Current understanding of an Emerging Coronavirus using in silico approach: Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2)

Abstract Novel coronavirus (nCoV) namely SARS-CoV-2 is being found responsible for current PANDEMIC commenced from Wuhan (China) since December 2019 and has been described with epidemiological linkage to China in about 221 countries and territories until now. In this study we have characterized the genetic lineage of SARS-CoV-2 and report the recombination within the genus and subgenus of coronaviruses. Phylogenetic relationship of thirty nine coronaviruses belonging to its four genera and five subgenera was analyzed by using the Neighbor-joining method using MEGA 6.0. Phylogenetic trees of full length genome, various proteins (spike, envelope, membrane and nucleocapsid) nucleotide sequences were constructed separately. Putative recombination was probed via RDP4. Our analysis describes that the SARS-CoV-2 although shows great similarity to Bat-SARS-CoVs sequences through whole genome (giving sequence similarity 89%), exhibits conflicting grouping with the Bat-SARS-like coronavirus sequences (MG772933 and MG772934). Furthermore, seven recombination events were observed in SARS-CoV-2 (NC_045512) by RDP4. But not a single recombination event fulfills the high level of certainty. Recombination mostly housed in spike protein genes than rest of the genome indicating breakpoint cluster arises beyond the 95% and 99% breakpoint density intervals. Genetic similarity levels observed among SARS-CoV-2 and Bat-SARS-CoVs advocated that the latter did not exhibit the specific variant that cause outbreak in humans, proposing a suggestion that SARS-CoV-2 has originated possibly from bats. These genomic features and their probable association with virus characteristics along with virulence in humans require further consideration.

Resumo O novo coronavírus (nCoV), nomeadamente SARS-CoV-2, foi considerado responsável pela pandemia atual iniciada em Wuhan (China) desde dezembro de 2019 e foi descrito com ligação epidemiológica à China em cerca de 221 países e territórios até agora. Neste estudo, caracterizamos a linhagem genética do SARS-CoV-2 e relatamos a recombinação dentro do gênero e subgênero dos coronavírus. A relação filogenética de 39 coronavírus pertencentes a seus quatro gêneros e cinco subgêneros foi analisada usando o método de Neighbour-joining usando MEGA 6.0. Árvores filogenéticas do genoma de comprimento total, várias proteínas (espícula, envelope, membrana e nucleocapsídeo), sequências de nucleotídeos foram construídas separadamente. A recombinação putativa foi testada via RDP4. Nossa análise descreve que o SARS-CoV-2, embora mostre grande semelhança com as sequências de Bat-SARS-CoVs em todo o genoma (dando semelhança de sequência de 89%), exibe agrupamento conflitante com as sequências de coronavírus do tipo Bat-SARS (MG772933 e MG772934) Além disso, sete eventos de recombinação foram observados em SARS-CoV-2 (NC045512) por RDP4. Mas nem um único evento de recombinação preenche o alto nível de certeza. A recombinação está alojada mais em genes de proteína de pico, principalmente, do que no resto do genoma, indicando que o cluster de ponto de interrupção surge além dos intervalos de densidade de ponto de interrupção de 95% e 99%. Os níveis de similaridade genética observados entre SARS-CoV-2 e Bat-SARS-CoVs defendem que o último não exibe a variante específica que causa surto em humanos, sugerindo que SARS-CoV-2 tenha se originado possivelmente de morcegos. Essas características genômicas e sua provável associação com as características do vírus, juntamente com a virulência em humanos, requerem uma consideração mais aprofundada.

Current understanding of an Emerging Coronavirus using in silico approach: Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) / Compreensão atual de um coronavírus emergente usando abordagem in silico: síndrome respiratória aguda grave - coronavírus-2 (SARS-CoV-2)

