Virus Isolation Research Articles

Squash vein yellowing virus from California emerged in the Middle East via intragenic and intergeneric recombination events in the hypervariable potyvirus P1 and ipomovirus P1a genes.

We present the complete sequence of the genomic RNA of an isolate of squash vein yellowing virus (Ipomovirus cucurbitavenaflavi) from California (SqVYV-CA) and show it is a recombinant virus with a highly divergent 5' UTR and proximal P1a gene. The evolution of SqVYV-CA involved an intrageneric event between unknown potyviruses, related to isolates of papaya ringspot virus (Potyvirus papayanuli) from the Old World, and an intergeneric event between this recombinant potyvirus (minor parent) and an isolate of SqVYV from Israel (SqVYV-IL) (major parent). These events occurred in mixed infections and in the potyvirus P1 and ipomovirus P1a recombination hotspots and resulted in SqVYV-CA having a potyvirus 5' UTR and chimeric P1-P1a gene/protein and the remainder of the genome from SqVYV-IL. The SqVYV-CA chimeric P1-P1a gene is under positive selection, and the protein is intrinsically disordered and may localize to the nucleus via nuclear localization signals in the P1 part. The C-terminal SqVYV-IL P1a part also diverged but retained the conserved serine protease motif. Furthermore, substantial divergence in SqVYV isolates from the Middle East was associated with genetic drift and a long evolutionary history in this region. The finding that the host range and symptomatology in cucurbits of SqVYV-CA is similar to those of SqVYV from Florida and SqVYV-IL, indicated that the recombinant part of the genome had no obvious effect on the virus-host interaction. A divergent part of the P1 sequence of the SqVYV-CA P1-P1a gene was used to develop a primer pair and RT-PCR test for specific detection of SqVYV-CA. This test was used to detect spread of SqVYV-CA to a new production area of California in 2021 and 2022. Together, these results demonstrate (i) a high level of genetic diversity exists among isolates of SqVYV and involved intra- and intergeneric recombination and genetic drift (mutation), (ii) evidence that SqVYV originated in the Middle East and that there were independent introductions into the New World and (iii) the remarkable genetic flexibility of the 5' proximal genes of these viruses.

Evaluation blackgram and greengram germplasm for resistance against tobacco streak virus (TSV) and peanut bud necrosis virus (PBNV) isolates of blackgram and greengram of Andhra Pradesh under glasshouse conditions

Evaluation blackgram and greengram germplasm for resistance against tobacco streak virus (TSV) and peanut bud necrosis virus (PBNV) isolates of blackgram and greengram of Andhra Pradesh under glasshouse conditions

Survivability of low pathogenic avian influenza virus in aqueous poultry manure fertilizer

Avian influenza has been a growing problem in the United States for decades. Low pathogenic avian influenza (LPAI) virus causes low morbidity, while highly pathogenic avian influenza (HPAI) has a devastating effect on the poultry industry causing high morbidity and mortality worldwide. Manure from large and small poultry operations is spread on crop fields as a fertilizer. During an outbreak of avian influenza in a farm it is critical to adequately process the manure to kill the virus before its use in agriculture. Aqueous extraction of poultry manure at high temperature (55-65°C) is an attractive method for treatment of poultry manure, which extracts the nutrients and kills harmful microbes from the manure. The end product is a nutrient rich liquid that can be safely applied to fields or used in hydroponic operations, with nutrients that are more bioavailable to the plant compared to dry litter. However, we do not know whether aqueous high temperature extraction processes completely kill avian influenza virus present in the manure. Our aim in this study was to determine the competence of the aqueous extraction of poultry manure on avian influenza virus inactivation. We optimized the procedure using a LPAI virus isolate in a biosafety level 2 cabinet. Our data indicated that LPAI virus including the hemagglutinin protein of the virus were completely destroyed when the poultry manure was processed by aqueous extraction at temperatures ≥ 55°C for one hour. Future research will identify the conditions required for inactivating HPAI virus using this optimized procedure by performing the study in a BSL3 facility.

