Alpha, Delta, Omicron—Oh My! A SARS-CoV-2 Genome Alignment Activity to Understand Mutations and COVID Variants

COVID took over the world starting in 2020. Everyone quickly "knew" about the novel coronavirus, but how much do they actually know about the virus behind COVID-19? This classroom activity gives students real-world practice in evaluating actual genetic sequences from SARS-CoV-2 and working with genome alignments to identify mutations and cluster different emergence patterns. This activity works through alignments, mutations/variants, protein folding, structure and function, and medical/ immunology implications of the different variants. There are seven parts to this activity, and each one can be incorporated alone into a lesson or collectively used for a lab, case study, or other supplemental activity to strengthen learning objectives in genetics, biology, immunology, and public health. This learning activity is scalable to different levels and has successfully been incorporated into K–12 education as well as college and graduate education. [ FROM AUTHOR] Copyright of American Biology Teacher (University of California Press) is the property of University of California Press and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . (Copyright applies to all s.)

Metavirome in Sewage and Fecally-Tainted River Waters in the Philippines: Highlighting the Role of Environmental Surveillance in the Covid-19 Pandemic

Intro: The COVID-19 pandemic has triggered global collaborative efforts on response and research to detect SARS-CoV-2 particles not just in the human population but also in wastewater. While the examination of clinical samples from COVID-19 patients links SARS-CoV-2 to specific individuals, the analysis of an amalgam of human feces through environmental surveillance (ES) links SARSCoV-2 to populations and communities served by the wastewater system. Studies on SARS-CoV-2 in the environment were already done in high-resource countries. However, its epidemiology in wastewater bodies in the Philippines is limited. In this study, we used the National ES for Polio and Other Pathogens Network to investigate the molecular epidemiology and transmission dynamics of SARS-CoV-2 at the outset of the pandemic. Method(s): This is a retrospective study of 250 wastewater samples collected from May 2020 to July 2021. Samples were processed using the two-phase concentration technique. Pepper mild mottle virus RNAs were quantified as the internal control. Real-time PCR was used to detect the N-gene of the SARS-CoV-2. Whole genomes were sequenced using the COVID-19 ARTIC v4.0. Phylogenetic and mutation analysis were done and lineage assignments were established using the PANGOLIN software. Finding(s): Forty-two percent (107/250) of the environmental samples detected SARS-CoV-2 particles. Fifty-nine samples with Ct values <=38 were sequenced and the whole genome analysis revealed B.1.1 and B.6. lineages of SARS-CoV-2. When viral load were plotted with the weekly cases in the respective site, we observed that SARS-CoV2 can be detected in wastewater weeks before the spike of cases in the community. Conclusion(s): This is the first report on the detection of B.1.1 and B.6 SARS-CoV-2 particles in waste/surface waters in the Philippines. With the declining incidence of COVID-19 cases, this study provided data regarding the feasibility of establishing environmental surveillance for SARS-CoV-2 as a supplemental tool for human or case monitoring especially in resource-limited settings.Copyright © 2023

Comparative analysis of SARS-CoV-2 variants with two high-throughput sequencing platforms

Whole-genome sequencing of upper respiratory tract specimens from patients with confirmed COVID-19 in Henan Province was performed to compare the performance of the Illumina and Oxford Nanopore sequencing platforms, thus providing a reference for whole-genome monitoring of the novel coronavirus (SARS-CoV-2). Ten samples from COVID-19 cases in Henan Province from June 2021 to January 2022 were collected and sequenced with Illumina and Nanopore high-through-put sequencing technology to obtain full genome sequences of the novel coronavirus, which were compared with the Wuhan reference sequence (Wuhan-Hu-1). Bioinformatics software (CLC) was used for sequence alignment analysis. Three of the ten samples were Omicron (BA.1) variants with 55,61 nucleotide variation sites. One sample was an Alpha (B.1.1.7) variant with 41 nucleotide variation sites. Six samples were Delta (8.1.617.2) variants with 35,42,47 nucleotide variation sites. The sequence identity of mutation sites in six samples was 100%, and the mutation sites in the S genome segment of seven samples were consistent. For samples with a Ct value < 33, both next-generation and third-generation sequencing achieved high genome coverage and sequencing depth. A significant difference in coverage was observed between second-generation sequencing and third-generation sequencing (t=-2.037, P < 0.06). However, the coverage at different time points of the third-generation sequencing did not significantly differ (F=2.498, P > 0.05). The needs for SARS-CoV-2 mutant detection could be met through use of either high-throughput sequencing platform. The identification of mutations in the novel coronavirus through Illumina high-throughput sequencing was more accurate, whereas Nanopore high-throughput sequencing technology could be used for rapid detection and typing of different novel coronaviruses.

