B1 Gene Research Articles

Analysis of the complete genome sequence of cucumber mosaic virus from Vinca minor and Wisteria sinensis in Iran

We present here the first complete sequence of cucumber mosaic virus (CMV) from RNA sequencing of a dwarf periwinkle (Vinca minor) and a Wisteria sinensis in Iran by de novo assembly and annotation of contigs. The tripartite genome of CMV-Ir-VM and Ir-WS consists of a 3391-nucleotide (nt) RNA1, a 3038-nt RNA2, and a 2197-nt RNA3 segment. The sequence comparisons and phylogenetic analyses revealed that all three RNA segments of these two isolates belonged to the CMV subgroup II. RNA1, RNA2, and RNA3 of these two isolates, respectively shared 97.61–99.06%, 97.83–98.88%, and 97.19–98.86% nucleotide identities to those of CMV subgroup II isolates. In genetic analysis, the 2b gene revealed more genetic variability (π = 0.2614) compared with other regions. Our results indicated that purifying selection pressure was the major force acting upon the CMV genome, although some positively selected sites were identified for all encoded proteins.

Mitochondrial Fatty Acid β-Oxidation Inhibition Promotes Glucose Utilization and Protein Deposition through Energy Homeostasis Remodeling in Fish

Fish cannot use carbohydrate efficiently and instead utilize protein for energy supply, thus limiting dietary protein storage. Protein deposition is dependent on protein turnover balance, which correlates tightly with cellular energy homeostasis. Mitochondrial fatty acid β-oxidation (FAO) plays a crucial role in energy metabolism. However, the effect of remodeled energy homeostasis caused by inhibited mitochondrial FAO on protein deposition in fish has not been intensively studied. This study aimed to identify the regulatory role of mitochondrial FAO in energy homeostasis maintenance and protein deposition by studying lipid, glucose, and protein metabolism in fish. Carnitine-depleted male Nile tilapia (initial weight: 4.29±0.12g; 3 mo old) were established by feeding them with mildronate diets (1000mg/kg/d) for 6wk. Zebrafish deficient in the carnitine palmitoyltransferase 1b gene (cpt1b) were produced by using CRISPR/Cas9 gene-editing technology, and their males (154±3.52mg; 3 mo old) were used for experiments. Normal Nile tilapia and wildtype zebrafish were used as controls. We assessed nutrient metabolism and energy homeostasis-related biochemical and molecular parameters, and performed 14C-labeled nutrient tracking and transcriptomic analyses. The mitochondrial FAO decreased by 33.1-88.9% (liver) and 55.6-68.8% (muscle) in carnitine-depleted Nile tilapia and cpt1b-deficient zebrafish compared with their controls (P <0.05). Notably, glucose oxidation and muscle protein deposition increased by 20.5-24.4% and 6.40-8.54%, respectively, in the 2 fish models compared with their corresponding controls (P <0.05). Accordingly, the adenosine 5'-monophosphate-activated protein kinase/protein kinase B-mechanistic target of rapamycin (AMPK/AKT-mTOR) signaling was significantly activated in the 2 fish models with inhibited mitochondrial FAO (P <0.05). These data show that inhibited mitochondrial FAO in fish induces energy homeostasis remodeling and enhances glucose utilization and protein deposition. Therefore, fish with inhibited mitochondrial FAO could have high potential to utilize carbohydrate. Our results demonstrate a potentially new approach for increasing protein deposition through energy homeostasis regulation in cultured animals.