Re-emergence of Oropouche virus between 2023 and 2024 in Brazil: an observational epidemiological study

Oropouche virus is an arthropod-borne virus that has caused outbreaks of Oropouche fever in central and South America since the 1950s. This study investigates virological factors contributing to the re-emergence of Oropouche fever in Brazil between 2023 and 2024. In this observational epidemiological study, we combined multiple data sources for Oropouche virus infections in Brazil and conducted in-vitro and in-vivo characterisation. We collected serum samples obtained in Manaus City, Amazonas state, Brazil, from patients with acute febrile illnesses aged 18 years or older who tested negative for malaria and samples from people with previous Oropouche virus infection from Coari municipality, Amazonas state, Brazil. Basic clinical and demographic data were collected from the Brazilian Laboratory Environment Management System. We calculated the incidence of Oropouche fever cases with data from the Brazilian Ministry of Health and the 2022 Brazilian population census and conducted age-sex analyses. We used reverse transcription quantitative PCR to test for Oropouche virus RNA in samples and subsequently performed sequencing and phylogenetic analysis of viral isolates. We compared the phenotype of the 2023-24 epidemic isolate (AM0088) with the historical prototype strain BeAn19991 through assessment of titre, plaque number, and plaque size. We used a plaque reduction neutralisation test (PRNT50) to assess the susceptibility of the novel isolate and BeAn19991 isolate to antibody neutralisation, both in serum samples from people previously infected with Oropouche virus and in blood collected from mice that were inoculated with either of the strains. 8639 (81·8%) of 10 557 laboratory-confirmed Oropouche fever cases from Jan 4, 2015, to Aug 10, 2024, occurred in 2024, which is 58·8 times the annual median of 147 cases (IQR 73-325). Oropouche virus infections were reported in all 27 federal units, with 8182 (77·5%) of 10 557 infections occurring in North Brazil. We detected Oropouche virus RNA in ten (11%) of 93 patients with acute febrile illness between Jan 1 and Feb 4, 2024, in Amazonas state. AM0088 had a significantly higher replication at 12 h and 24 h after infection in mammalian cells than the prototype strain. AM0088 had a more virulent phenotype than the prototype in mammalian cells, characterised by earlier plaque formation, between 27% and 65% increase in plaque number, and plaques between 2·4-times and 2·6-times larger. Furthermore, serum collected on May 2 and May 20, 2016, from individuals previously infected with Oropouche virus showed at least a 32-fold reduction in neutralising capacity (ie, median PRNT50 titre of 640 [IQR 320-640] for BeAn19991 vs <20 [ie, below the limit of detection] for AM0088) against the reassortant strain compared with the prototype. These findings provide a comprehensive assessment of Oropouche fever in Brazil and contribute to an improved understanding of the 2023-24 Oropouche virus re-emergence. Our exploratory in-vitro data suggest that the increased incidence might be related to a higher replication efficiency of a new Oropouche virus reassortant for which previous immunity shows lower neutralising capacity. São Paulo Research Foundation, Burroughs Wellcome Fund, Wellcome Trust, US National Institutes of Health, and Brazilian National Council for Scientific and Technological Development. For the Portuguese translation of the abstract see Supplementary Materials section.

Correction: Isolation of a feline-derived feline panleukopenia virus with an A300P substitution in the VP2 protein and confirmation of its pathogenicity in dogs

Correction: Isolation of a feline-derived feline panleukopenia virus with an A300P substitution in the VP2 protein and confirmation of its pathogenicity in dogs

Partial Characterisation of Three Isolates of Potato virus Y

Partial Characterisation of Three Isolates of Potato virus Y

Genomes of Alphanucleorhabdovirus Physostegiae Isolates from Two Different Cultivar Groups of Solanum melongena

Plant rhabdoviruses cause considerable economic losses and are a threat to the agriculture of Solanaceae plants. Two novel virus isolates belonging to the family Rhabdoviridae are identified by high-throughput sequencing (HTS) in Russian eggplant cultivars grown in the Volga river delta region for the first time. The phylogenetic inference of L protein (polymerase) shows that these virus isolates belong to Alphanucleorhabdovirus physostegia (Physostegia chlorotic mottle virus—PhCMoV), and their minus-sense RNA genomes have the typical gene order 3′-nucleocapsid (N)—X protein (X)—phosphoprotein (P)—Y protein (Y)—matrix protein (M)—glycoprotein (G)—polymerase (L)-5′ observed in some plant-infecting alphanucleorhabdoviruses. One of the PhCMoV isolates from the eggplant cultivar Almaz is genetically very similar to the Russian PhCMoV isolate from tomato and grouped in a subclade together with four isolates from Belgium, Germany, the Netherlands, and France. However, another eggplant-infecting isolate from the Russian cultivar Boggart is the most divergent compared with the other 45 virus genomes of European PhCMoV isolates. Thus, our comparative analysis reveals that two virus isolates from Russia may either share a close evolutionary relationship with European isolates or significantly diverge from all known virus isolates. The potential to use the protein sequence comparative analysis of accessory polypeptides, along with the early developed strategy of the nucleotide sequence comparison of the RNA genomes, is shown.

