This work received funding from the German Centre for Infection Research (DZIF), TTU Hepatitis Projects 5.807 and 5.704, the Deutsche Forschungsgemeinschaft (DFG) TRR179 (TP 15), and the Australian Centre for HIV and Hepatitis Virology Research.
We are indebted to Professor William Mason for his part in developing the original invPCR method and demonstrating it to us. We would like to thank Drs. Yi Ni and Florian A. Lempp for reagents (cell lines and HBV inoculum). We acknowledge Anja Rippert, Franziska Schlund, Sarah Engelhardt, and Dr. Katrin Sch&#246;neweis for technical assistance. We are grateful to Miriam Kleinig for proofreading, and to Professors Nicholas Shackel and Ralf Bartenschlager for continuous support.

1. Cell Infection and DNA Extraction
<ol>
	<li>Maintain cultured Huh7-NTCP cells8,9 in Dulbecco&#39;s Modified Eagle&#39;s Medium (DMEM) supplemented with 10% v/v fetal bovine serum, 1x Penicillin/Streptomycin, and 2 mM L-glutamine. 
	NOTE: This has previously been reported in detail40.</li>
	<li>Seed 2 x 105 cells/mL Huh7-NTCP cells into a 12-well plate with 1 mL of DMEM.</li>
	<li>If testing cell treatments (e.g., HBV inhibitors), apply them to the culture supernatant 4 h after seeding (1 day prior to HBV infection). For a negative control, apply 200 nM Myrcludex B (a potent HBV entry inhibitor41).</li>
	<li>Use heparin-column purified42 supernatant from HepAD3843 as an inoculum to infect cells at 1,000 VGE/cell in 500 &#181;L of culture media (DMEM supplemented with 10% v/v fetal bovine serum, 1x Penicillin/Streptomycin, 2 mM L-glutamine, and 2.5% v/v DMSO), containing 4% w/v polyethylene glycol 8000 [dissolved in 1x phosphate-buffered saline (PBS)].</li>
	<li>Culture the cells in a 37 &#176;C incubator (set at 5% CO2 and 90% humidity).</li>
	<li>Wash the cells twice with 1 mL of sterile 1x PBS at 16&#8211;24 h post-infection.</li>
	<li>Replace the culture media every 2 days following HBV infection until harvest.</li>
	<li>At day 3 post-infection, treat the cells with 5 &#181;M Tenofovir disoproxil and 10 &#181;M Lamivudine to limit production of HBV replicative intermediates that are amplifiable by invPCR.</li>
	<li>At day 5 post-infection, trypsinize the cells with 200 &#181;L of Trypsin-EDTA and resuspend them in 2 mL of DMEM (supplemented with 10% v/v fetal bovine serum, 1x Penicillin/Streptomycin, and 2 mM L-glutamine), also containing 5 &#181;M Tenofovir disoproxil and 10 &#181;M Lamivudine.</li>
	<li>Transfer the cell suspensions to a 6-well plate to induce one round of mitosis (which has been reported to induce loss of HBV cccDNA44 and other HBV DNA intermediates that are amplifiable by invPCR).</li>
	<li>At day 7 post-infection, trypsinize the expanded cells in 400 &#181;L of Trypsin-EDTA and resuspend the mixture in 1 mL of DMEM. Place the suspension in a 1.5 mL tube, pellet the cells by centrifugation at 500 x g for 5 min, and remove the supernatant by aspiration.</li>
	<li>(Optional) Store the cell pellets at -20 &#176;C until they are ready for DNA extraction.</li>
	<li>Extract the DNA from the cell pellet using a DNA extraction kit, as per the manufacturer&#8217;s instructions. Estimate the final DNA concentration using optical densitometry. 