Evaluation of SARS-CoV-2 in Tears of Patients with Moderate to Severe COVID-19

PurposeTo investigate the presence of SARS-CoV-2 RNA in tears of patients with moderate to severe coronavirus disease 2019 (COVID-19).DesignCross-sectional study.ParticipantsPatients with laboratory-proven moderate to severe COVID-19.MethodsTears were collected within 48 hours of laboratory confirmation using 3 methods: conjunctival swab plus Schirmer’s test strips (group 1), conjunctival swab (group 2), and Schirmer’s test strips (group 3). Samples from both the eyes of each patient were transported in a single viral transport media for real-time RT-PCR. Detailed demographic profiles, systemic symptoms, comorbidities, and ocular manifestations were noted.Main Outcome MeasuresViral load of a sample was determined using cycle threshold (Ct) value of E gene. A specimen was considered to show positive results if the amplification curve for the E gene crossed the threshold line within 35 cycles and if it showed positive results on an RNA-dependent RNA polymerase or open reading frame 1b gene assay.ResultsOf the 78 patients enrolled in the study, samples from 3 patients were found to be inadequate for analysis. Thirty-six patients (48%) had moderate disease, whereas 39 patients (52%) had severe disease, with no ocular involvement in any patient. In the 75 patients, RT-PCR analysis of tears showed positive results in 18 patients (24%), and 29 of 225 samples (12.9%) showed positive results. Positive results were found in 11 (14.7%), 11 (14.7%), and 7 (9.3%) patients in groups 1, 2, and 3, respectively (P = 0.3105). Mean Ct values in groups 1, 2, and 3 were 28.36 ± 6.15, 29.00 ± 5.58, and 27.86 ± 6.46 (P = 0.92), respectively. Five patients showed positive RT-PCR results by all 3 methods (mean Ct value, 25.24 ± 6.33), and 12 patients showed positive results by any of the 3 methods (mean Ct value, 32.16 ± 1.94), the difference in Ct values being statistically significant (P = 0.029). The median value of symptomatology in patients with positive RT-PCR results from tears was 5 days (range, 4–9 days).ConclusionsSARS-CoV-2 RNA was detected in tears of 24% of patients with laboratory-proven moderate to severe COVID-19. Conjunctival swab remains the gold standard of tear collection for RT-PCR assay. A significantly higher possibility of viral transmission exists through tears in patients with moderate to severe COVID-19.

SEROLOGICAL AND MOLECULAR DIAGNOSIS OF TOXOPLASMA GONDII AMONG EWES AND HORSES IN DUHOK PROVINCE-IRAQ

This study was aimed to demonstrate the seroprevalence and molecular detection of Toxoplasma gondii among ewes and horses as well as to determine the risk factors for infection in Duhok province. Sera and blood samples from 700 ewes and 62 horses were collected. Sera were examined by indirect ELISA for detection of anti-T. gondii IgM antibodies and in molecular study, DNA was extracted, then by PCR, B1 gene was amplified and the product visualized and sent off for sequencing. Serologically, the prevalence of toxoplasmosis was 17.7 (11/62) and 28.9 (202/700) in horses and ewes by ELISA respectively. Present of cats on the farm was significantly associated with T. gondii infected ewes in the farm. While, Age, number of abortion and history of abortion has no role in infection in ewes. On the other hand, age and sex have no role in prevalence of toxoplasmosis among the horses. Only 2 samples among 11 seropositive samples by ELISA were give positive results by PCR in rate 18.2% in horse, while in ewes 13 samples from 60 randomly selected seropositive by ELISA were found to be positive by PCR in rate 21.7%. Results of this study indicate that prevalence of T. gondii among ewes and horses was high and cats have a role in prevalence of infection among the ewes.

A Genome-Wide CRISPR-Cas9 Screen Reveals the Requirement of Host Cell Sulfation for Schmallenberg Virus Infection.