Assessment of porcine reproductive and respiratory syndrome virus (PRRSV) farm surface contamination through environmental sampling

BackgroundDuring the fall of 2020, the porcine reproductive and respiratory syndrome virus (PRRSV) L1C.5 variant emerged and rapidly spread throughout southern Minnesota generating questions regarding possible transmission routes. This study aimed to investigate whether PRRSV could be detected on surfaces inside and outside pig barns housing L1C.5 variant PRRSV-positive pigs to illustrate the potential for indirect transmission of PRRSV. Seven Midwestern U.S. PPRS-positive breeding or growing pig farms and one PRRS-negative farm were conveniently selected. Internal and external barn surfaces were wiped using a PBS moistened cloth and the resulting liquid was submitted to the University of Minnesota Veterinary Diagnostic Laboratory for PRRSV RT-PCR testing and virus isolation.ResultsAll (n = 26) samples from PRRSV-negative farm tested negative. Nineteen (13%) out of 143 samples from positive farms yielded positive RT-PCR results. Positive samples originated primarily from exhaust fan cones and doorknobs, followed by anteroom floor and mortality carts/sleds. Virus isolation attempted on two samples did not yield positive results.ConclusionsPRRSV contamination can occur on surfaces inside and outside pig barns that are in frequent contact with farm personnel. Although virus isolation attempts were negative, our results illustrate the potential for PRRSV to be transmitted indirectly through contaminated materials or farm personnel. The study supports the implementation of biosecurity practices by farm personnel to prevent the introduction of PRRSV into farms and the prevention of PRRSV transmission between farms.

Genomic identification of Oryctes rhinoceros nudivirus isolates, a biocontrol agent for coconut rhinoceros beetle

The coconut rhinoceros beetle (Oryctes rhinoceros, CRB) is a serious pest of coconut and oil palms. It is native to South and Southeast Asia and was inadvertently introduced to Samoa in 1909. It has invaded many other Pacific countries throughout the last century. Oryctes rhinoceros nudivirus (OrNV), a natural pathogen of CRB in its native range, was successfully introduced as a classical biocontrol agent and has effectively suppressed invasive CRB populations for decades. However, resurgence of CRB has been recorded, with new invasions detected in several Pacific Island Countries and Territories. Additionally, new populations of CRB are emerging in some invaded areas that have a degree of resistance to the virus isolates commonly released for CRB biocontrol. Here, we designed a fast and reliable tool for distinguishing between different OrNV isolates that can help with the selection process to identify effective isolates for management of new CRB invasions. A comparison of 13 gene/gene region sequences within the OrNV genome of 16 OrNV isolates from native and invaded ranges allowed us to identify unique Single Nucleotide Polymorphisms (SNPs). With these SNPs, we developed an assay using multiplex PCR-amplicon-based nanopore sequencing to distinguish between OrNV isolates. We found that as few as four gene fragments were sufficient to identify 15 out of 20 OrNV isolates. This method can be used as a tool to monitor the establishment and distribution of OrNV isolates selected for release as biocontrol agents in CRB-infected areas.

Complete coding sequence of Tembusu virus isolate 2211-5 isolated in Taiwan.

We reported the complete coding sequence of a Tembusu virus from sick geese in Taiwan in 2022. The nucleotide sequence of the 2211-5 isolate was most closely related to the strain CTLN isolated from chicken in China and classified into Cluster 3 of Tembusu virus.

(Re-)Emergence of Oropouche Virus (OROV) Infections: Systematic Review and Meta-Analysis of Observational Studies.