	NOTE: The DNA yield in a 100 &#956;L elution volume is generally ~250-400 ng/&#956;L.</li>
</ol>
2. Inversion of DNA
<ol>
	<li>Aliquot ~1.5&#8211;2.5 &#956;g of the total DNA extract from step 1 into a 200 &#956;L PCR tube. Add the appropriate amount of restriction enzyme master-mix to result in a 40 &#956;L reaction volume containing 1x digest reaction buffer (e.g., CutSmart buffer) and 10 U NcoI-HF.</li>
	<li>Mix the reactions thoroughly and spin down in a small tube centrifuge. Incubate the restriction enzyme reaction in a PCR machine at 37 &#176;C for 1 h for optimal digestion efficiency.</li>
	<li>Inactivate the restriction enzyme by incubating at 80 &#176;C for 20 min.</li>
	<li>Transfer the entire restriction enzyme reaction to a 1.5 mL tube. Add 400 &#956;L of 1x T4 DNA ligase buffer and 500 U of T4 DNA ligase and mix it thoroughly. The large reaction volume encourages intra-molecular (as opposed to inter-molecular) ligation of the digested DNA fragments.</li>
	<li>Incubate the ligation reaction at room temperature for 2 h to ensure complete ligation.</li>
	<li>Inactivate the T4 DNA ligase at 70 &#176;C for 20 min.</li>
	<li>Add 10 &#956;L of 10% w/v sodium dodecyl sulfate to ensure complete inactivation of the T4 ligase.</li>
	<li>Mix the tubes by pulse vortexing and briefly spin down the reaction mix. Add NaCl to a final concentration of 100 mM and dextran (35&#8211;45 kDa) to a final concentration of 90 &#181;g/mL. Mix the tubes by pulse vortexing and briefly spin down the reaction mix.</li>
	<li>Add 900 &#956;L of 100% ethanol and mix by inversion. Precipitate the DNA at -20 &#176;C overnight.</li>
	<li>Pellet the precipitated DNA by centrifugation at 14,000 x g for 15 min. Remove the supernatant by aspiration with a P200 pipette. Wash the pellet with 500 &#956;L of 70% v/v ethanol and centrifugation at 14,000 x g for 15 min.</li>
	<li>Remove the ethanol by aspiration with a P200 pipette. Air-dry the DNA pellet at room temperature for 20 min.</li>
	<li>Dissolve the pellet in 20 &#956;L of H2O. Add 20 &#956;L of a restriction enzyme master-mix to result in a 40 &#956;L reaction volume containing 1x digest reaction buffer, 5 U of BsiHKAI, and 5 U of SphI-HF. Incubate the restriction enzyme reaction in a heat-block at 37 &#176;C (the optimal temperature for SphI-HF) for 1 h.</li>
	<li>Briefly spin down the reaction mix. Incubate the restriction enzyme reaction in a heat-block at 65 &#176;C (the optimal temperature for BsiHKAI) for 1 h.</li>
	<li>Briefly spin down the reaction mix.</li>
	<li>Store the inverted DNA at -20 &#176;C until the next step.</li>
</ol>
3. Nested PCR
<ol>
	<li>Remove potential amplicons from a reusable silicon mat seal using a DNA degradation solution, rinse the mat thoroughly with DNA-free water, and air-dry it at room temperature while preparing the PCR mixture.</li>
	<li>Prepare 1 mL of a 1x PCR mix containing the outer forward (5&#8217;-TTC GCT TCA CCT CTG CAC G-3&#8217;) and reverse (5&#8217;-AAA GGA CGT CCC GCG CAG-3&#8217;) primers at a concentration of 0.5 &#181;M.</li>
	<li>Add 170 &#956;L of the 1x PCR mix to wells A1 and E1 in a 96-well PCR plate.</li>
	<li>Add 120 &#956;L of the 1x PCR mix to wells B1 to H1.</li>
	<li>Add 10 &#956;L of the inverted DNA from step 2 to wells A1 and E1 (2 different inverted samples can be analyzed on the same PCR plate). Mix the reaction in each well by gently pipetting each about 10 times using a P1000 set to 100 &#956;L.</li>
	<li>Serially dilute samples from wells A1 to D1 at a ratio of 1:3 by transferring 60 &#956;L at each step. Mix the wells at each step by gently pipetting them about 10 times using a P1000 set to 100 &#956;L. Avoid forming bubbles. Repeat step 3.6 for well E1, diluting down to well H1.</li>