Abstract Novel coronavirus (nCoV) namely "SARS-CoV-2" is being found responsible for current PANDEMIC commenced from Wuhan (China) since December 2019 and has been described with epidemiological linkage to China in about 221 countries and territories until now. In this study we have characterized the genetic lineage of SARS-CoV-2 and report the recombination within the genus and subgenus of coronaviruses. Phylogenetic relationship of thirty nine coronaviruses belonging to its four genera and five subgenera was analyzed by using the Neighbor-joining method using MEGA 6.0. Phylogenetic trees of full length genome, various proteins (spike, envelope, membrane and nucleocapsid) nucleotide sequences were constructed separately. Putative recombination was probed via RDP4. Our analysis describes that the "SARS-CoV-2" although shows great similarity to Bat-SARS-CoVs sequences through whole genome (giving sequence similarity 89%), exhibits conflicting grouping with the Bat-SARS-like coronavirus sequences (MG772933 and MG772934). Furthermore, seven recombination events were observed in SARS-CoV-2 (NC_045512) by RDP4. But not a single recombination event fulfills the high level of certainty. Recombination mostly housed in spike protein genes than rest of the genome indicating breakpoint cluster arises beyond the 95% and 99% breakpoint density intervals. Genetic similarity levels observed among "SARS-CoV-2" and Bat-SARS-CoVs advocated that the latter did not exhibit the specific variant that cause outbreak in humans, proposing a suggestion that "SARS-CoV-2" has originated possibly from bats. These genomic features and their probable association with virus characteristics along with virulence in humans require further consideration.

Resumo O novo coronavírus (nCoV), nomeadamente "SARS-CoV-2", foi considerado responsável pela pandemia atual iniciada em Wuhan (China) desde dezembro de 2019 e foi descrito com ligação epidemiológica à China em cerca de 221 países e territórios até agora. Neste estudo, caracterizamos a linhagem genética do SARS-CoV-2 e relatamos a recombinação dentro do gênero e subgênero dos coronavírus. A relação filogenética de 39 coronavírus pertencentes a seus quatro gêneros e cinco subgêneros foi analisada usando o método de Neighbour-joining usando MEGA 6.0. Árvores filogenéticas do genoma de comprimento total, várias proteínas (espícula, envelope, membrana e nucleocapsídeo), sequências de nucleotídeos foram construídas separadamente. A recombinação putativa foi testada via RDP4. Nossa análise descreve que o "SARS-CoV-2", embora mostre grande semelhança com as sequências de Bat-SARS-CoVs em todo o genoma (dando semelhança de sequência de 89%), exibe agrupamento conflitante com as sequências de coronavírus do tipo Bat-SARS (MG772933 e MG772934) Além disso, sete eventos de recombinação foram observados em SARS-CoV-2 (NC045512) por RDP4. Mas nem um único evento de recombinação preenche o alto nível de certeza. A recombinação está alojada mais em genes de proteína de pico, principalmente, do que no resto do genoma, indicando que o cluster de ponto de interrupção surge além dos intervalos de densidade de ponto de interrupção de 95% e 99%. Os níveis de similaridade genética observados entre "SARS-CoV-2" e Bat-SARS-CoVs defendem que o último não exibe a variante específica que causa surto em humanos, sugerindo que "SARS-CoV-2" tenha se originado possivelmente de morcegos. Essas características genômicas e sua provável associação com as características do vírus, juntamente com a virulência em humanos, requerem uma consideração mais aprofundada.

Effect of Spermine-NONOate on acrosome reaction and associated protein tyrosine phosphorylation in Murrah buffalo (Bubalus bubalis) spermatozoa.