Oropouche Virus (OROV; genus of Orthobunyavirus) is the causal agent of Oropouche Fever (OF). Due to the lack of specific signs and symptoms and the limited availability of diagnostic tests, the actual epidemiology of OROV infections and OF has been extensively disputed. In this systematic review with meta-analysis, a literature search was carried out in PubMed, Scopus, EMBASE, and MedRxiv in order to retrieve relevant articles on the documented occurrence of OROV infections. Pooled detection rates were then calculated for anti-OROV antibodies and virus detection (i.e., viral RNA detected by viral cultures and/or real-time polymerase chain reaction [RT-qPCR]). Where available, detection rates for other arboviruses (i.e., Dengue [DENV], Chikungunya [CHKV], and Zika Virus [ZIKV]) were calculated and compared to those for OROV. A total of 47 studies from South America and the Caribbean were retrieved. In individuals affected by febrile illness during OROV outbreaks, a documented prevalence of 0.45% (95% confidence interval [95%CI] 0.16 to 1.12) for virus isolation, 12.21% (95%CI 4.96 to 27.09) for seroprevalence (including both IgM and IgG class antibodies), and 12.45% (95%CI 3.28 to 37.39) for the detection of OROV-targeting IgM class antibodies were eventually documented. In the general population, seroprevalence was estimated to be 24.45% (95%CI 7.83 to 55.21) for IgG class antibodies. The OROV detection rate from the cerebrospinal fluids of suspected cases of viral encephalitis was estimated to be 2.40% (95%CI 1.17 to 5.03). The occurrence of OROV infections was consistently lower than that of DENV, CHKV, and ZIKV during outbreaks (Risk Ratio [RR] 24.82, 95%CI 21.12 to 29.16; RR 2.207, 95%CI 1.427 to 3.412; and RR 7.900, 95%CI 5.386 to 11.578, respectively) and in the general population (RR 23.614, 95%CI 20.584 to 27.129; RR 3.103, 95%CI 2.056 to 4.685; and RR 49.500, 95%CI 12.256 to 199.921, respectively). In conclusion, our study stresses the possibly high underestimation of OROV prevalence in the general population of South America, the potential global threat represented by this arbovirus infection, and the potential preventive role of a comprehensive "One Health approach".

New isolate of sweet potato virus 2 from Ipomoea nil: molecular characterization, codon usage bias, and phylogenetic analysis based on complete genome

BackgroundViral diseases of sweet potatoes are causing severe crop losses worldwide. More than 30 viruses have been identified to infect sweet potatoes among which the sweet potato latent virus (SPLV), sweet potato mild speckling virus (SPMSV), sweet potato virus G (SPVG) and sweet potato virus 2 (SPV2) have been recognized as distinct species of the genus Potyvirus in the family Potyviridae. The sweet potato virus 2 (SPV2) is a primary pathogen affecting sweet potato crops.MethodsIn this study, we detected an SPV2 isolate (named SPV2-LN) in Ipomoea nil in China. The complete genomic sequence of SPV2-LN was obtained using sequencing of small RNAs, RT-PCR, and RACE amplification. The codon usage, phylogeny, recombination analysis and selective pressure analysis were assessed on the SPV2-LN genome.ResultsThe complete genome of SPV2-LN consisted of 10,606 nt (GenBank No. OR842902), encoding 3425 amino acids. There were 28 codons in the SPV2-LN genome with a relative synonymous codon usage (RSCU) value greater than 1, of which 21 end in A/U. Among the 12 proteins of SPV2, P3 and P3N-PIPO exhibited the highest variability in their amino acid sequences, while P1 was the most conserved, with an amino acid sequence identity of 87-95.3%. The phylogenetic analysis showed that 21 SPV2 isolates were clustered into four groups, and SPV2-LN was clustered together with isolate yu-17-47 (MK778808) in group IV. Recombination analysis indicated no major recombination sites in SPV2-LN. Selective pressure analysis showed dN/dS of the 12 proteins of SPV2 were less than 1, indicating that all were undergoing negative selection, except for P1N-PISPO.ConclusionThis study identified a sweet potato virus, SPV2-LN, in Ipomoea nil. Sequence identities and genome analysis showed high similarity between our isolate and a Chinese isolate, yu-17-47, isolated from sweet potato. These results will provide a theoretical basis for understanding the genetic evolution and viral spread of SPV2.