Isolation, identification and genetic evolution analysis of porcine epidemic diarrhea virus SNJ-P strain in Sichuan Province

Purpose: To investigate the epidemic variation of porcine epidemic diarrhea virus (PEDV) strains in Sichuan Province, and to analyze the causes of poor vaccination effect. Methods: Piglet intestinal samples were collected from a pig farm in Sichuan Province for PCR detection, virus purification, determination of virus titer and virus infection experiments. Whole genome sequencing of isolated strains was determined. The S gene sequence of the isolated strain was compared with the strains from other regions and vaccine strains, and the phylogenetic tree was established. The amino acid site variation of S protein between the isolated strain and the classical vaccine strain CV777 was compared. Results: A PEDV strain was successfully isolated and named as PEDV SNJ-P. The determination of virus titer was 1..107.5/100 L. Animal infection experiments showed that the isolated strain could cause diarrhea, dehydration and other symptoms and lead to death in piglets. Genome sequencing and phylogenetic tree analysis showed that the whole gene of PEDV SNJ-P strain was 28003 bp, and the genotype of the strain was S non-INDEL type. The strains were closely related to the strains of PEDV-WS, CH/JLDH/2016 and CH/HNLH/2015 isolated from China, and were relatively distant with the same type vaccine strain, and were far from the classical vaccine strain. Compared with the classical vaccine strain CV777, the S protein of SNJ-P strain had multiple amino acid mutations, deletions and insertions. Conclusion: Due to the continuous variation of strains, SNJ-P strain is far from the vaccine strain, and the current vaccines cannot provide effective protection. The results of this study are expected to provide reference for the study of PEDV strains and vaccine development in China.

Identification of feline corona- virus in breeding catteries by molecular biological methods and shedding persistency

Infectious peritonitis virus (FIPV) causes a fatal disease in cats. This virus occurs both in cats bred in households with optimal welfare and outdoor cats. Feline patients with the effusive form of disease usually survive a few days to weeks from the appearance of the first clinical signs. Cats with the non- effusive form survive for weeks to months. FIPV is caused by a mutation from feline enteric coronavirus (FECV). In our study, we diagnosed feline coronavirus from the feces of 82% of the tested cats. The persistence of the feline coronavirus in the organism is influenced by environmental factors, the genome of the host and the causative agent. Negative environmental conditions that increase the likelihood of FIPV disease are long-term stress, mainly more labile individuals and a high concentration of domesticated cats in one place. In the host, there are important factors such as immune system performance, age, breed and genetic background. In our study, we primarily verified the real time RT-PCR method for identifying the virus from the feces of 71 cats and subsequently gaine the valuable data on the dynamics of feline coronavirus excretion, primarily for epizootological purposes and for the purposes of genetic analyzes of susceptibility to infection.

New Short RNA Motifs Potentially Relevant in the SARS-CoV-2 Genome

Background: The coronavirus disease has led to an exhaustive exploration of the SARS-CoV-2 genome. Despite the amount of information accumulated, the prediction of short RNA motifs encoding peptides mediating protein-protein or protein-drug interactions has received limited attention. Objective(s): The study aims to predict short RNA motifs that are interspersed in the SARS-CoV-2 genome. Method(s): A method in which 14 trinucleotide families, each characterized by being composed of triplets with identical nucleotides in all possible configurations, was used to find short peptides with biological relevance. The novelty of the approach lies in using these families to search how they are distributed across genomes of different CoV genera and then to compare the distributions of these families with each other. Result(s): We identified distributions of trinucleotide families in different CoV genera and also how they are related, using a selection criterion that identified short RNA motifs. The motifs were reported to be conserved in SARS-CoVs;in the remaining CoV genomes analysed, motifs contained, exclusively, different configurations of the trinucleotides A, T, G and A, C, G. Eighty-eight short RNA motifs, ranging in length from 12 to 49 nucleotides, were found: 50 motifs in the 1a polyprotein-encoding orf, 27 in the 1b polyprotein-encoding orf, 5 in the spike-encoding orf, and 6 in the nucleocapsid-encoding orf. Although some motifs (~27%) were found to be intercalated or attached to functional peptides, most of them have not yet been associated with any known functions. Conclusion(s): Some of the trinucleotide family distributions in different CoV genera are not random;they are present in short peptides that, in many cases, are intercalated or attached to functional sites of the proteome.Copyright © 2022 Bentham Science Publishers.

