Observing inhibition of the SARS-CoV-2 helicase at single-nucleotide resolution.

The genome of SARS-CoV-2 encodes for a helicase (nsp13) that is essential for viral replication and highly conserved across related viruses, making it an attractive antiviral target. Here we use nanopore tweezers, a high-resolution single-molecule technique, to gain detailed insight into how nsp13 turns ATP-hydrolysis into directed motion along nucleic acid strands. We measured nsp13 both as it translocates along single-stranded DNA or unwinds double-stranded DNA. Our data reveal nsp13's single-nucleotide steps, translocating at ∼1000 nt/s or unwinding at ∼100 bp/s. Nanopore tweezers' high spatiotemporal resolution enables detailed kinetic analysis of nsp13 motion. As a proof-of-principle for inhibition studies, we observed nsp13's motion in the presence of the ATPase inhibitor ATPγS. We construct a detailed picture of inhibition in which ATPγS has multiple mechanisms of inhibition. The dominant mechanism of inhibition depends on the application of assisting force. This lays the groundwork for future single-molecule inhibition studies with viral helicases.

Infection with Decapod iridescent virus 1: an emerging disease in shrimp culture.

For the last 3 decades the shrimp industries has been plagued by many destructive diseases, which have resulted in severe production and economic losses to many aquaculture countries. These include viral, bacterial and parasitic diseases. Recently, another emerging viral disease is threatening the shrimp culture industry in Asia. The virus originally called Cherax quadricarinatus iridovirus (CQIV) or Shrimp hemocyte iridescent virus (SHIV) and now classified within the proposed genus Decapodiridovirus and formally named as Decapod iridescent virus 1 (DIV1) by International Committee on Taxonomy of Viruses (ICTV). The virus was first detected as early as 2014 from Cherax quadricarinatus samples in Fujian Province and farmed white leg shrimp Penaeus vannamei samples from Zhejiang Province. This review article encompasses the significance of the DIV1 and their implications for the future of the global aquaculture.

Inhibition of the SARS-CoV-2 helicase at single-nucleotide resolution.

The genome of SARS-CoV-2 encodes for a helicase called nsp13 that is essential for viral replication and highly conserved across related viruses, making it an attractive antiviral target. Here we use nanopore tweezers, a high-resolution single-molecule technique, to gain detailed insight into how nsp13 turns ATP-hydrolysis into directed motion along nucleic acid strands. We measured nsp13 both as it translocates along single-stranded DNA or unwinds short DNA duplexes. Our data confirm that nsp13 uses the inchworm mechanism to move along the DNA in single-nucleotide steps, translocating at ~1000 nt/s or unwinding at ~100 bp/s. Nanopore tweezers' high spatio-temporal resolution enables observation of the fundamental physical steps taken by nsp13 even as it translocates at speeds in excess of 1000 nucleotides per second enabling detailed kinetic analysis of nsp13 motion. As a proof-of-principle for inhibition studies, we observed nsp13's motion in the presence of the ATPase inhibitor ATPγS. Our data reveals that ATPγS interferes with nsp13's action by affecting several different kinetic processes. The dominant mechanism of inhibition differs depending on the application of assisting force. These advances demonstrate that nanopore tweezers are a powerful method for studying viral helicase mechanism and inhibition.

Inhibition of the SARS-CoV-2 helicase at single-nucleotide resolution.

The genome of SARS-CoV-2 encodes for a helicase called nsp13 that is essential for viral replication and highly conserved across related viruses, making it an attractive antiviral target. Here we use nanopore tweezers, a high-resolution single-molecule technique, to gain detailed insight into how nsp13 turns ATP-hydrolysis into directed motion along nucleic acid strands. We measured nsp13 both as it translocates along single-stranded DNA or unwinds short DNA duplexes. Our data confirm that nsp13 uses the inchworm mechanism to move along the DNA in single-nucleotide steps, translocating at ~1000 nt/s or unwinding at ~100 bp/s. Nanopore tweezers high spatio-temporal resolution enables observation of the fundamental physical steps taken by nsp13 even as it translocates at speeds in excess of 1000 nucleotides per second enabling detailed kinetic analysis of nsp13 motion. As a proof-of-principle for inhibition studies, we observed nsp13s motion in the presence of the ATPase inhibitor ATP{gamma}S. Our data reveals that ATP{gamma}S interferes with nsp13s action by affecting several different kinetic processes. The dominant mechanism of inhibition differs depending on the application of assisting force. These advances demonstrate that nanopore tweezers are a powerful method for studying viral helicase mechanism and inhibition.