Schmallenberg virus (SBV) is an insect-transmitted orthobunyavirus that can cause abortions and congenital malformations in the offspring of ruminants. Even though the two viral surface glycoproteins Gn and Gc are involved in host cell entry, the specific cellular receptors of SBV are currently unknown. Using genome-wide CRISPR-Cas9 forward screening, we identified 3'-phosphoadenosine 5'-phosphosulfate (PAPS) transporter 1 (PAPST1) as an essential factor for SBV infection. PAPST1 is a sulfotransferase involved in heparan sulfate proteoglycan synthesis encoded by the solute carrier family 35 member B2 gene (SLC35B2). SBV cell surface attachment and entry were largely reduced upon the knockout of SLC35B2, whereas the reconstitution of SLC35B2 in these cells fully restored their susceptibility to SBV infection. Furthermore, treatment of cells with heparinase diminished infection with SBV, confirming that heparan sulfate plays an important role in cell attachment and entry, although to various degrees, heparan sulfate was also found to be important to initiate infection by two other bunyaviruses, La Crosse virus and Rift Valley fever virus. Thus, PAPST1-triggered synthesis of cell surface heparan sulfate is required for the efficient replication of SBV and other bunyaviruses.IMPORTANCE SBV is a newly emerging orthobunyavirus (family Peribunyaviridae) that has spread rapidly across Europe since 2011, resulting in substantial economic losses in livestock farming. In this study, we performed unbiased genome-wide CRISPR-Cas9 screening and identified PAPST1, a sulfotransferase encoded by SLC35B2, as a host entry factor for SBV. Consistent with its role in the synthesis of heparan sulfate, we show that this activity is required for efficient infection by SBV. A comparable dependency on heparan sulfate was also observed for La Crosse virus and Rift Valley fever virus, highlighting the importance of heparan sulfate for host cell infection by bunyaviruses. Thus, the present work provides crucial insights into virus-host interactions of important animal and human pathogens.

Generation and characterization of iPSC lines (BGUi004-A, BGUi005-A) from two identical twins with polyalanine expansion in the paired-like homeobox 2B (PHOX2B) gene

Congenital central hypoventilation syndrome (CCHS) is a rare life-threatening condition affecting the autonomic nervous system that usually presents shortly after birth as hypoventilation or central apnea during sleep. In the majority of cases, heterozygous polyalanine expansion mutations within the third exon of the paired-like homeobox 2B (PHOX2B) gene underlie CCHS. Here, we report the generation of two induced pluripotent stem cell (iPSC) lines from two identical twins with a heterozygous PHOX2B expansion mutation (+5 alanine residues). Both generated lines highly express pluripotency markers, can differentiate into the three germ layers, retain the disease-causing mutation and display normal karyotypes.

Toxoplasmagondii oocysts, Giardia cysts and Cryptosporidium oocysts in outdoor swimming pools in Brazil.

The accidental ingestion of treated recreational water is an important transmission route of waterborne protozoa worldwide. The present study aimed to provide the first evaluation of swimming pools in Brazil, analysing the presence of pathogenic protozoa (Toxoplasma gondii, Cryptosporidium spp. and Giardia spp.) by parasitological and molecular methods. A total of 57 samples were collected from 21 public swimming pools, either directly from the pool or filter backwash water and concentrated using the membrane filtration technique. Giardia cysts and Cryptosporidium oocysts were visualized by direct immunofluorescence assay after purification by immunomagnetic separation. Toxoplasma gondii oocysts were detected by autofluorescence visualization using the supernatant discarded during the purification step as a sample. Positive samples were submitted to molecular analysis. The molecular markers were used: SSU-rRNA, tpi, gdh and bg, for Giardia DNA amplification, and 18S rRNA gene fragment amplification was used for the Cryptosporidium oocysts. The 529-bp repeat element (REP529) fragment and the 35-fold repetitive B1 gene were employed as a target for T.gondii. Amplified products were submitted to sequencing and phylogenetic analysis. Giardia cysts were detected in 19.0% and Cryptosporidium oocysts in 9.5% of swimming pools. In one swimming pool (4.7%), both protozoa were detected on at least one occasion. Structures similar to T.gondii oocysts were detected in 33.3% of the samples, ranging from one to 23 per slide. Giardia was confirmed by DNA amplification in three swimming pools; Giardia duodenalis Assemblage A was identified by the phylogenetic positioning of the β-giardin gene. Toxoplasma gondii DNA was detected in 14.2% of swimming pools. The present study represents the first report of the occurrence of T.gondii oocysts in swimming pools. Recreational activity in swimming pools contaminated by chlorine-resistant protozoa can represent a high risk of infection for bathers and swimmers.