Genomic characterization and phylogenetic analysis of sars-cov-2 in libya

The COVID-19 epidemic started in Libya in March 2020 and rapidly spread. To shed some light on the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) strains circulating in Libya, viruses isolated from 10 patients in this country were sequenced, characterized at the genomic level, and compared to genomes isolated in other parts of the world. As nine genomes out of 10 belonged to the SS1 cluster and one to SS4, three datasets were built. One included only African strains and the other two contained internationally representative SS1 and SS4 genomes. Genomic analysis showed that the Libyan strains have some peculiar features in addition to those reported in other world regions. Considering the countries in which the strains are genetically more similar to the Libyan strains, SARS-CoV-2 could have entered Libya from a North African country (possibly Egypt), sub-Saharan Africa (e.g., Ghana, Mali, Nigeria), the Middle East (e.g., Saudi Arabia), or Asia (India, Bangladesh).Copyright © 2021 by the authors. Licensee MDPI, Basel, Switzerland.

Complete genome sequencing and molecular genetic evolution analysis of Guangxi mutant of porcine epidemic diarrhea virus

In order to understand the genomic characteristics and molecular genetic diversity of porcine epidemic diarrhea virus(PEDV) in Guangxi in recent years, 11 pairs of specific primers were designed to detect the whole genome of PEDV GXNN isolated from porcine diarrhea in Nanning, Guangxi, China, and similarity comparison, genetic evolution, gene variation and S gene recombination were also analyzed. The results showed that full length of the GXNN strain was 28 035 bp, had similar genomic characteristics with other PEDV isolates, about 96.4%-98.7% nucleotide similarity with different reference strains, and the nucleotide similarity of S, ORF3, M and N genes was 93.7%-98.9%, 90.9%-99.4%, 97.4%-99.7% and 95.6%-99.2%;the amino acid similarity of them was 92.9%-99.5%, 91.3%-99.1%, 97.4%-99.1% and 96.4%-99.5%. GXNN is closely related to most domestic isolates in recent years. Phylogenetic tree showed that GXNN closely related to most strains isolated in China recent years, belonged to GII-b subtype. However, it was low relatedness to classic vaccine strains, domestic early epidemic strains, foreign epidemic strains and Guangxi CH-GX-2015-750 A, they belong to different subtypes. Compared with the 5 vaccine strains, the S gene of GXNN stain has a large variation, by inserting amino acid Q at positions 118 844 and 905 sizes, four unique amino acid mutations in the core neutralizing epitope(COE)region and the main epitope region, and 14 mutations in other regions. 126 T/A, 199 A/V and 103 T/A site mutations of ORF3, M and N genes were happened at position 126, 4 D4 region and PN-D4 region, respectively. Recombination analysis revealed that there was a potential recombination region in the hypervariable region of S gene at 826-3 142 nt. This study successfully obtained the complete genome sequence of a PEDV strain, and analyzed its genetic variation and provided a reference for PEDV molecular epidemiology research and new vaccine development.

Whole-Genome Analysis of Influenza A(H3N2) and B/Victoria Viruses Detected in Myanmar during the COVID-19 Pandemic in 2021.

An influenza circulation was observed in Myanmar between October and November in 2021. Patients with symptoms of influenza-like illness were screened using rapid diagnostic test (RDT) kits, and 147/414 (35.5%) upper respiratory tract specimens presented positive results. All RDT-positive samples were screened by a commercial multiplex real-time polymerase chain reaction (RT-PCR) assay, and 30 samples positive for influenza A(H3N2) or B underwent further typing/subtyping for cycle threshold (Ct) value determination based on cycling probe RT-PCR. The majority of subtyped samples (n = 13) were influenza A(H3N2), while only three were B/Victoria. Clinical samples with low Ct values obtained by RT-PCR were used for whole-genome sequencing via next-generation sequencing technology. All collected viruses were distinct from the Southern Hemisphere vaccine strains of the corresponding season but matched with vaccines of the following season. Influenza A(H3N2) strains from Myanmar belonged to clade 2a.3 and shared the highest genetic proximity with Bahraini strains. B/Victoria viruses belonged to clade V1A.3a.2 and were genetically similar to Bangladeshi strains. This study highlights the importance of performing influenza virus surveillance with genetic characterization of the influenza virus in Myanmar, to contribute to global influenza surveillance during the COVID-19 pandemic.