The present study was conducted to know the role of Nitric Oxide (NO) on the acrosome reaction (AR) in Murrah buffalo (Bubalus bubalis) spermatozoa. Ejaculated buffalo spermatozoa were washed, suspended in sp-TALP media containing 6 mg BSA/mL and cell concentration was adjusted to 50×10(6) cells/mL. The cells were incubated for 6h in the absence or presence of heparin (10 µg/mL) to induce capacitation. Fully capacitated spermatozoa were incubated in presence of 100 µg/mL Lysophosphatidyl choline (LPC, T1) or 100 µM Spermine-NONOate (T2) or 100 mM L-NAME (T3) or 100 µM Spermine-NONOate+100 mM L-NAME (T4) or 1 mM db-cAMP + 0.1 mM IBMX (T5) or 100µM H-89 (T6) or 100 µM Spermine-NONOate+100 µM H-89 (T7) in combination to induce acrosome reaction. The extent of AR was assessed by dual-staining of spermatozoa with trypan blue/Giemsa stain. AR-associated tyrosine-phosphorylated proteins were detected by SDS-PAGE followed by immunoblotting using monoclonal anti-phosphotyrosine antibody. Significant (P<0.05) number of spermatozoa were acrosome reacted in Spermine-NONOate (T2) treated cells but it was significantly (P<0.05) lower than LPC (T1) induced AR. Addition of Spermine-NONOate + L-NAME (T4) resulted in non significant (P>0.05) decrease in acrosome reaction. On addition of H-89 + Spermine-NONOate (T7) to sperm culture medium, resulted in significant (P<0.05) decrease in the percent acrosome reaction. Conversely, addition of db-cAMP+IBMX (T5, cAMP analogue) resulted in the significantly (P<0.05) higher number of acrosome reacted spermatozoa. Pattern of sperm protein tyrosine phosphorylation was also different in NO induced acrosome reaction compared to that of LPC. The present study concluded that nitric oxide is involved in acrosome reaction of buffalo spermatozoa by causing the tyrosine phosphorylation of proteins mainly p17 and p20 and through activation of cAMP/PKA pathway.

Ondansetron versus granisetron in the prevention of chemotherapy induced nausea and vomiting in children with acute lymphoblastic leukemia.

Effect of ondansetron and granisetron were evaluated in sixty (60) children (age 4-11 years) irrespective of sex, diagnosed case of acute lymphoblastic leukemia (ALL) who received high dose methotrexate and did not receive any antiemetic 24 hours prior to HDMTX. This was a prospective, randomized, double-blind, single center study. Of 60 children, 30 received oral ondansetron (4mg) and rest 30 granisetron (1mg) half an hour before therapy. Drugs were randomly allocated with appropriate code. The patients were followed up from day 1 to day 5 of therapy. Episodes of nausea and vomiting were recorded and scorings was done every 24 hours following chemotherapy. No significant difference was found between two groups according to acute emesis (Day-1) (p=0.053). In day two and day three it was significant (p<0.05). In day four it was significant (p=0.002). Early chemotherapy induced nausea and vomiting (CINV) were controlled 90% in children who received granisetron and 70% in children who received ondansetron. Delayed (Day 2-4) CINV were controlled in 80% of children who received granisetron and 43.4% who received ondansetron (p<0.05). Granisetron group required additional doses only 3.3% cases and ondanseton group 30% cases on the second day (p<0.05). Result was significant between two groups. About 36.7% patients had episodes of nausea on day four of chemotherapy in ondansetron group and it was only 3.3% in granisetron group due to adverse effects of antiemetic drug itself (p=0.001). Maximum episodes of vomiting were found on the second day in ondansetron group 33.3% and in granisetron group 3.3% (p=0.003). Though adverse effects like headache, constipation, abdominal pain and loose motion were common in both group of children but their number was much less in children who received granisetron. On second day of therapy score of nausea and vomiting was maximum in ondansetron and minimum in granisetron treated on day 4 and the result was significant. So, to prevent acute and delayed CINV in children with ALL, oral graniseteron can be considered as more effective and well tolerated with minimum adverse effects compared with ondansetrons.

Back pain and vertebral compression: an unusual presentation of childhood acute lymphoblastic leukemia.

Junayet, a nine years and six months old boy was admitted to the hospital because of back pain and vertebral compression fractures. The boy had been well until two months earlier, when he began to have back pain after falling on his back along with occasional fever. The pain was intermittent initially but gradually it became constant. One month before admission, he fell again and the back pain became deteriorated. He was mildly pale, liver was palpable, skin survey revealed normal, BCG scar mark was present. He had bone pain, cervical lymphadenopathy and a tender swelling on the lumbusacral region. Two weeks before admission, the hematological findings were suggestive of leukemia of lymphoblastic type. Biochemical values were normal except high level of serum lactate dehydrogenase (LDH). Cerebrospinal fluid (CSF) examination was free of malignant cell. Skeletal survey showed diffuse osteopenia of the thoracic and lumber spine with multiple compression fracture of the vertebral bodies of D7, D8, D12 and L1, L3 and L5 with increased disc space. Radiograph of the chest also showed diffuse osteopenia of ribs. Magnetic resonance (MRI) showed uniform signal intensity in the marrow throughout the spine with compressed fracture of the same vertebrae. Bone marrow morphology study and the cytochemistry of the aspirated marrow were consistent with acute lymphoblastic leukemia (ALL-L2). Then, he was started protocol based chemotherapy for induction of remission, consolidation, high dose methotrexate and maintenance therapy. Now, he is on regular follow up with repeated hematological and radiological examinations. Following six month of chemotherapy the boy was found with significant improvement of his physical, hematological and radiological abnormalities.

