Early diagnosis and treatment of human immunodeficiency virus type 1 (HIV-1) infection in infants can greatly reduce mortality rates. However, current infant HIV-1 diagnostics cannot reliably be performed at the point of care, often delaying treatment and compromising its efficacy. Recombinase polymerase amplification (RPA) is a novel technology that is ideal for an HIV-1 diagnostic, as it amplifies target DNA in pol ) and can reliably detect 3 copies of proviral DNA by the use of fluorescence detection and lateral-flow strip detection. These pol and LTR primers amplified 98.6% and 93%, respectively, of the diverse HIV-1 variants tested. This is the first example of an isothermal assay that consistently detects all of the major HIV-1 global subtypes. IMPORTANCE Diagnosis of HIV-1 infection in infants cannot rely on the antibody-based tests used in adults because of the transfer of maternal HIV-1 antibodies from mother to child. Therefore, infant diagnostics rely on detection of the virus itself. However, current infant HIV-1 diagnostic methods require a laboratory setting with complex equipment. Here we describe the initial development of an HIV-1 diagnostic for infants that may be performed at the point of care in rural health clinics. We utilize a method that can amplify and detect HIV-1 DNA at an incubation temperature within the range of 25 to 42°C, eliminating the need for thermocycling equipment. HIV-1 diagnostics are challenging to develop due to the high diversity seen in HIV-1 strains worldwide. Here we show that this method detects the major HIV-1 strains circulating globally.

Rapid Detection of HIV-1 Proviral DNA for Early Infant Diagnosis Using Recombinase Polymerase Amplification

Review of global rotavirus strain prevalence data from six years post vaccine licensure surveillance: Is there evidence of strain selection from vaccine pressure?

The rampant spread of COVID-19 and the worldwide prevalence of infected cases demand a rapid, simple, and cost-effective Point of Care Test (PoCT) for the accurate diagnosis of this pandemic. The most common molecular tests approved by regulatory bodies across the world for COVID-19 diagnosis are based on Polymerase Chain Reaction (PCR). While PCR-based tests are highly sensitive, specific, and remarkably reliable, they have many limitations ranging from the requirement of sophisticated laboratories, need of skilled personnel, use of complex protocol, long wait times for results, and an overall high cost per test. These limitations have inspired researchers to search for alternative diagnostic methods that are fast, economical, and executable in low-resource laboratory settings. The discovery of Loop-mediated isothermal Amplification (LAMP) has provided a reliable substitute platform for the accurate detection of low copy number nucleic acids in the diagnosis of several viral diseases, including epidemics like Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS). At present, a cocktail of LAMP assay reagents along with reverse transcriptase enzyme (Reverse Transcription LAMP, RT-LAMP) can be a robust solution for the rapid and cost-effective diagnosis for COVID-19, particularly in developing, and low-income countries. In summary, the development of RT-LAMP based diagnostic tools in a paper/strip format or the integration of this method into a microfluidic platform such as a Lab-on-a-chip may revolutionize the concept of PoCT for COVID-19 diagnosis. This review discusses the principle, technology and past research underpinning the success for using this method for diagnosing MERS and SARS, in addition to ongoing research, and the prominent prospect of RT-LAMP in the context of COVID-19 diagnosis.

Loop-Mediated Isothermal Amplification (LAMP): A Rapid, Sensitive, Specific, and Cost-Effective Point-of-Care Test for Coronaviruses in the Context of COVID-19 Pandemic.

A device is described having a first surface having a plurality of first areas and a second surface having a plurality of second areas. The first surface and the second surface are opposed to one another and can move relative to each other from at least a first position where none of the plurality of first areas, having a first substance, are exposed to plurality of second areas, having a second substance, to a second position. When in the second position, the plurality of first and second areas, and therefore the first and second substances, are exposed to one another. The device may further include a series of ducts in communication with a plurality of first second areas to allow for a substance to be disposed in, or upon, the plurality of second areas when in the first position.

Slip chip device and methods

Studies on genetic diversity of rotaviruses have been primarily based on the genes encoding the antigenically significant VP7 and VP4 proteins. Since the rotavirus genome has 11 segments of RNA that are vulnerable to reassortment events, analyses of the VP7 and VP4 genes may not be sufficient to obtain conclusive data on the overall genetic diversity, or true origin of strains. In the last few years following the advent of the whole-genome-based genotype classification system, the whole genomes of at least 167 human group A rotavirus strains have been analyzed, providing a plethora of new and important information on the complex origin of strains, inter- and intra-genogroup reassortment events, animal-human reassortment events, zoonosis, and genetic linkages involving different group A rotavirus gene segments. In addition, the whole genomes of a limited number of human group B, C and novel group rotavirus strains have been analyzed. This article briefly reviews the available data on whole-genomic analysis of human rotavirus strains. The significance and future prospects of whole-genome-based studies are also discussed.

Whole-genomic analysis of rotavirus strains: current status and future prospects.

Rapid detection of human immunodeficiency virus type 1 group M by a reverse transcription-loop-mediated isothermal amplification assay.