Intra-Host SARS-CoV-2 Evolution Dynamics

Background. Our understanding of SARS-CoV-2 evolution is limited. Most estimates arise from analysis of global databases populated with unrelated sequences and is currently estimated at ~27.7 substitutions/genome/year. SARS-CoV-2 polymerase contains a proofreading function encoded by NSP-14 limiting change. Additionally, virus evolution may be influenced by patient comorbidity. Intra-host mutational rate (MR) during infection remain poorly studied. Methods. To minimize effect of vaccination and/or natural immunity on MR analysis, paired samples from adults originating from the initial pandemic wave (3/17/2020 through 5/27/2020) were retrieved and analyzed at Cleveland Clinic. Viral genome analysis was performed using next generation sequencing, and mutations between paired samples were quantified at allele frequencies (AF) >= 0.1, >= 0.5 and >= 0.75 and compared. MR was calculated employing F81 and JC69 evolution models and compared between isolates with (DELTA NSP-14) and without (wildtype, wt) non-synonymous mutations in NSP-14 and by comorbidity. Results. A total of 40 patients (80 sample pairs) were identified. Median interval between paired tests was 15 days [range 5-32]. The estimatedMRby F81 modeling was 317.2 (95%CI 312.0-322.3), 54.6 (95%CI 52.5-56.7) and 45.1 (95%CI 43.1-47.0) substitutions/ genome/year at AF of >=0.1, >=0.5, >=0.75 respectively. Rates in DELTANSP-14 (n=13) vs wt (n=27) groups were 557.7 (95%CI 537.0-578.2) vs 193.1 (95%CI 187.1-199.1) p-value 0.001, 50.8 (95%CI 44.3-57.3) vs 56.3 (95%CI 53.1-59.4) p-value 0.144, and 31.0 (95%CI 25.9-36.1) vs 51.3 (95%CI 48.3-54.3) p- value < 0.001 at AF >=0.1, >=0.5, >=0.75 respectively. Patients with immune comorbidities (n=6) had significantly higher MR of 137.6 (95%CI 114.6-160.5) vs 40.5 (95%CI 38.4-42.7) p-value < 0.001, and 113.7 (95%CI 92.8-134.5) vs 33.4 (95%CI 31.5-35.4) p-value < 0.001 at AF >=0.5 and >=0.75 respectively. Similar results were obtained when using the JC69 model. Conclusion. Intra-host SARS-CoV-2 mutation rates are higher than those reported through population analysis. Virus strains with altered NSP-14 have accelerated MR at low AF. Immunosuppressed patients have elevated MR at higher AF. Understanding intra-host virus evolution will aid in current and future pandemic modeling.

Genomic Data Science And COVID -19 Genome Analysis Using Bio Python

The last few years have been amazing for biology and healthcare and the best thing that happens in this field was the human genome project .it was an international research project with the goal of mapping and understanding the entire human genome .data science is the field in which we study data, understand the data to get valuable insight from that. Data science has already become an umbrella under which every industry and field comes. We can work in medical, marketing, Information technology, and every other field, even far before data science comes into the real world, we were using statistical and computational knowledge to get an outcome from our data. But today with the grace of the internet and social media our ability to decipher the information from that data is out of our range, where data science has come as a saviour. Because of the amount of genomic data being generated it become essential that the field of genomics or biology must be combined with modern technology and tools so that we can properly analyze such big data for precise and accurate prediction of disease and prevention mechanisms for that, which ultimately will result in improved human health. The data collected from a single week-long sequence today can create more data than whole genome research done a few years ago. "Bioinformatics", "computational genomics" and "genomic data science" are all very similar fields. To provide biological insights in these disciplines, we must be able to process and analyse huge genomics datasets, as well as validate the processed data's quality and transform it. Afterwards, depending on the nature of our issue, we must apply statistical or machine-learning models. The most likely scenario is to first perform some dimension reduction and clustering, then visualisation. In this paper, I will use python to pass my accountancies over genomic data science and genomic data analysis. Copyright © 2022 Wolters Kluwer Medknow Publications. All rights reserved.