	<li>Aliquot 10 &#956;L of the reaction mixture using a multi-channel pipette from wells A1-H1 into wells A2-H2, A3-H3, and so on until reaching wells A12-H12 of the 96-well plate. Cover the PCR plate with the dry silicon mat from step 3.1, pressing firmly.</li>
	<li>Place the plate in a PCR machine and run the following program: 10 min at 95 &#176;C; 35 cycles of 15 s at 95 &#176;C, 15 s at 54 &#176;C and 3 min at 72 &#176;C; 7 min at 72 &#176;C; then, hold the plate at room temperature.</li>
	<li>Heat the pins of a 96-pin replicator to red-hot with a Bunsen burner and then cool for at least 5 min at room temperature.</li>
	<li>Fill the wells of a second PCR plate with 10 &#956;L of 1x PCR mix (containing a gel load-ready buffer) and the inner forward (5&#8217;-CGC ATG GAG ACC ACC GTG A-3&#8217;) and reverse (5&#8217;-CAC AGC CTA GCA GCC ATG G-3&#8217;) at 0.5 &#181;M.</li>
	<li>Carefully remove the silicon mat from the PCR plate of the 96-well plate from the first-round PCR, and avoid cross-contamination between wells.</li>
	<li>Use the cooled replicator to transfer the PCR products of the 96-well plate from first-round PCR to the newly-aliquoted 96-well plate. Carry out the nested PCR using the same conditions as in step 3.8, except for changing the initial denaturation step at 95 &#176;C from 10 min to 2 min.</li>
</ol>
4. PCR Product Isolation and Gel Extraction
<ol>
	<li>Analyze the PCR products by gel electrophoresis using a 96-well with 1.3% w/v agarose gel. For a 100 mL agarose gel, run at 200 V for 10&#8211;15 min.</li>
	<li>Excise the DNA bands from the agarose gels using disposable drinking straws. For each PCR product, place the straw and agarose gel plug into a 1.5 mL tube and trim the straw to size with scissors. 
	NOTE: It is sufficient to isolate bands only from those dilutions in which single PCR products can be resolved.</li>
	<li>(Optional) Store the tubes at -20&#176;C for later extraction.</li>
	<li>Eject the agarose plugs into each tube by squeezing on the end of the straw fragment. Add 300 &#956;L of gel extraction buffer and 5 &#956;L of gel extraction glass bead slurry to each tube.</li>
	<li>Extract the PCR products as per the manufacturer&#8217;s instructions for the gel extraction kit (except using half-volumes for washing steps) and elute the DNA from the beads with 30 &#956;L of water.</li>
	<li>Submit the purified DNA for Sanger sequencing (as per the supplier&#8217;s instructions) with the Forward primer used in the second-round nested PCR.</li>
</ol>
5. Sequence Analysis
<ol>
	<li>Confirm virus-cell DNA junctions by performing nucleotide BLAST analysis (using default settings aligning to the entire nucleotide collection). 
	NOTE: Representative results are detailed in Figure 3 below.
	<ol>
		<li>If only partial alignment of the sequence is observed, trim the 5&#8217; HBV DNA sequence before re-running a BLAST analysis.</li>
	</ol>
	</li>
	<li>Apply stringent selection criteria to determine if a given sequence represents a true integration junction as follows:
	<ol>
		<li>Include only sequences containing &#62;20 bp of a cellular sequence for confident mapping to the cellular genome.</li>
		<li>Disregard any sequences that contain restriction sites of any enzymes used within 10 bp of the supposed virus-cell integration junction, as they likely represent in vitro ligation events rather than true integration junctions.</li>
		<li>Disregard any sequences with obvious dissimilar peak fluorescence levels on either side of the supposed integration junction in sequencing chromatographs, as these are likely artifacts generated by cross-contamination during the sequencing reaction or capillary chromatography.</li>
		<li>Define unique integration events as those with the exact HBV and cellular sequences at the virus-cell junction. 