Evidence of vertical transmission of Senecavirus A in naturally infected sows

Senecavirus A (SVA) is a Picornaviridae RNA virus that causes vesicular disease (VD) and transitory neonatal losses in pigs. The major ways SVA is spread are by oral, nasal, and feces. Vertical transmission of SVA was investigated during a VD epidemic in a farrow-to-finish herd in Brazil. Vesicular lesions were observed on sows before farrowing and on piglets within 24 h of birth. Analyses included RT-qPCR, viral isolation, sequencing, and virus-neutralization assays on serum, vesicular fluid, colostrum, and milk. Five out of ten sows were viremic before farrowing, and 46.7% of tested piglets had high viral loads in the first 24 h after birth. Infectious virus was detected in colostrum and milk from one postnatal sow. Despite high levels of neutralizing antibodies (nAbs) in piglet serum, colostrum, and milk, piglets were not protected from viremia and clinical illness. These findings support the vertical and congenital transmission of SVA.

Sputnik V-Induced Antibodies against SARS-CoV-2 Variants during the Dissemination of the Gamma Variant in Venezuela.

The COVID-19 pandemic was characterized by the emergence and succession of SARS-CoV-2 variants able to evade the antibody response induced by natural infection and vaccination. To evaluate the IgG reactivity and neutralizing capacity of the serum of individuals vaccinated with Sputnik V (105 volunteers vaccinated) against different viral variants. IgG reactivity to the Spike protein (S) was evaluated by ELISA. A plaque reduction neutralization test was performed using different viral variant isolates. At 42 days post-vaccination, the frequency of recognition and reactivity to the S protein of the Omicron variant was lower compared to that of the other variants. In general, a higher average neutralization titer was seen against the ancestral variant compared to the variants, especially Omicron. However, some sera exhibited a higher neutralization titer to the Gamma variant compared to the ancestral variant, suggesting unapparent exposure during the clinical trial. Antibodies induced by Sputnik V can recognize, persist, and neutralize SARS-CoV-2 variants, with Omicron being the one that best evades this response. These results represent a unique report on the humoral response induced by a globally lesser-studied vaccine in terms of efficacy and immune escape, offering insights into developing vaccines targeting unknown coronaviruses.

Logistics for Rapid Isolation of Viruses From Humans.

An important aspect of microbiological surveillance is the ability to access live viruses for microneutralization assays, which enables the study of viral characteristics and mechanisms in vitro and production of positive controls for diagnostic methods. During the COVID-19 pandemic, the Public Health Agency of Sweden established a protocol for the rapid collection of clinical samples and subsequent isolation of novel virus variants.

Characterization and genetic diversity of grapevine Pinot gris virus in Serbian vineyards

Sixty-five samples of grapevine from commercial vineyards in the Rasina district of Serbia were tested for the presence of grapevine Pinot gris virus (GPGV), using the reverse transcription-polymerase chain reaction. Fourteen samples of the grapevine varieties ‘Red Globe’, ‘Victoria’ and ‘Preobraženje’ were infected with GPGV. All the infected plants showed symptoms of leaf chlorotic mottling, puckering, and deformation, stunting, and reduced yields. The coding regions of the movement and coat protein (MP/CP) and a region of the RNA-dependent RNA polymerase (RdRP) domains of eight virus isolates were sequenced. Phylogenetic analyses of these genomic regions showed high nucleotide similarity among the Serbian GPGV isolates. This study is the first to describe genetic diversity of GPGV isolates in Serbia.

First detection of recombinant variant of African swine fever virus in the Russian Federation (brief communication)

As part of extensive molecular and genetic research into African swine fever virus isolates circulating in Russia, a recombinant variant with a mosaic genome structure has been identified. The one that caused an outbreak on a pig farm in the Primorsky Krai, in 2023. The characterized strain ASFV/Primorsky_2023/DP-4560.Recdemonstrates hemadsorption, active propagation in porcine primary macrophage cell culture, 99.9917% identity with the first recombinant isolates from the People’s Republic of China, recovered in 2021. Recombination sites included 79 open reading frames homologous to genotype II isolates; 49 ones homologous to genotype I and 12 mixed ones. Testing biomaterial from dead pigs in real-time polymerase chain reaction showed no changes in sensitivity or specificity, despite significant genetic distinctions between the recombinant and genotype II isolates that are enzootic to the Russian Federation. However, in 2023, D. Zhao et al. reported on high virulence of the virus related variants as revealed by the challenge tests in domestic pigs. Given the accelerating rates of AFSV molecular evolution in the East Asian countries (China, Vietnam and the Far Eastern regions of Russia), it is required to improve control measures, general and specific prevention, national and international surveillance over the economically significant animal disease.