BEACON: Scalable Near-Data-Processing Accelerators for Genome Analysis near Memory Pool with the CXL Support

Genome analysis benefits precise medical care, wildlife conservation, pandemic treatment (e.g., COVID-19), and so on. Unfortunately, in genome analysis, the speed of data processing lags far behind the speed of data generation. Thus, hardware acceleration turns out to be necessary. As many applications in genome analysis are memory-bound, Processing-In-Memory (PIM) and Near-Data-Processing (NDP) solutions have been explored to tackle this problem. In particular, the Dual-Inline-Memory-Module (DIMM) based designs are very promising due to their non-invasive feature to the cost-sensitive DRAM dies. However, they have two critical limitations, i.e., performance bottle-necked by communication and the limited potential for memory expansion. In this paper, we address these two limitations by designing novel DIMM based accelerators located near the dis-aggregated memory pool with the support from the Compute Express Link (CXL), aiming to leverage the abundant memory within the memory pool and the high communication bandwidth provided by CXL. We propose BEACON, Scalable Near-Data-Processing Accelerators for Genome Analysis near Memory Pool with the CXL Support. BEAC-ON ad-opts a software-hardware co-design approach to tackle the above two limitations. The BEACON architecture builds the foundation for efficient communication and memory expansion by reducing data movement and leveraging the high communication bandwidth provided by CXL. Based on the BEACON architecture, we propose a memory management framework to enable memory expansion with unmodified CXL-DIMMs and further optimize communication by improving data locality. We also propose algorithm-specific optimizations to further boost the performance of BEACON. In addition, BEACON provides two design choices, i.e., BEACON- D and BEACON-S. BEACON-D and BEACON-S perform the computation within the enhanced CXL-DIMMs and enhanced CXL-Switches, respectively. Experimental results show that compared with state-of-the-art DIMM based NDP accelerators, on average, BEACON-D and BEACON-S improve the performance by 4. 70x and 4. 13x, respectively. © 2022 IEEE.

Genome Analysis for Sequence Variants in Sars-Cov -2 in Symptomatic Individuals at Tertiary Care Hospital

Background: COVID-19 is an acute viral illness caused by severe acute respiratory syndrome corona virus 2(SARS-CoV-2). Since the onset of the SARS-CoV-2 pandemic, multiple new variants of concern have emerged which are associated with enhanced transmissibility and increased virulence? It also highlights the role of the clinical interprofessional teams, public health agencies, and community participation in improving patientcare. An analysis of genomic sequencing variants of SARS-CoV-2 in symptomatic patients during 2nd and 3rd wave of pandemic by next-generation sequencing (NGS). Material(s) and Method(s): A total of 200 symptomatic patients, throat/nasopharyngeal swab were collected for real-time reverse transcription-polymerase chain reactions (RT-PCR) at tertiary care hospital, Ongole. The specimens were transported under cold chain according to guidelines to Centre for Cellular & Molecular biology (CCMB), Hyderabad, for genome sequence analysis by next generation sequencing (NGS). Study period - 2ndwave i.e., MARCH 2021 -NOVEMBER 2021 & 3rdwave i.e., DECEMBER 2021 -MARCH 2022 according to WHO. Result(s): Out of 200 samples analysed, 132 samples of 2nd wave & 68 samples in 3rd wave. Out of 132 samples, 57 Delta (B.1.617.2), 75 Delta sub-lineages. Out of 68 samples 41 Omicron (B.1.1.529), 11 Omicron lineages (BA.1), 16 Omicron (BA.2). Conclusion(s): During the 2ndwave the symptomatic patients were detected with more delta and delta sub lineages showing high mortality rate. During 3rdwave omicron and omicron sub lineages were detected more than delta showing very high transmissibility and less mortality. Continuous monitoring and analysis of the sequence variants to understand the genetic heterogenicity. Copyright © 2022 Ubiquity Press. All rights reserved.