		NOTE: Repetition of unique integration events can result from clonal expansion of cells containing those integrations or cross-contamination during the PCR (which can be tested using negative-control reactions, further detailed in the representative results below). Repeated integrations into specific cellular sequences are expected to display different HBV terminal sites for each integration event, as non-homologous end-joining pathways are used15.</li>
	</ol>
	</li>
	<li>Calculate the integration frequency by multiplying the dilution factor of inverted DNA templates by the number of virus-cell junctions detected at that dilution, followed by normalization to the amount of total DNA input into the inversion reaction. Generally, the integration frequency is on the order of 1:104 cells.</li>
</ol>

S.U. is a co-applicant and co-inventor of patents protecting Myrcludex B as an HBV/HDV entry inhibitor. T.T. declares no conflicts of interest.

Before performing the protocol, it is important to note that this invPCR assay is a highly sensitive technique, capable of amplifying single copies of DNA template. Therefore, limiting contamination from PCR products is of utmost importance. General strategies to limit PCR product contamination include the following. (i) Establish physically separate areas for different steps of the method. Each area should have separate lab coats, and gloves should be changed when moving between these areas. We have listed these areas below in order from most to least likely to be contaminated: PCR product extraction and sequencing reaction set-up area (post-PCR); PCR template addition and flamed-pin transfer area (we have used PCR hoods with a decontaminating UV lamp with good results); DNA extraction and inversion area (pre-PCR); and a &#34;DNA template-free&#34; area used solely for preparing stock and PCR solutions. (ii) Be aware of air flow in the lab as a potential driver of cross-contamination. In particular, cross-contamination of PCR reactions during the flamed pin transfer step is most likely to occur and will lead to inaccurate quantification of integration frequency. PCR hoods can be used to limit these cross-currents. Negative control wells (e.g., Myrcludex B-treated samples or no template controls) in the PCR can be also used to test for cross-contamination. (iii) Limit potential PCR contaminants on pipettes and work surfaces by regularly wiping them down with a DNA degradation solution.
The protocol specified here is arranged to detect integration of a known infectious HBV clone generated from the HepAD38 cell line42. If the inoculum used is of a different HBV DNA sequence (e.g., from patient serum), then the HBV genome should be first sequenced to confirm compatibility of PCR primers and inversion design. In previously published studies19, we have used 3 sets of primers that bind conserved HBV DNA sequences flanking the expected site of HBV DNA integration junctions. Other primer sequences and protocols have been described to determine the genomic sequence of HBV44,45,46,47,48&#160;and may work successfully.
Furthermore, different HBV-susceptible cells (e.g., primary human hepatocytes, differentiated HepaRG, HepG2-NTCP cells) can be used; however, we have found that Huh7-NTCP cells provide the greatest signal-to-noise ratio, when considering the number of virus-cell DNA junctions that are amplified compared to the virus intermediate DNA that is amplified13. In particular, terminally differentiated cells such as primary human hepatocytes or differentiated HepaRG do not efficiently undergo mitosis, resulting in a high level of amplifiable HBV DNA replicative intermediates remaining within the cells. We have found that ~90% of amplified sequences represent HBV DNA rearrangements (and not integration events) in terminally-differentiated cells, compared to 70&#8211;50% in hepatoma cell lines13. These products are generally HBV DNA genomes containing large deletions in the surface and core open reading frames, or they can represent HBV quasi-species with an additional NcoI site prior to the SphI site. The amplification of these HBV species (including a schematic diagram) have been described in detail previously13.
There are several drawbacks to this method. Due to the laborious and multi-day nature of this protocol, invPCR is not suited to high-throughput analyses of a large number of samples. Furthermore, as it relies on limiting dilution titration, our method is not highly precise in quantification; although, it should easily measure log-level changes in integration frequency.
Moreover, our inversion protocol is only suited to detect integrations occurring between the DR2 and DR1 region of the HBV genome, as the majority of HBV integrations occur within this region49. NGS analysis of HBV patient tissues has shown that a large minority (up to ~50%) may also occur outside of this region49. New invPCR designs are theoretically able to detect these other integration sites, though they have not (to our knowledge) been carried out yet. Relatedly, due to the necessary restriction enzyme sites required downstream from the virus-cell junction sequence for the inversion reaction, invPCR does not detect all integrations occurring within the DR2 and DR1 regions of the HBV genome (i.e., we have estimated that ~10% of all integrations are detectable using in silico simulations13). However, when applied to a focused batch of samples with small numbers of different treatments, invPCR is one of the only practical methods for detecting integrated HBV DNA at a single base-pair resolution.
