Volume 02 · Issue 02 · 2020

The infrastructure needed to detect Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection (COVID-19) that complies completely with WHO guidelines is lacking across many parts of the globe, especially in developing countries, including Nepal. We outline the problems faced by such countries and suggest that the national and international community should collaborate in the development and adoption of novel protocols for the rapid detection of COVID-19 according to locally available infrastructure, in order to fight against the outbreak.

As of March 12^th Italy has the largest number of SARS-CoV-2 cases in Europe as well as outside China. The infections, first limited in Northern Italy, have eventually spread to all other regions. When controlling an emerging outbreak of an infectious disease it is essential to know the key epidemiological parameters, such as the basic reproduction number R₀, i.e. the average number of secondary infections caused by one infected individual during his/her entire infectious period at the start of an outbreak. Previous work has been limited to the assessment of R₀ analyzing data from the Wuhan region or Mainland China. In the present study the R₀ value for SARS-CoV-2 was assessed analyzing data derived from the early phase of the outbreak in Italy. In particular, the spread of SARS-CoV-2 was analyzed in 9 cities (those with the largest number of infections) fitting the well-established SIR-model to available data in the interval between February 25–March 12, 2020. The findings of this study suggest that R₀ values associated with the Italian outbreak may range from 2.43 to 3.10, confirming previous evidence in the literature reporting similar R₀ values for SARS-CoV-2.

The aim of this study was to perform an epidemiological analysis of the viral strains isolated from outpatients with acute gastroenteritis in Dalian, Liaoning province, China to determine the epidemiology of Norovirus (NoV). Fecal samples were collected from 789 outpatients with acute gastroenteritis in the Xigang district of Dalian, Liaoning province, China from July 2015 to December 2016. Norovirus was detected by real-time reverse transcriptase-polymerase chain reaction (RT-PCR). A selection of the positive samples identified was subsequently sequenced, and these data were analyzed by using the Norovirus Typing tool. Results showed that 38.02% (300/789) of the fecal samples were positive for NoV, of which 95.67% (287/300) were identified as genotype GII with 1.33% (4/300) identified as GI. A further 3.00% (9/300) were combined infections with both GI and GII Norovirus. When analyzing the age distribution, the infections primarily occurred in adults especially the elderly whose NoV positive rate was much higher than the average. Winter was the season when most cases were recorded during 2015 and 2016; however, another infection peak was observed in July 2016. Thirty Norovirus positive samples were successfully sequenced, and results showed that GII.4 was the most commonly identified genotype, along with GII.3 and GII.17. Norovirus is the most common pathogen for acute gastroenteritis in Dalian, Liaoning province of China. The current NoV genotype prevalence in Dalian was found to be similar to that in other regions of China. Genotype GII.4 was the most common genotype in our study, GII.3 and GII.17 were also identified.

Anti-influenza drugs are one of the most critical pathways for control of influenza virus infection. Drugs that have been developed or are developing may function via different mechanisms, and so far, inhibitors of influenza virus polymerase are among the most promising types of drugs. Favipiravir and Baloxavir, also named T-705 and Xofluza respectively, have been approved for influenza treatment in Japan and the United States. Favipiravir effectively and selectively inhibits the RNA-dependent RNA polymerase (RdRp) of RNA viruses while Baloxavir specifically targets the cap-dependent endonuclease PA of influenza viruses. These two drugs have been suggested as the first candidate drugs for influenza infection treatment, especially for strains resistant to other anti-influenza drugs. This review will focus on the pharmaceutical mechanisms and anti-influenza activity of these two drugs.

Colistin is an old antimicrobial that has been revitalized as last-resort treatment against multidrug-resistant (MDR) gram-negative bacterial infections. However, colistin has been widely used in agricultural production and veterinary medicine for decades, and the recent global dissemination of mobilized colistin resistance (mcr) genes from animals to humans seriously threats the clinical use of colistin. Most of the mcr-harboring isolates have been Enterobacteriaceae, such as Escherichia coli and Salmonella enterica which are common to animals and humans. An understanding of the origin, dissemination and transmission of mcr genes in bacteria common to animals and humans will facilitate the management of colistin use and relevant interventions to prevent further spread of resistance. This review aims to provide a comprehensive assessment of the global prevalence and transmission of mcr genes of animal and human commensal/pathogenic bacteria.