Molecular detection of the B1 gene of Toxoplasma gondii in blood samples of female sheep and goats in Tebessa, northeastern Algeria

Toxoplasmosis, caused by Toxoplasma gondii, is a parasitic zoonosis of crucial medical and veterinary importance. It is mainly diagnosed by serological methods which are limited by insufficient sensitivity. Therefore, it is necessary to rely on direct detection of the parasite. The present study was aimed for direct detection of the parasite DNA in the blood samples of sheep and goats using PCR targeting the B1 gene. The study was carried out in 20 small ruminant farms between 2016 and 2018 in Tebessa region, part of north-eastern Algeria, and concerned 227 and 91 aborted female sheep and goats respectively. DNA of T. gondii was detected in 35.24 % and 18.68 % blood samples of sheep and goats respectively (p < 0.001). Molecular prevalence was higher in 13−24 month old female sheep (93.33 %) than 1−12 month old female sheep (14.37 %) (p < 0.0001). While, in goats no significant difference was observed in relation to age. Female sheep that aborted between 1−60 days of gestation were found to be more infected (46.41 %) compared to females that aborted between 61−120 days of gestation (12.16 %) (p < 0.001). Whereas, female goats that aborted between 61−120 days of gestation were found to be more infested (30.77 %) compared to females that aborted between 1−60 days of gestation (16.67 %) (p < 0.001). This study revealed that small ruminants are highly infected with T. gondii, which represents a major risk for the consumer in Tebessa. Further studies are needed to improve our knowledge of the different genotypes of T. gondii infecting small ruminant population.

Depression and Toxoplasma gondii infection: assess the possible relationship through a seromolecular case-control study.

Depression disorder is one of the most common psychological recognitions that characterized by sadness, low self-confidence, and disinterest in every activity. Considering evidence showing the effects of toxoplasmosis on the psychological disease, this study conducted to investigate the serological and molecular aspects of Toxoplasma gondii infection among patients with depression. In this study, after selecting the patients with depression and control groups under the supervision of a psychologist, the blood samples were collected and the serum samples and buffy coat were separated. The specific anti-Toxoplasma IgG antibodies in serum samples were evaluated using the commercial ELISA kit. Then the desired region of the Toxoplasma B1 gene was amplified using the specific primers. To confirm the specificity of primers to amplify the B1 gene of Toxoplasma, the extracted PCR product was sequenced. The overall prevalence of toxoplasmosis in patients with depression was 59.8 and 60.19% by ELISA and PCR, respectively. In the control group, the prevalence of Toxoplasma was 56.3 and 40.2% by serology and PCR. There was a significant correlation between the prevalence of toxoplasmosis and depression. Moreover, a significant difference was found between the variables of age, sex, kind of nutrition, level of education and toxoplasmosis among the two cases and control groups. The higher prevalence of Toxoplasma infection among patients with depression compared with the control group indicates the probable impact of this parasite on depression and exacerbates its symptoms, which requires special attention of specialist physicians and patient's relatives.

From the Literature

From the Literature

The association between genetic variants in the genes for cytochrome P450 B1 and ATP-binding cassette transporter genes and breast cancer risk.

