ABSTRACT
INTRODUCTION: Human mastadenovirus (HAdV) types 8, 37, 64 have been considered the major contributors in Epidemic keratoconjunctivitis (EKC) epidemics, but recent surveillance data have shown the involvement of emerging recombinants, including HAdV-53, HAdV-54, and HAdV-56. In our initial work, positive samples for adenovirus revealed that our strains were closer to HAdV-54 than HAdV-8. Hence, the current study aimed to use whole genome technology to identify the HAdV strain correctly. METHODOLOGY: Oxford Nanopore technique was used, wherein a Targeted sequencing approach using long-range PCR amplification was performed. Primers were designed using HAdV-54 (AB448770.2) and HAdV-8 (AB897885.1) as reference sequences. Amplicons were sequenced on the GridION sequencer. Sequences were annotated using Gatu software, and similarities with standard reference sequence was calculated using Bioedit software. The phylogenetic tree was built after alignment in MEGA v7.0 using Neighbour joining method for each of the genes: Penton, Hexon, and Fiber. The effect of novel amino acid changes was evaluated using the PROVEAN tool. The Recombination Detection Program (RDP) package Beta 4.1 was used to identify recombinant sequences. RESULTS: Of the five samples sequenced, OL450401, OL540403, and OL540406 showed nucleotide similarity to HAdV-54 in the penton region. Additionally, OL450401 showed a statistically significant recombination event with HAdV-54 as minor and HAdV-8 as major parents. This was further supported by phylogenetic analysis as well. CONCLUSIONS: In the present study, we have found evidence of a shift from HAdV-8 towards HAdV-54, thus stressing the need for surveillance of HAdVs and to stay updated on the rise of new recombinants.
Subject(s)
Adenovirus Infections, Human , Adenoviruses, Human , Keratoconjunctivitis , Mastadenovirus , Humans , Adenovirus Infections, Human/epidemiology , Adenovirus Infections, Human/genetics , Adenoviruses, Human/genetics , Genome, Viral , India/epidemiology , Keratoconjunctivitis/epidemiology , Mastadenovirus/genetics , Phylogeny , Sequence Analysis, DNAABSTRACT
BACKGROUND AND OBJECTIVES: India has witnessed significant number of cases of co-infection of malaria or dengue with COVID-19, especially during the monsoon season. It has been speculated that anti-malarial immunity might have a protective role in co-infection. Retrospective analysis of co-infection of vector-borne diseases with COVID-19 was done for comparing their remission with matched controls with COVID-19 by means of epidemiological data. METHODS: Medical case records of patients with co-infection of malaria or dengue with COVID-19 admitted at TNMC and BYL Nair Charitable Hospital from 1 March 2020 to 31 October 2020 were analyzed retrospectively. Out of 91 cases of co-infection of SARS-CoV-2 infection with vector-borne diseases, virus clearance (VC) analysis was done for 61 co-infections with malaria. RESULTS: Median duration of VC for co-infection with malaria was 8 days whereas, it was 12 days for controls with COVID-19 (p=0.056). Young patients (≤50 years) with co-infection recovered faster than controls age (p=0.018). INTERPRETATION & CONCLUSION: Co-infection with malaria is associated with less severe disease and early recovery in the form of early VC. Genetic and immunological studies are necessary to confirm malaria protection against SARS-CoV-2 infection.