Source tracing of the COVID-19 infection case in Guangxi, China

The study describing the process of discovery and source tracing of a native case of coronavirus disease 2019 (COVID-19) infection on Jan 2021, in Guangxi, China, to provide methodology for source investigation better in the future. Following the Epidemiological Investigation Plan for COVID-19 (version 7), information of the native COVID-19 case and related close contacts were collected. Real time reverse transcription-quantitative polymerase chain reaction was performed to detect the nucleic acids of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in samples collected from the infection case, related close contacts, and the environment, combined with serum specific antibody detection. The positive nucleic acid samples were undergone whole genome sequencing, phylogenetic analysis and analyses of variation of amino acids. The whole genome sequence from the native case and the imported asymptomatic infected case from Indonesia containing 25 nucleotide mutation sites belong to L-Lineage European Branch II. 3. The imported asymptomatic case was the source of infection of this native case. The possible route of infection was that native case was exposed to contaminated environment by imported case, due to improper personal protective equipment. A focus on local outbreaks of COVID-19 caused by SARS-CoV-2-infected people from outside China is needed.

Genome characterization and potential risk assessment of the novel SARS-CoV-2 variant Omicron (B.1.1.529)

As the novel coronavirus SARS-CoV-2 spread around the world, multiple waves of variants emerged, thus leading to local or global population shifts during the pandemic. A new variant named Omicron (PANGO lineage B.1.1.529), which was first discovered in southern Africa, has recently been proposed by the World Health Organization to be a Variant of Concern. This variant carries an unusually large number of mutations, particularly on the spike protein and receptor binding domain, in contrast to other known major variants. Some mutation sites are associated with enhanced viral transmission, infectivity, and pathogenicity, thus enabling the virus to evade the immune protective barrier. Given that the emergence of the Omicron variant was accompanied by a sharp increase in infection cases in South Africa, the variant has the potential to trigger a new global epidemic peak. Therefore, continual attention and a rapid response are required to decrease the possible risks to public health.

Covid-19 infection and hepato-biliary surgeries: From diamond princess cruise ship toward the daily routine at the end of 2021

Objectives: Since the admission of the critically ill American patients from Diamond Princess on February 11, 2020, our hospital has accepted a total of 300 Covid-19 infected patients. Materials and Methods: On January 29, 2020, we established our own PCR test method based on the SARS-CoV-2 genome data (Hirotsu Y, et al. J Virol Methods. 2020). In the PCR test for screening of all hospitalized patients, the minimum detection limit was determined based on the data of positive sample dilution experiments, and a method for testing multiple samples at once was established using the ''Pooling Strategy'' (Hirotsu Y, et al. Sci Rep. 2020). To date, the total number of PCR tests performed at our hospital has exceeded 25,832 cases. In addition, we have established a system that allows us to perform antigen/antibody testing and PCR testing at the same time for urgent hospitalization and emergency surgery cases without interfering with the emergency system. Results: With these systems in place, we have been able to achieve zero nosocomial infections and no staff waiting at home, and have been able to perform surgical operations as usual. Conclusion: Currently, the Genome Analysis Center has resumed genome analysis of the accumulated liver cancer resection specimens. Panel analysis of hepatocarcinoma-associated mutated genes (72 SMGs) using next-generation sequencers has shown a trend toward early recurrence and poor prognosis after hepatic resection in cases of multinodular hepatocarcinoma that share multiple oncogenic mutations.

Complete genome sequence and phylogenetic analysis of avian infectious bronchitis virus isolated in India

Emergence of avian infectious bronchitis virus (IBV) variants with altered tissue tropism and host range has been reported from different parts of the world. Little is known about the different IBV variants existing and emerging in India. To explore the same, an IBV isolate, namely B17 isolated from backyard chicken in Tamil Nadu was used in the present study. The complete genome of B17 was sequenced and its phylogenetic relationship with the existing vaccine strain genotypes was analysed. The phylogenetic analysis of both S1 gene and complete genome sequence grouped B17 under Mass41 genotype comprising of M41, Beaudette, H120 and H120 variant with bootstrap value of 95-100%. Further, genomic analysis of B17 revealed the possibilities of emergence of the same from H120 vaccine strain through mutations at various genes.

