


2021 ◽  
Vol 43 (3) ◽  
pp. 1937-1949
Author(s):  
Laura A. E. Van Poelvoorde ◽  
Mathieu Gand ◽  
Marie-Alice Fraiture ◽  
Sigrid C. J. De Keersmaecker ◽  
Bavo Verhaegen ◽  
...  

The worldwide emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) since 2019 has highlighted the importance of rapid and reliable diagnostic testing to prevent and control the viral transmission. However, inaccurate results may occur due to false negatives (FN) caused by polymorphisms or point mutations related to the virus evolution and compromise the accuracy of the diagnostic tests. Therefore, PCR-based SARS-CoV-2 diagnostics should be evaluated and evolve together with the rapidly increasing number of new variants appearing around the world. However, even by using a large collection of samples, laboratories are not able to test a representative collection of samples that deals with the same level of diversity that is continuously evolving worldwide. In the present study, we proposed a methodology based on an in silico and in vitro analysis. First, we used all information offered by available whole-genome sequencing data for SARS-CoV-2 for the selection of the two PCR assays targeting two different regions in the genome, and to monitor the possible impact of virus evolution on the specificity of the primers and probes of the PCR assays during and after the development of the assays. Besides this first essential in silico evaluation, a minimal set of testing was proposed to generate experimental evidence on the method performance, such as specificity, sensitivity and applicability. Therefore, a duplex reverse-transcription droplet digital PCR (RT-ddPCR) method was evaluated in silico by using 154 489 whole-genome sequences of SARS-CoV-2 strains that were representative for the circulating strains around the world. The RT-ddPCR platform was selected as it presented several advantages to detect and quantify SARS-CoV-2 RNA in clinical samples and wastewater. Next, the assays were successfully experimentally evaluated for their sensitivity and specificity. A preliminary evaluation of the applicability of the developed method was performed using both clinical and wastewater samples.


Science ◽  
2021 ◽  
Vol 374 (6564) ◽  
pp. 182-188
Author(s):  
Arthur Kocher ◽  
Luka Papac ◽  
Rodrigo Barquera ◽  
Felix M. Key ◽  
Maria A. Spyrou ◽  
...  

Author(s):  
Alexander L. Greninger ◽  
Ksenia Rybkina ◽  
Michelle J. Lin ◽  
Jennifer Drew-Bear ◽  
Tara C. Marcink ◽  
...  

2021 ◽  
Author(s):  
Alba Torrents de la Peña ◽  
Iván del Moral Sánchez ◽  
Judith A. Burger ◽  
Ilja Bontjer ◽  
Gözde Isik ◽  
...  

The HIV-1 envelope glycoprotein (Env) trimer is responsible for viral entry into target cells and is the sole target of neutralizing antibodies. The Env protein is therefore the focus of HIV-1 vaccine design. Env consists of two non-covalently linked subunits (gp120 and gp41) that form a trimer of heterodimers and this 6-subunit complex is metastable and conformationally flexible. Several approaches have been pursued to stabilize the Env trimer for vaccine purposes, which include structure-based design, high-throughput screening and selection by mammalian cell display. Here, we employed directed virus evolution to improve Env trimer stability. Accordingly, we deliberately destabilized the Env gp120-gp41 interface by mutagenesis in the context of replicating HIV-1 LAI virus and virus evolution over time. We identified compensatory changes that pointed at convergent evolution as they were largely restricted to specific Env regions, namely the V1V2-domain of gp120, and the the HR1 and HR2 domain of gp41. Specifically, S614G in V1V2 and Q567R in HR1 were frequently identified. Interestingly, the majority of the compensatory mutations were at distant locations from the original mutations and most likely strengthen inter-subunit interactions. These results show how the virus can overcome Env instability and illuminate the regions that play a dominant role in Env stability. Importance A successful HIV-1 vaccine most likely requires an envelope glycoprotein (Env) component, as the Env is the only viral protein on the surface of the virus and the target for neutralizing antibodies. However, HIV Env is metastable and flexible because of the weak interactions between the Env subunits, complicating the generation of recombinant mimics of native Env. Here, we used directed viral evolution to study Env stability. We deliberately destabilized the interface between Env subunits and explored the capacity of the virus to repair trimer instability by evolution. We identified compensatory mutations that converged in specific Env locations: the apex and the trimer interface. Selected mutations enhanced the stability of recombinant soluble Env trimer proteins. These results provided clues on understanding the structural mechanisms involved in Env trimer stability, which can guide future immunogen design.