Breast cancer is among the most common malignancies in women. Recent studies have shown that polymorphisms in genes involved in the metabolism and transport of anticancer drugs are associated with outcomes of several malignancies, e.g., breast cancer. In this study we evaluate whether CYP1B1/rs1056836 and ABCB1/rs2032582 gene variants are associated with breast cancer. Eighty eight cases and 200 controls, were genotyped for polymorphisms of the CYP1B1 and ABCB1 genes using Taqman®-based methods. Logistic regression was also used to test the associations between breast cancer risk and the various genotypes involved. The GG genotype of rs2032582 locus had a frequency of 43.5% with 0.38 MAF; while the GT and TT genotypes in the control group were 40% and 16.5%, respectively. The GG, GT and TT genotype frequencies in the patients with breast cancer were 45.5%, 12.5% and 26.1%, respectively. An association was observed between the TT genotype of ABCB1/rs2032582 locus and a larger breast cancer tumor size (P < 0.05). However, neither the relationship between the CYP1B1 polymorphism and breast cancer type nor the risk of breast cancer were statistically significant. Our data suggest a potential association of the ABCB1 genetic variant with breast cancer tumor size, however further investigation in a larger population is necessary to show its value as a risk stratification biomarker.

Development of two TaqMan real-time reverse transcription-PCR assays for the detection of severe acute respiratory syndrome coronavirus-2

The outbreak of coronavirus disease 2019 (COVID-19) in Wuhan, China, was caused by a novel coronavirus (CoV), named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The rapid detection of viral nucleic acids is critical for the early identification of infected cases. We have developed two TaqMan real-time reverse transcription-PCR assays to detect SARS-CoV-2. The designed primers target the nucleocapsid (N) and open reading frame (ORF) 1b gene regions, where the probes discriminate SARS-CoV-2 from other human and animal CoVs. The sensitivities are one genomic copy per reaction for the N gene assay and ten copies for the ORF 1b gene assay. The overall linear detection ranges are 1–106 and 10–106 copies per reaction for the N gene assay and the ORF 1b gene assay, respectively. Surveillance of 23 suspected COVID-19 patients demonstrated that SARS-CoV-2 could be detected from 100% (23/23) and 62.5% (16/23) of clinical specimens by the N gene assay and the ORF 1b gene assay, respectively. All of the samples not detected by the ORF 1b gene assay were throat swabs, indicating a lower viral load in the upper respiratory tract and the relatively lower sensitivity of the ORF 1b gene assay. The assays developed in the present study offer alternative diagnostic tests for COVID-19.

Molecular Detection and Genetic Diversity of Toxoplasma gondii Oocysts in Cat Faeces from Klang Valley, Malaysia, Using B1 and REP Genes in 2018.

The major route for Toxoplasma gondii (T. gondii) infection is through the ingestion of foods contaminated with oocyst from cat faeces. The microscopic detection of T. gondii oocysts in cat faeces is challenging, which contributes to the failure of detecting or differentiating it from other related coccidian parasites. This study aims to detect T. gondii oocysts in cat faeces using two multicopy-target PCR assays and to evaluate their genetic diversity. Cat faecal (200) samples were collected from pet cats (PCs; 100) and free-roaming cats (FRCs; 100) within Klang Valley, Malaysia, and screened for coccidian oocysts by microscopy using Sheather’s sucrose floatation. PCR assays were performed on each faecal sample, targeting a B1 gene and a repetitive element (REP) gene to confirm T. gondii oocysts. Additionally, the PCR amplicons from the REP gene were sequenced to further confirm T. gondii-positive samples for phylogenetic analysis. Microscopy detected 7/200 (3.5%) T. gondii-like oocysts, while both the B1 gene and the REP gene detected 17/200 (8.5%) samples positive for T. gondii. All samples that were microscopically positive for T. gondii-like oocysts were also shown to be positive by both B1 and REP genes. The BLAST results sequenced for 16/200 (8.0%) PCR-positive T. gondii samples revealed homology and genetic heterogeneity with T. gondii strains in the GenBank, except for only one positive sample that did not show a result. There was almost perfect agreement (k = 0.145) between the two PCR assays targeting the B1 gene and the REP gene. This is the first report on microscopic, molecular detection and genetic diversity of T. gondii from cat faecal samples in Malaysia. In addition, the sensitivities of either the B1 gene or REP gene multicopy-target PCR assays are suitable for the accurate detection of T. gondii from cat faeces.