In this study, we explored the viral diversity and community structures of the ticks collected from dogs and detected possible tick-borne viruses (TBVs) using metagenomic analysis. Additionally, full-length sequences and the structural, phylogenetic and molecular features of the possible TBVs were characterized using bioinformatics tools. The sequence run produced 12,254,268 reads and 6,667,259 unique reads from the tick pools. Further analysis of the viral reads revealed that 92.73% were similar to ssRNA viruses, and 90.5% of the total viral sequences belonged to Non-classified viral families. Of the 29 classified viral families, most virome sequences were homologous with vertebrate viruses from Circoviridae, plant viruses from Virgaviridae, phages from Microviridae, insect viruses from Baculoviridae, and giant viruses from Mimiviridae. In the process of assembly of reads, large contigs representing four virus families were identified, including Phenuiviridae, Chuviridae, Parvoviridae and Non-classified families. Some sequences of Non-classified family shared a highly divergent amino acid sequence identities from existing virus sequences. The importance of these newly identified virus contigs to public and veterinary health needs additional researches. Because of the lack of the acquired viral reads from these families, we only demonstrated the complete sequences of Circoviridae in detail. The complete canine circovirus (CaCV)-NC21 genome detected from police dogs was 2,063 bp long with a GC content of 53.6%. Our results suggested that tick viromes collected from dogs contained diverse sequences with a broad range of animal, insect, plant, and phage viruses, which may reflect the ecological characteristics of the dogs and their ticks. Furthermore, our study revealed the existence of the partial contigs belonging to the four virus families in ticks. More researches are needed to verify their importance to public and veterinary health. As well, our detection of CaCv-NC21 demonstrated that ticks can harbor and potentially transmit canine circoviruses.

Fever and rash illnesses (FRIs) are a series of common diseases with fever and rashes as clinical manifestations, most of which are caused by viral infection. The rashes of FRIs are generally nonspecific; therefore it is difficult to identify FRI-associated viruses solely based on clinical symptoms. To achieve rapid and accurate identification of FRI pathogens, a multiplex one-step real-time reverse transcription-polymerase chain reaction (RT-PCR) assay was developed and evaluated in this study. Primers and probes were selected for the detection of measles virus (MeV), rubella virus (RV), human enterovirus (EV), varicella-zoster virus (VZV), dengue virus (DENV), human parvovirus B19 (B19), Epstein-Barr virus (EBV), and human herpes virus 6 (HHV-6), which cover the most common pathogenic viruses of FRIs. Detection of the eight FRI-associated viruses, which was divided into two groups/tubes, was simultaneously performed under universal optimized reaction conditions in multiplex one-step real-time RT-PCR assay. The multiplex realtime RT-PCR showed high sensitivity and specificity in detecting the eight FRI-associated viruses. The limits of detection (LODs) for the eight viruses were in the range of 47–177 copies/reaction, and no cross reactions for the eight FRI-associated viruses were found in the multiplex assay. In addition, the results of the multiplex real-time RT-PCR assay were consistent with the results of a monoplex real-time RT-PCR assay and sequencing for clinical specimens obtained from FRI patients. With its advantages of high efficiency and rapid and accurate diagnosis, multiplex real-time RT-PCR was very feasible for the early diagnosis of FRI pathogenic viruses and would be of great help for the proper treatment, monitoring, and initiation of preventive measures for FRI cases.

Infectious diseases remain as an important public health threat to humans. Research into pathogens can be useful for planning an organized response to infectious diseases. Bibliometric analysis is an important method for scientific research and assessing capability. In this study, 100 pathogens of public health importance were selected, and the distributions of annual, national, institutional, and journal publications on Science Citation Index (SCI) journals were statistically analyzed. The United States of America ranked the first in terms of the number of relevant studies published. China attaches great importance to the prevention and control of infectious diseases, but still needs to improve in the following areas: for example, insufficient SCI reports on particular pathogens, institutions SCI reports on pathogens lower than world top pathogen research institutions, and lack of influential international pathogen-related journals. Scientific literature databases are important tools for science-of-science analysis. The findings of this study shed light on the hot spots and the ignored spots in pathogen researches, and thus would be useful for drawing a national and institutional research plan.

This study aimed to determine the clinical characteristics of patients diagnosed with the coronavirus disease 2019 (COVID-19). Clinical data of COVID-19 patients diagnosed between January 28, 2020 and February 23, 2020 at the Beijing You'an Hospital were summarized and analyzed. Overall, 45 (18 men and 27 women) patients were included in this study. The average age of patients was 58 years (range, 7–94 years). Furthermore, 21 patients (47%) experienced underlying chronic diseases, with another four patients (9%) having three or more chronic diseases simultaneously. The first symptoms appeared at the onset of illness onset include fever in 36 patients (80%), cough in 23 patients (51%), and expectoration in 15 patients (33%), respectively. Patients may experience hepatic and renal injury as well as abnormal myocardial enzymes in varying degrees. Senior patients (≥58) and accompanying chronic diseases were considered as independent predictors for developing a severe and critically ill population with increased mortality. Laboratory results regarding the NEU percentage, NLR, ALC, and C-reactive protein levels were considered significant in predicting clinically critical disease or for prognosis assessment and thus require further studies. COVID-19 may affect multiple organs of the human body. Glucocorticoid is considered effective in the treatment of patients diagnosed with severe COVID-19.