Classification of Highly Divergent Viruses from DNA/RNA Sequence Using Transformer-Based Models.

Viruses infect millions of people worldwide each year, and some can lead to cancer or increase the risk of cancer. As viruses have highly mutable genomes, new viruses may emerge in the future, such as COVID-19 and influenza. Traditional virology relies on predefined rules to identify viruses, but new viruses may be completely or partially divergent from the reference genome, rendering statistical methods and similarity calculations insufficient for all genome sequences. Identifying DNA/RNA-based viral sequences is a crucial step in differentiating different types of lethal pathogens, including their variants and strains. While various tools in bioinformatics can align them, expert biologists are required to interpret the results. Computational virology is a scientific field that studies viruses, their origins, and drug discovery, where machine learning plays a crucial role in extracting domain- and task-specific features to tackle this challenge. This paper proposes a genome analysis system that uses advanced deep learning to identify dozens of viruses. The system uses nucleotide sequences from the NCBI GenBank database and a BERT tokenizer to extract features from the sequences by breaking them down into tokens. We also generated synthetic data for viruses with small sample sizes. The proposed system has two components: a scratch BERT architecture specifically designed for DNA analysis, which is used to learn the next codons unsupervised, and a classifier that identifies important features and understands the relationship between genotype and phenotype. Our system achieved an accuracy of 97.69% in identifying viral sequences.

A case of acquired immunodeficiency syndrome-related Kaposi sarcoma in a patient with COVID-19 - A brief review of HIV-COVID Co-infection and its Therapeutic challenges!

Barriers posed by the COVID-19 pandemic have led to reduced access to Human Immunodeficiency virus (HIV) care, leaving untreated patients at risk for various superimposed infections and malignancies such as Kaposi sarcoma (KS). We recently encountered a 37-year-old African-American male with a past medical history of HIV who tested positive for SARS-CoV-2 and was diagnosed with AIDS-related disseminated KS, representing the first reported case of COVID-19 infection with a newly diagnosed concomitant KS. The patient experienced multi-organ failure requiring tracheostomy, renal replacement therapy, and a prolonged intensive care unit (ICU) stay. Goals of care were changed to comfort measures and the patient passed away shortly afterwards. He was made comfort measures and passed away shortly afterwards. AIDS-related KS is a vascular tumor seen in association with Human Herpes Virus-8 (HHV-8). Management of limited AIDS-related KS typically includes combined antiretroviral therapy (ART) while multi-organ KS disease demands systemic chemotherapy. Immunosuppression should be avoided in patients with AIDS-related KS as it can lead to progression of KS. This recommendation is in conflict with the usual standard of care for patients with COVID-19 pneumonia, requiring clinical judgment and a customized approach based on the stage and severity of both the KS and the COVID-related disease. We briefly review HIV-COVID-19 coinfection, AIDS related KS and challenges associated with their management.

IgG4 related lung disease- a rare and novel mimic of malignancy and infections-a case series of three patients with a brief review of updated literature.

IgG4-related lung disease is an extremely rare and novel entity which is still poorly understood. We reviewed the 16 patients diagnosed with IgG4-related disease from October 2014 through December 2019 at our institution. The three cases that showed pulmonary involvement are included in this series. Of these, two patients had cavitary lung disease and developed aspergilloma and chronic cavitating aspergillosis after a prolonged course of steroid therapy, and one had isolated pulmonary nodule and ground glass opacity. We reviewed the updated literature and briefly described disease epidemiology, clinical characteristics, diagnostic approaches, and management strategies for IgG4-related lung disease.

Pancreatic cancer Masquerading as lung nodules: A Diagnostic Dilemma.

To our knowledge, this is the first report of isolated pulmonary nodules as an initial presentation of underlying pancreatic cancer. We present a case of metastatic pancreatic cancer which manifested as worsening bilateral pulmonary nodules and normal abdominal imaging in a 72-year-old female patient. A navigational bronchoscopy with biopsy of lung nodules was performed which showed poorly differentiated adenocarcinoma. Carcinoembryonic antigen and CA 19-9 levels were elevated so endoscopic ultrasound with fine needle aspiration was done which revealed an underlying occult pancreatic adenocarcinoma. The patient was treated with chemotherapy. Patients with pulmonary metastasis have been shown to confer longer survival as compared to metastatic disease involving other organs. We have briefly reviewed the epidemiology, clinical characteristics and management of such cases in our report.

Maltoma veiled in the lung-a rare case of pulmonary and gastric maltoma.

Mucosa associated lymphoid tissue (MALT) is a type of B-cell lymphoma that is commonly observed in the gastrointestinal site, most frequently occurring in the stomach. However, the incidence of this type of lymphoma in the respiratory tract is very uncommon. We report a case of this rare clinical entity in a patient who presented with non-symptomatology and was diagnosed with pulmonary MALT lymphoma (pMALToma).