MTNR1B gene on susceptibility to gestational diabetes mellitus: a two-stage hospital-based study in Southern China.

Large-scale studies on genetic risk loci for melatonin receptor 1B (MTNR1B) gene and GDM risk have not been well generalized to the Chinese population. In this study, we performed two-stage case-control study: 1.429 pregnant women: 753 GDM/676 controls in the Southern Chinese population by genotyping 5 SNPs (rs10830963, rs1387153, rs2166706, rs1447352, and rs4753426) in MTNR1B. Genotypes were determined using the Sequenom MassARRAY platform and TaqMan allelic discrimination assay. Interactions between genetic variants and age/BMI as predictors of GDM risk were evaluated under the logistic regression model. In the first stage, the SNP rs10830963 was discovered to be potentially related to GDM risk (additive model: OR = 1.27, 95%CI = 1.05-1.55, P = 0.025), which was further confirmed in the second stage with a similar effect (additive model: OR = 1.53, 95%CI = 1.19-1.98, P = 0.005). In the combined stage, the G allele of rs10830963 was potentially associated with GDM risk (additive model: OR = 1.36, 95%CI = 1.17-1.59, P < 0.001; dominant model: OR = 1.45, 95%CI = 1.15-1.83, P = 0.005). The rs10830963 interacted with age and BMI to contribute to GDM risk in the combined participants. And, the similar interactive effects for the other four SNPs also exist. These findings offer the potential to improve our understanding of the etiology of GDM, and particularly of biological mechanisms.

Seroprevalence and Risk Factors of Toxoplasma gondii in Ruminant Meats from Wet Markets in Klang Valley and Abattoirs in Selangor, Malaysia.

Simple SummaryThis study investigated the prevalence of Toxoplasma. gondii in meats of cattle, goat and sheep from wet markets and abattoirs in Selangor, Malaysia. Meat samples from wet markets in various districts and diaphragm samples from abattoirs were analyzed using ELISA to check for T. gondii IgG antibodies. Furthermore, attempts were made to detect T. gondii DNA from meat samples using the nested PCR technique. Twenty-five percent of the samples were positive for T. gondii antibodies, with the highest recorded in goat (55%), followed by sheep (35%) and cattle meat (9%). T. gondii DNA was not detected in any of the meat samples. Being the first report in Malaysia, the findings highlight the need for proper control in reducing exposure of ruminant meats to the parasite, especially those destined for human consumption.(1) Background: The objective of this study was to determine the prevalence of T. gondii in meats of cattle, goat and sheep from wet markets in Klang Valley, and abattoirs in Selangor, Malaysia; (2) Methods: A total of 192 meat samples were purchased from 51 wet markets in six districts in Klang Valley (Gombak, Klang, Kuala Lumpur, Hulu Langat, Petaling and Putrajaya). Meanwhile, a total of 200 diaphragm samples were collected from two government abattoirs located in Shah Alam and Banting, Selangor. All meat juices from samples were subjected to an indirect-ELISA kit for the presence of T. gondii IgG antibodies. Furthermore, all 184 meat samples of goat and sheep were subjected to conventional nested PCR (B1 genes) for the detection of T. gondii DNA; (3) Results: T. gondii antibodies were detected in 25% (n = 98/392) of the samples with seroprevalence of 9.1% (19/208, CI: 5.9%–13.8%) in cattle meat; 54.7% (41/75, 95% CI: 43.5%–65.4%) in goat meat and 34.9% (38/109, CI: 26.6%–44.2%) in sheep meat. No T. gondii DNA was detected in any of the meat samples of goat and sheep. T. gondii seropositivity in wet market samples was higher in goat (OR = 37.1 CI 12.4–110.3) and sheep meat (OR 9.03 CI: 3.28–24.8) compared to cattle meat (OR = 1.0) At univariate level, meat from non-licensed abattoirs (OR = 6.0 CI: 2.9–12.3) and female animals (OR = 6.7; CI 1.9–22.6) had higher risks of being seropositive for T. gondii antibodies than licensed abattoirs and male animals, respectively. (4) Conclusions: This is the first report of seroprevalence of T. gondii in ruminant meats for human consumption in Malaysia. The findings signified high exposure of meat samples from wet markets to T. gondii and the need for control measures to reduce the likelihood of infection when such raw or undercooked meats are consumed.