Research status and trend of zoonosis and zoonotic microorganisms based on pubmed database retrieval

Objective: To gather information on the research status and the hot spots of zoonosis and zoonotic microorganisms worldwide, and to provide references for the prevention and control of zoonotic diseases in China. Method: COOC 12.6 and Citespace 5.8 R1 software were used to carry out frequency statistics, co-occurrence analysis, cluster analysis, timeline analysis and burst analysis on the keywords associated with zoonosis and zoonotic microorganisms in PubMed database. Result: According to the keywords frequency statistics and co-occurrence analysis results from the year of 2001 to 2021 in pubMed database, the zoonosis and zoonotic microorganisms arousing high international attentions were classified into the following three categories: the first category was commonly observed zoonotic microorganisms such as Brucella, hepatitis E virus, Streptococcus, Escherichia coli (E. coli) and Salmonella, to which continuous public attentions were still needed to be paid;the second category was the zoonotic microorganisms worldwide concerned in recent years such as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and influenza A virus, which were worthy of more in-depth research to control the spread of these diseases as soon as possible;the third category was the zoonosis that had massively prevailed in specific regions abroad such as Q fever and middle east respiratory syndrome (MERS), and these diseases were expected to be noticed in terms of imported risks to avoid their outbreaks in China. In addition to the above mentioned zoonosis and zoonotic microorganisms, some keywords associated with detection and diagnosis such as phylogeny and PCR were also of high interests. The cluster analysis generated a total of 10 clusters, in which the tick-borne infectious disease cluster suggested the role of ticks in the transmission of zoonotic diseases;the results of timeline and burst analysis demonstrated that among the zoonotic microorganisms, the attentions being paid to influenza A virus and SARS-CoV-2 were gradually increasing. At the same time, the detection technology of zoonotic microorganisms was evolving from specific sequence detection to whole genome sequencing. These fields were likely to be the research direction and trend in the future.

SARS-CoV-2 mutation hotspots incidence in different geographic regions

SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) is RNA virus with a positive-sense single-strand that belongs to the beta-coronavirus group that causes COVID-19 (Coronavirus Disease 2019) which originally emerged in China. Viruses with RNA genomes are known by a high mutation rate potential. The mutation rate determines genome variability and evolution of the virus;therefore, allowing viruses to evade the immune system, gain more infectivity potentials, virulence modifications, and probably resistance development to antivirals. A total of 311 SARS-CoV-2 virus whole genome sequences have been retrieved from the GISAID database from 1st of January 2020 to 31th of August 2020. The sequences were analyzed for sequence purity and multiple sequence alignment together with reference sequence was conducted through using Clustal Omega that is imbedded in Jalview software and Blast tools. We recorded the occurrence of 4 newly incident high frequently occurring mutations in all six geographic regions, namely at positions 2416, 18877, 23401, and 27964. The majority of all recorded hotspots were detected in Asia, Europe, and North America. The findings of our study suggest that the SARS-CoV-2 is in continuous evolution. For the impact of these mutations, further investigations are required and to understand whether these mutations would lead to the appearance of Drug-resistance viral strains, strains with increased infectivity and pathogenicity, and also their effect on the vaccine development and immunogenesis.

Identification and molecular characteristics of infectious bronchitis virus isolated from Shanxi Province

Chicken infectious bronchitis (IB) is one of the epidemic diseases that cause severe economic loss to poultry industry and induced by the infection of infectious bronchitis virus (IBV). IBV was prone to mutation and recombination due to its genomic characteristics, resulting in new antigenic variants. In order to understand the prevalence and variation of IBV in Shanxi province and provide reference for IB epidemic prevention and control in this area, tissues of a broiler flock suspected of respiratory virus infection were collected in Jinzhong city, Shanxi province. Through PCR identification, chicken embryo inoculation, and sequencing verification, an IBV strain was isolated and named CK/Shanxi-01/2021. On the basis of S1 gene sequencing, the sequence was compared with those of the representative IBV strains of different genotypes deposited in NCBI database, and the phylogenetic tree was constructed. The results of genetic evolution analysis showed that the IBV strain isolated in this study was belonged to GI-19 genotype. The sequence alignment of CK/Shanxi-01/2021 with common IBV vaccine strains H120, M41, H52, 4/91, and LDT3-A showed that the nucleotide homology between the isolated strain and the current common vaccine strain was 78.1%-85.2%, and the amino acid homology was only 75.2%-78.4%. Compared with the sequences of GI-19 genotype strains, some new mutations, including V68I, S120A, A271T, N282T, and N291S, were identified in the S1 protein hypervariable region(HVR). Therefore, it is of great significance for the prevention and control of IB epidemic to strengthen the epidemiological monitoring of IBV and timely grasp the current epidemic IBV genotype and its variation characteristics.