Identification of severe fever with thrombocytopenia syndrome virus isolates in the northwest of Hubei Province, China

Severe fever with thrombocytopenia syndrome (SFTS) is a tick-borne viral disease that is increasingly affecting human being worldwide. The clinical manifestations and mortality rates of SFTS can vary depending on the geographic region and the specific genotype of the SFTS virus (SFTSV). From July 2022 to August 2023, we collected serum samples from 83 patients with suspected SFTSV infection in the northwest of Hubei Province, China. From which, 13 patients tested positive for SFTSV. Phylogenetic analysis of the SFTSV L, M, and S gene segments was performed using the maximum likelihood method to determine the genetic diversity of the isolates. At least 2 SFTSV genotypes (A and F) were identified in the northwest of Hubei Province. The clinical manifestations and laboratory findings on the first day of admission were investigated. Results showed that bleeding and disturbance of consciousness, and significant elevated AST and APTT, are valuable for assessing the prognosis for SFTS patients. This study disclosed the genomic sequences and genotypes of SFTSV spreading in the northwest of Hubei Province for the first time, providing information of genetically etiology for SFTS in the local district. Furthermore, certain symptoms and/or laboratory findings may indicate adverse clinical outcomes, highlighting the importance of identifying the symptoms and monitoring specific laboratory markers. Future research is needed to investigate the threshold values of these markers and to closely observe the indicative symptoms in order to early identify and timely management of critically ill patients within clinical settings.

Waste management and disease spread potential: A case study of SARS-CoV-2 in garbage dumping sites in Bangkok and its vicinity

During the coronavirus disease 2019 (COVID-19) pandemic, hospitals and households have used personal protective equipment (PPE), such as masks and gloves. Some of these potentially infectious materials were discarded with other household wastes in garbage dumping sites. Thus, this study aimed to detect the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in contaminated wastes, environments, and mammals scavenging around these sites. From September to October 2022, we visited three garbage dumping sites located in Bangkok, Nakhon Pathom, and Nonthaburi provinces of Thailand. Oral, nasal, rectal swabs, and blood samples were collected from small mammals, stray dogs, and cats. Masks, gloves, soil, and water samples from the sites were additionally collected. Of the 582 samples collected from 238 animals, none tested positive for SARS-CoV-2 in the virus isolation, real-time reverse-transcription polymerase chain reaction, and neutralizing antibody detection. However, one sample (1.18 %; 1/85) from a rat (Rattus spp.) captured in Nonthaburi was serologically positive in the indirect enzyme-linked immunosorbent assay. The surveillance of coronaviruses in rats is strongly encouraged because rats may harbor different zoonotic pathogens, including unknown potentially zoonotic coronaviruses. Moreover, two face mask samples (4.65 %; 2/43) collected from the dumping site in Nakhon Pathom tested positive for SARS-CoV-2 by real-time RT-PCR. To reduce environmental contamination, detecting the SARS-CoV-2 viral genome in contaminated face masks highlights the critical need for proper waste management in households and communities in Thailand. Thus, to minimize exposure and prevent onward transmission, waste management personnel, including garbage dump staff and waste pickers, should be equipped with appropriate PPE and receive regular training on safe handling and disposal.

DETERMINATION OF E PROTEIN MUTATION IN SARS-COV-2 VIRUS ISOLATES

The emergence of new variants of the SARS-CoV-2 coronavirus is caused by mutations in the main structural proteins of severe acute respiratory syndrome coronavirus 2. Vaccination and other therapeutic approaches can help stop the epidemic. Scientists are currently developing drugs and vaccines that specifically target the structural proteins of the SARS-CoV-2 coronavirus. As a result, taking into account mutations in proteins and determining their impact on function will help in high-quality production and development of preventive and therapeutic agents. As a result of sequencing, it was possible to obtain the complete nucleotide sequence of the E gene of the SARS-CoV-2 coronavirus. The presence and location of mutations in the envelope protein (E) of SARS-CoV-2 virus isolates were investigated by aligning the sequences with the reference sequence of the SARS-CoV-2 virus. The results showed that the most relative mutations in the amino acid sequence of the E protein of the SARS-CoV-2 coronavirus occurred in regions 9 and 11. Two mutations, T9I and T11A, were found compared with the Severe acute respiratory syndrome coronavirus 2 (NC 045512.2) strain. The identified structural mutations of the E protein can be used in the strategy for developing drugs and vaccines.