Extensive genetic diversity and host range of rodent-borne coronaviruses.

To better understand the genetic diversity, host associations and evolution of coronaviruses (CoVs) in China we analyzed a total of 696 rodents encompassing 16 different species sampled from Zhejiang and Yunnan provinces. Based on reverse transcriptase PCR-based CoV screening of fecal samples and subsequent sequence analysis of the RNA-dependent RNA polymerase gene, we identified CoVs in diverse rodent species, comprising Apodemus agrarius, Apodemus chevrieri, Apodemus latronum, Bandicota indica, Eothenomys cachinus, Eothenomys miletus, Rattus andamanensis, Rattus norvegicus, and Rattus tanezumi. CoVs were particularly commonplace in A. chevrieri, with a detection rate of 12.44 per cent (24/193). Genetic and phylogenetic analysis revealed the presence of three groups of CoVs carried by a range of rodents that were closely related to the Lucheng Rn rat CoV (LRNV), China Rattus CoV HKU24 (ChRCoV_HKU24), and Longquan Rl rat CoV (LRLV) identified previously. One newly identified A. chevrieri-associated virus closely related to LRNV lacked an NS2 gene. This virus had a similar genetic organization to AcCoV-JC34, recently discovered in the same rodent species in Yunnan, suggesting that it represents a new viral subtype. Notably, additional variants of LRNV were identified that contained putative non-structural (NS)2b genes located downstream of the NS2 gene that were likely derived from the host genome. Recombination events were also identified in the open reading frame (ORF) 1a gene of Lijiang-71. In sum, these data reveal the substantial genetic diversity and genomic complexity of rodent-borne CoVs, and extend our knowledge of these major wildlife virus reservoirs.

Identification of nsp1 gene as the target of SARS-CoV-2 real-time RT-PCR using nanopore whole-genome sequencing.

Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has caused the coronavirus disease 2019 (COVID‐19) pandemic. Accurate detection of SARS‐CoV‐2 using molecular assays is critical for patient management and the control of the COVID‐19 pandemic. However, there is an increasing number of SARS‐CoV‐2 viruses with mutations at the primer or probe binding sites, and these mutations may affect the sensitivity of currently available real‐time reverse transcription‐polymerase chain reaction (RT‐PCR) assays targeting the nucleocapsid (N), envelope (E), and open reading frame 1a or 1b genes. Using sequence‐independent single‐primer amplification and nanopore whole‐genome sequencing, we have found that the nonstructural protein 1 (nsp1) gene, located at the 5′ end of the SARS‐CoV‐2 genome, was highly expressed in the nasopharyngeal or saliva specimens of 9 COVID‐19 patients of different clinical severity. Based on this finding, we have developed a novel nsp1 real‐time RT‐PCR assay. The primers and probes are highly specific for SARS‐CoV‐2. Validation with 101 clinical specimens showed that our nsp1 RT‐PCR assay has a sensitivity of 93.1% (95% confidence interval [CI]: 86.2%‐97.2%), which was similar to those of N and E gene RT‐PCR assays. The diagnostic specificity was 100% (95% CI: 92.9%‐100%). The addition of nsp1 for multitarget detection of SARS‐CoV‐2 can avoid false‐negative results due to mutations at the primers/probes binding sites of currently available RT‐PCR assays.