Infestation of Lernaeenicus seeri (Copepoda: Pennellidae) and Hirudinella ventricosa (Digenea: Hirudinellidae) on wahoo Acanthocybium solandri collected from Parangipettai, southeast coast of India.

A commercially important fish, wahoo Acanthocybium solandri (Cuvier, 1832) (Scombridae), was collected to study the infestation of parasites from Parangipettai landing center, Tamil Nadu, southeast coast of India for a period of one year from January to December 2011. A total of 644 fish were captured and screened for parasites. Off 644 fish, 270 were infested by a parasitic copepod Lernaeenicus seeri Kirtisinghe, 1934 (Siphonostomatoida: Pennellidae) on the body surface. It is a mesoparasite, since the head and neck are inserted and attached to the muscle by making a wound/hole on the body and the rest of the parasite body with the egg sacs hanging outside. Prevalence was recorded as 42.29% with mean and maximum intensity at 3.22 and 33, respectively. Seasonal study showed that the prevalence was highest (62.82 %) during postmonsoon. Simultaneously, some of the fish (n = 144) were internally observed for the presence of parasites and we found that 101 fish were infested with an endoparasite digenean Hirudinella ventricosa (Pallas, 1774) (Hirudinellidae) in the stomach. Prevalence was recorded as 70.9%, and mean intensity of 1.62 and maximum intensity of 3 were also noted. The overall percentage of both copepod and digenean infestation were recorded as 60.42%. The infestation was high in postmonsoon season for both parasites. This is the first record of L. seeri from Indian waters and the second record of occurrence worldwide. Significant interactions were observed between season and infestation of both parasites (P<0.05).

Occurrence of heavy copepod infestation on Hemiramphus lutkei and double parasitisms on Hemiramphus far with copepod (Lernaeenicus hemiramphi) and isopod (Mothocya plagulophora).

In the present study about, 66 copepod parasites of Lernaeenicus hemiramphi of two Hemiramphus sp., H. far (17 copepod) and H. lutkei (49 copepod), and an isopod (Mothocya plagulophora) on the gill chamber were observed. H. lutkei was added as a new host for L. hemiramphi. The copepod infestation was almost on the ventral side of the hosts.

Occurrence of tumour (odontoma) in marine fish Sphyraena jello from the southeast coast of India.

We examined the occurrence of odontoma in the marine fish Sphyraena jello sourced from 3 different landing centers (Cuddalore, Parangipettai and Nagapattinam) in Tamil Nadu (southeast India). A total of 19783 fishes were examined for odontoma presence, of which 2393 were affected with odontoma. The overall prevalence was 12.1% among the 3 stations. Fish landed at Parangipettai showed the highest peak prevalence of odontoma (16.8%) during the pre-monsoon, followed by Nagapatinam (9.1%) during summer 2011. The tumour lengths in premaxilla, supermaxilla and dentary bone were 1.1-3.6, 1.4-5.9 and 1.2-4.1 cm, respectively, and tumour widths were 0.3-1.9, 0.7-3.1 and 0.5-1.9 cm. Higher prevalence (0.206%) of tongue tumour along with odontoma was observed at Nagapattinam whereas it was lower (0.162%) at Cuddalore. Odontoma histopathology showed dense fibrous tissue with fine teeth roots. TEM analysis showed virus-like particles associated with odontoma. Radiography of the odontoma showed that the tumour masses were bony in nature and tissues were merged with upper and lower jaw.