We therefore envision applications of this method serving a key role in finding viral (via mutations of the HBV inoculum), cellular (through knockout or overexpression of specific cellular genes, or through application of various drugs), and environmental (e.g., exposure to oxidative stress) factors that induce HBV DNA integration. With this method and newly developed HBV infection systems, we enable unprecedented control of these factors so that they can be well-isolated and better characterized. We also expect that this will lead to a key understanding of the cellular consequences of HBV DNA integration, including to what extent viral antigens (e.g., HBx or HBsAg50) are expressed from the integrated form, what controls this expression, and whether or not HBV integration significantly changes the cellular phenotype towards a more pro-oncogenic state. The results of these future studies will have a profound impact on the therapeutic strategies used to treat chronic hepatitis B and on the basic understanding of the virus itself.

HBV is a double-stranded DNA virus that can cause life-long chronic infection, leading to liver cirrhosis and hepatocellular carcinoma (HCC)1,2,3. While there are multiple molecular mechanisms driving HBV persistence4 (e.g., high stability of the epigenetic viral transcriptional template, evasion of immune surveillance, and low turnover of hepatocytes in the liver) and its associated risk of HCC initiation5,6 (e.g., chronic inflammation and activation of cellular stress pathways), HBV DNA integration into the host cell genome (a reported mechanism for both of these phenomena) has been poorly studied. A major reason is the lack of suitable in vitro infection systems for HBV that allow reliable detection of integration events. Here, we describe a recently-developed protocol for both in vitro generation and detection of HBV DNA integrations that can be used to elucidate the underlying molecular mechanisms and consequences thereof.
HBV replication and the formation of HBV DNA integration has been previously reviewed in detail7. Briefly, HBV enters hepatocytes using the Sodium Taurocholate Co-transporting Peptide (NTCP) as the main cellular receptor for infection8,9. The HBV nucleocapsids containing the HBV-relaxed circular DNA (rcDNA) genome enters the nucleus, where the rcDNA is converted into episomal covalently closed circular DNA (cccDNA). The nuclear cccDNA acts as the transcriptional template for viral mRNAs and pre-genomic RNA (pgRNA)10. HBV polymerase and pgRNA are then packaged into newly-formed nucleocapsids (composed of HBV core protein dimers). HBV pgRNA is reverse-transcribed within the nucleocapsid, resulting in either an rcDNA genome or a double-stranded linear DNA (dslDNA) genome11,12. These mature nucleocapsids containing HBV DNA genomes are finally enveloped and exported as virions.
Infection of hepatocytes by enveloped particles containing dslDNA molecules can result in viral integration into the host cell genome13, leading to replication-incompetent forms of HBV DNA7,14,15. HBV DNA integration occurs at the site of chromosomal double-stranded DNA breaks15. Accumulating evidence suggests that each integration event occurs in an essentially random position within the host cell genome16,17. In addition, HBV DNA integration occurs somewhat rarely, at a rate of 1 per 104 cells13,18,19,20. Important questions regarding HBV DNA integration remain unanswered, particularly regarding the exact molecular pathways involved, the dependence on viral and host factors, the viral antigens expressed from integrated forms, and their possible contribution to viral persistence7. We have set up an in vitro model to shed light on some of these questions.
The rarity of HBV DNA integration events (both with respect to integration rate per cell and to the copy number of each unique integration) in in vitro HBV infection models make them challenging to detect. Cell mitosis is limited in our in vitro system, as dividing cells do not support efficient infection. Thus, unlike in patient liver tissues where significant clonal expansion of hepatocytes occurs18,19,20, very few (1 to 2) copies of each integration are present in a given pool of cells infected in vitro. We have also found that integration mainly occurs during the initial infection of hepatocytes (and not continuously in chronically-infected hepatocytes)13. Accordingly, HBV DNA integration cannot be increased by simply culturing cells for a longer period.