A national inpatient cost estimate of percutaneous endoscopic gastrostomy (PEG)-associated aspiration pneumonia.

OBJECTIVE: To present national estimates of the prevalence and costs of inpatient admissions for aspiration pneumonia (AP) associated with percutaneous endoscopic gastrostomies (PEGs) inserted before or during an admission. STUDY DESIGN: Retrospective analysis using medical claims. PATIENTS AND METHODS: National estimates of the prevalence of inpatient admissions associated with AP and mortality rates were developed, using data from the Nationwide Inpatient Sample of the Hospital Cost and Utilization Project (HCUP-3) Database. The MEDSTAT Group's MarketScan Private Pay Fee-for-Service (FFS) and Medicare FFS databases were used to calculate the percentage of admissions for AP that were preceded by a PEG or that entailed a PEG placement. Associated statistics, such as average length of stay and mean payments for these admissions, also were estimated. RESULTS: Approximately 300,000 inpatient admissions for AP took place in the United States in 1995, of which roughly 70,000 (23.9%) resulted in death. Approximately 10% of all AP admissions occurred after or entailed a PEG placement. After adjusting for differences in patients' age, gender, and health status, the total mean payments were estimated to be $26,618 per patient. This per-patient estimate translates into a national estimate of the cost of PEG-associated AP of approximately $808.2 million. CONCLUSION: The cost of PEG-associated AP is relatively high, as estimated in this study. The high inpatient mortality rates of AP imply that future efforts should be directed toward preventing AP.

Thirty-day case-fatality rates for pulmonary embolism in the elderly.

BACKGROUND: Short-term race- and sex-specific case- fatality rates for pulmonary embolism (PE) in the elderly have not been studied previously, to our knowledge. OBJECTIVES: To examine 30-day race- and sex-specific case-fatality rates of PE in the Medicare population and to determine the risk of fatality when PE was a secondary diagnosis in 6 primary concurrent conditions and 3 surgical procedures. METHODS: Case-fatality rates were determined using the Medicare Provider Analysis and Review Record tiles from 1984 through 1991. All Medicare Part A beneficiaries aged 65 years or older were included, yielding more than 400,000 patients with PE. Case-fatality rates 30 days from hospital admission were calculated for both a primary discharge diagnosis of PE and a secondary discharge diagnosis of PE. RESULTS: Blacks with PE as a primary discharge diagnosis had an overall age-adjusted case-fatality rate of 16.1% compared with a rate of 12.9% for whites. When PE was a secondary diagnosis, blacks also had higher rates than whites (34.7% vs 30.2%). Men had a fatality rate of 13.7% whereas women had a rate of 12.8% when PE was the primary diagnosis. For a secondary diagnosis of PE, men had a rate of 32.8% compared with a rate of 28.6% for women. The risk of fatality was very high when PE was a secondary discharge diagnosis in 6 primary concurrent conditions (congestive heart failure, cancer, chronic obstructive pulmonary disease, myocardial infarction, hip fracture, and stroke) and 3 common surgical procedures (coronary artery bypass graft, hip replacement, and knee replacement) relative to the case-fatality rate when PE was not present in these conditions. CONCLUSIONS: Our results indicate that there are racial and gender differences in 30-day case-fatality rates for PE in elderly patients. The high fatality risk associated with PE as a comorbid factor among common primary concurrent conditions and procedures calls attention to the need for more effective prophylaxis of deep vein thrombosis and rapid diagnosis and treatment of PE when it occurs.