Author(s):  
Longlong Si ◽  
Haiqing Bai ◽  
Crystal Yuri Oh ◽  
Lei Jin ◽  
Rachelle Prantil-Baun ◽  
...  

The rapid evolution of viruses, such as influenza viruses and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is challenging the use and development of antivirals and vaccines. Studies of within-host viral evolution can contribute to our understanding of the evolutionary and epidemiological factors that shape viral global evolution as well as development of better antivirals and vaccines.


2021 ◽  
Author(s):  
NARENDRAN PRADEEP KUMAR ◽  
PRASANTA SAINI ◽  
PHILIP SAMUEL ◽  
P.M. AJITHLAL ◽  
ABIDHA SURESH ◽  
...  

Abstract The recent global outbreaks of the ZIKA Virus (ZIKV) reported in 85 countries and territories caused severe complications such as microcephaly among neonates and Guillain-Barre Syndrome among the older population. Recently, an outbreak of ZIKV was reported from Thiruvananthapuram, the capital city of Kerala, India with 66 cases being reported so far. We conducted an outbreak investigation and the primary findings are described here. A cluster of ZIKV cases from the Kadakampalli / Anamugham administrative wards of the Thiruvananthapuram Municipal Corporation area was reported where Kerala Institute of Medical Sciences (KIMS) is located. Later many ZIKV cases were reported from other wards of the city. The density of known Aedes vectors was high in this region of the metropolitan city. Aedes albopictus, Aedes aegypti and Aedes vittatus collected from the focal area of the outbreak were found to be naturally infected with ZIKV. Male specimens of Ae. albopictus were naturally infected, indicating trans-ovarian transmission of the virus. This is first report of incrimination of Ae. albopictus and Ae. vittatus in ZIKV transmission from India. The virus was characterized and the partial sequences clustered with the Asian strain of ZIKV reported from India. The NS5 sequences of human and Ae. albopictus pools from Thiruvananthapuram were 100% similar indicating an ongoing active ZIKV transmission. The state health authorities were sensitized and appropriate containment and vector control measures have been initiated to contain the outbreak. This report underscores the importance of continued human and vector surveillance as well as genomic sequencing to understand the virus evolution and implications on public health.


Viruses ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1827
Author(s):  
Daniel Udenze ◽  
Ivan Trus ◽  
Henry Munyanduki ◽  
Nathalie Berube ◽  
Uladzimir Karniychuk

The host’s immune status may affect virus evolution. Little is known about how developing fetal and placental immune milieus affect virus heterogeneity. This knowledge will help us better understand intra-host virus evolution and how new virus variants emerge. The goal of our study was to find out whether the isolated in utero environment—an environment with specialized placental immunity and developing fetal immunity—supports the emergence of RNA and DNA virus variants. We used well-established porcine models for isolated Zika virus (RNA virus) and porcine circovirus 2 (DNA virus) fetal infections. We found that the isolated in utero environment was conducive to the emergence of RNA and DNA virus variants. Next-generation sequencing of nearly whole virus genomes and validated bioinformatics pipelines identified both unique and convergent single nucleotide variations in virus genomes isolated from different fetuses. Zika virus and PCV2 in utero evolution also resulted in single nucleotide variations previously reported in the human and porcine field samples. These findings should encourage further studies on virus evolution in placenta and fetuses, to better understand how virus variants emerge and how in utero viral evolution affects congenital virus transmission and pathogenicity.


Author(s):  
Minetaro Arita

Each virus has a different strategy for its replication, which requires different host factors. Enterovirus, a model RNA virus, requires host factors PI4KB and OSBP, which form an obligatory functional axis to support viral replication.


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