A rare genotype G6P[9] was identified in two human group A rotavirus strains designated as KF14 and KF17, that were detected in stool specimens from children with diarrhea in Japan. VP7 gene sequences of these two strains were identical and genetically closely related to G6 human rotavirus strains reported in European countries and the United States. To our knowledge, this is the first report of detection of a G6 human rotavirus in Japan. For further genetic analysis to elucidate the origin of the G6 rotavirus, nearly full-length sequences of all 11 RNA segments were determined for the KF17 strain. The complete genomic constellation of KF17 was determined as G6-P[9]-I2-R2-C2-M2-A3-N2-T3-E3-H3, a novel genotype constellation for human rotavirus. Phylogenetic analysis indicated that VP6, VP1-3, and NSP2 genes of KF17 clustered with bovine-like G6 human strains and some animal strains into sub-lineages distinct from those of common DS-1-like G2 human rotaviruses. On the other hand, KF17 genes encoding VP4, NSP1, and NSP3-5 showed high sequence identities to the human G3P[9] strain AU-1, and clustered with AU-1 and some feline strains within the same lineage. These findings suggested that the G6P[9] human rotavirus detected in Japan may have occurred through reassortment among uncommon bovine-like human rotaviruses and human/feline AU-1-like rotaviruses.

Detection and full genomic analysis of G6P[9] human rotavirus in Japan

Aim Rotavirus infection is a serious gastrointestinal infection that is usually prevalent during winter months and often seen in infants and young children. Studies on genotypes of prevalent rotavirus strains are important for preventing infection, developing vaccines, and its evaluation. The purpose of this study was to make an investigation of a rotavirus infection in the Nasu Region of Tochigi, Japan and to compare findings to those of other regions. Materials and methods We examined the clinical findings in 147 patients who attended the Department of Pediatrics at International University of Health and Welfare Hospital in the Nasu-shiobara City, Tochigi Prefecture, Japan during April 1, 2008 to March 31, 2010. Results We analyzed the clinical findings of 37 patients with a fecal sample positive for rotavirus antigen. Furthermore, viral genotypes were determined using rotavirus-positive samples from 27 of these 37 patients. The genotypes were determined as G1P [8] in 5 samples, G3P [8] in 5 samples, G9P [8] in 3 samples, and G6P [9] in 2 samples. We were able to analyze the phylogenetic trees of these genotypes. Conclusion Of particular note, we detected G6P [9] which were extremely rare in humans but common in cattle. Studies on changes in prevalent strains after vaccine introduction need to be conducted.

Clinical and virological characteristics of rotavirus gastroenteritis and prevalence of strains in Tochigi, Japan.

Introduction: Relationships between adipokines, adiposity and severity of acute viral bronchiolitis in infancy have not been elucidated. Materials and Methods: We investigated the relationships bet...

Relationships Between Adipokine Profiles, Physique Index, and Severity of Bronchiolitis in Infancy

Background: Serious gastrointestinal infection of Rotavirus (RV) is usually prevalent during winter months and often seen in infants and young children. Studies on genotypes of prevalent rotavirus strains are quite important for preventing infection, developing vaccines, and its evaluation. While at least 11 G genotypes have been isolated from humans, G1, G2, G3, G4, and emerging G9 are major genotypes of human RV. Although G6 human rotavirus is quite rare, it is the major type among rotaviruses from cattle. In this study we investigated the characteristics and origin of bovine RV strains from the children of the Nasu district, Tochigi, Japan. Materials and methods: We examined the clinical findings in 147 patients who attended to the Department of Pediatrics at International University of Health and Welfare Hospital in Nasu-shiobara City, Tochigi, Japan during the time of April 1, 2008 to March 31, 2010. We analyzed the clinical findings of the 37 patients with a fecal sample positive for RV antigen on VP6, NSP4 gene RT-PCR genotyping. Viral genotypes were determined using rotavirus-positive samples from 27 of these 37 patients. Results: In 37 cases in VP6, NSP4 gene-based RT-PCR 24 samples were positive and the genotypes were determined as G1P[8] in 5 samples, G3P[8] in 5 samples, G9P[8] in 3 samples, and G6P[9] in 2 samples. Of particular note, we detected G6P[9] which were extremely rare in human beings but common in cattle. KF17 strain of a patient showed G6 type of bovine strains and P[9] was admitted to reconcile with human strains. Per match ratio in each gene of VP6, VP1, VP2, VP3, and NSP4 showed a high match rate (84.1-86.4%) with DS-1 type. Per match ratio in each gene of VP4, NSP1, NSP3, NSP4 and NSP5 also showed a high match rate (94.2-96.9%) with AU-1 type. Bovine type strain gene segments become reassortant rotaviruses major two genes in these stocks. Discussion: In the phylogenetic analysis the gene of a strain KF17 of G6P[9] was located in a human lineage including other human G6 strains. Similarly, all other genes of the strain except for the NSP3 gene were relatively closely related to at least one of the human G6 RVs reported in Europe and the U.S. In a study in Miyagi Prefecture G6P[9] (M72S11) per sample was found from a 2-year-old toddler in 2011. Also G6P[9] have been detected from more than 3 cats of Mie Prefecture. These findings suggest that human G6 RVs which had occurred by reassortment between human and bovine RVs are distributed worldwide, despite low prevalence. G6 RV may occur independently in different areas through reassortment among local strains.

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Kei Numazaki

Papers

Rapid detection of human immunodeficiency virus type 1 group M by a reverse transcription-loop-mediated isothermal amplification assay.

Detection and full genomic analysis of G6P[9] human rotavirus in Japan

Clinical and virological characteristics of rotavirus gastroenteritis and prevalence of strains in Tochigi, Japan.

Relationships Between Adipokine Profiles, Physique Index, and Severity of Bronchiolitis in Infancy

A Study on the Origin of Bovine Rotavirus Strains Detected from the Children of the Nasu District, Tochigi, Japan