Functional role of annexins in zebrafish caudal fin regeneration – A gene knockdown approach in regenerating tissue

Regeneration is an adaptive phenomenon with wide biological implications spread heterogeneously in almost all the organism including human beings. The ability of regeneration varies from species to species for its complexity. Epimorphic regeneration of zebrafish caudal fin tissue is the most widely studied regeneration mechanism for its discrete and rapid regenerative capability. Several genes and proteins were found to be associated with regenerative mechanisms of zebrafish caudal fin tissue. In this study we have evaluated the functional role of Annexin 2a and 2b genes during zebrafish caudal fin tissue regeneration using inventive electroporation techniques for targeting the gene involving CRISPR-Cas9 technology. The electroporation of the CRISPR was performed on the adult zebrafish caudal fin tissue post amputation. We report retarded growth during the regeneration of caudal fin tissue when Annexin 2a and 2b genes were knocked down, which was validated through gene expression & sequencing analysis and further supported by high-throughput quantitative proteomic analysis of the fin tissue. Annexin family genes such as ANXA13, ANXA1a, ANXA5b were also found to be repressed with their expression. Knocking down of ANXA2a and 2b in regenerating caudal fin tissue compromises regenerating capacity as these genes are involved in cell to cell communication and extracellular matrix growth. This study proves that ANXA2a and 2b plays a significant role in epimorphic regeneration of zebrafish caudal fin tissue.

Serological and molecular detection of Neospora caninum and Toxoplasma gondii in human umbilical cord blood and placental tissue samples

Neosporosis primarily affects cattle and dogs and is not currently considered a zoonotic disease. Toxoplasmosis is a zoonosis with a worldwide distribution that is asymptomatic in most cases, but when acquired during pregnancy, it can have serious consequences. The seropositivity rates determined by the indirect fluorescent antibody test for Neospora caninum (N. caninum) and Toxoplasma gondii (T. gondii) were 24.3% (49 samples) and 26.8% (54 samples), respectively. PCR positivity for N. caninum was observed in two samples of cord blood (1%) using the Nc5 and ITS1 gene, positivity for T. gondii was observed in 16 samples using the primer for the B1 gene (5.5% positivity in cord blood and 2.5% positivity in placental tissue). None of the samples showed structures characteristic of tissue cysts or inflammatory infiltrate on histopathology. Significant associations were observed only between N. caninum seropositivity and the presence of domestic animals (p = 0.039) and presence of dogs (p = 0.038) and between T. gondii seropositivity and basic sanitation (p = 0.04). This study obtained important findings regarding the seroprevalence and molecular detection of N. caninum and T. gondii in pregnant women; however, more studies are necessary to establish a correlation between risk factors and infection.

Toxoplasma gondii infection in patients with lung diseases in Shandong province, eastern China

Toxoplasma gondii, an intracellular protozoan parasite, can induce various clinical symptoms. T. gondii has been considered to play an important role in the pathogenesis of lung diseases. This survey was conducted to explore the correlation between T. gondii infection and lung diseases through a case-control study carried out in Shandong province, eastern China. In the present survey, T. gondii IgG antibodies were found in 76/398 (19.10%) of patients with lung diseases, which was significantly higher (P < 0.001) than the level found in the control subjects (35/398; 8.79%) through serological diagnosis. Patients with lung cancer have the highest T. gondii seroprevalence (26.19%), followed by Pulmonary cyst (25.00%), Tuberculosis (17.07%), Pneumonia (16.33%) and chronic obstructive pulmonary disease (COPD) (16.05%). Moreover, a semi-nest PCR targeted T. gondii B1 gene was employed to detect the T. gondii DNA in the blood samples. T. gondii DNA was detected in 5.53% blood samples of patients with lung diseases and 2.51% control subjects, respectively. The present study firstly shows that T. gondii has a high probability to infect the patients with lung diseases. Thus, the potential presence of T. gondii in patients with lung diseases should be appreciated during in the course of treatment and safeguard procedures should be implemented to protect vulnerable patients with lung diseases.