In general, methods previously used to detect integrated HBV DNA, including Southern blot hybridization21,22,23,24,25, Alu-PCR26,27, cassette-mediated ligation PCR28, and whole genome sequencing29,30,31,32,33, do not have the sensitivity to detect single-copies of integrations. We and other researchers have used inverse nested PCR (invPCR) to detect hepadnaviral DNA integration in duck, woodchuck, and human infected livers13,14,18,19,34,35,36. Others have introduced procedural modifications to the invPCR technique that may alter the generation of false-positive signals and restrict the ability for quantification37. If the assay is carried out as described in this protocol, invPCR represents a specific and sensitive assay that identifies and quantifies (in absolute copy numbers) multiple HBV DNA integrations. The HBV-cell DNA junction is sequenced at a single-base pair resolution, allowing bioinformatical studies of viral and host DNA sequences at the sites of integration13.
We have previously described38&#160;results from invPCR on DNA of HBV-infected tissue extracted from a large range of sources, including snap-frozen liver tissues, paraffin-embedded liver sections, and extremely small tissue samples isolated by laser-microdissection19. This protocol outlines an updated version of an invPCR assay using DNA extracted from cell culture-derived tissues after in vitro infection, in which low copy numbers of integrations (1&#8211;2 copies per integration) are generated. The HBV DNA integrations formed in vitro resemble those found in patient tissues with respect to their distribution over the cellular genome and junction within the viral sequence that is integrated13,16, suggesting a comparable pathway to within an infected liver.

<table>
	<tbody>
		<tr>
			<td>Dulbecco&#8217;s PBS</td>
			<td>PAA</td>
			<td>H15-002</td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM medium</td>
			<td>Thermo Fisher Scientific</td>
			<td>41965</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal bovine serum</td>
			<td>PAA</td>
			<td>A15-151</td>
			<td>Heat-inactivate before use</td>
		</tr>
		<tr>
			<td>Penicillin, 10000U/ml; Streptomycin 10mg/ml, 100&#215;</td>
			<td>PAA</td>
			<td>P11-010</td>
			<td></td>
		</tr>
		<tr>
			<td>L-glutamine, 200mM</td>
			<td>PAA</td>
			<td>M11-004</td>
			<td></td>
		</tr>
		<tr>
			<td>Trypsin, 0.5 mg/ml; EDTA, 0.22mg/ml, 1&#215;</td>
			<td>PAA</td>
			<td>L11-004</td>
			<td></td>
		</tr>
		<tr>
			<td>PEG, MW 8000</td>
			<td>Sigma-Aldrich</td>
			<td>89510</td>
			<td>Stock at 40% w/v in 1xPBS, autoclave before use</td>
		</tr>
		<tr>
			<td>DMSO for spectroscopy</td>
			<td>Merck</td>
			<td>102950</td>
			<td></td>
		</tr>
		<tr>
			<td>Tenofovir disoproxil</td>
			<td>Sigma-Aldrich</td>
			<td>CDS021622</td>
			<td>Dissolve in DMSO</td>
		</tr>
		<tr>
			<td>Lamivudine</td>
			<td>Sigma-Aldrich</td>
			<td>L1295</td>
			<td>Dissolve in DMSO</td>
		</tr>
		<tr>
			<td>NucleoSpin Tissue kit</td>
			<td>Macherey Nagel</td>
			<td>740952.250</td>
			<td></td>
		</tr>
		<tr>
			<td>NanoDrop 2000/2000c Spectrolphotometer</td>
			<td>Thermo Fisher Scientific</td>
			<td>ND-2000</td>
			<td></td>
		</tr>
		<tr>
			<td>NcoI-HF</td>
			<td>NEB</td>
			<td>R3193L</td>
			<td></td>
		</tr>
		<tr>
			<td>T4 DNA ligase</td>
			<td>NEB</td>
			<td>M0202T</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium dodecyl sulfate</td>
			<td>Sigma-Aldrich</td>
			<td>L3771</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium Chloride</td>
			<td>Sigma-Aldrich</td>
			<td>433209</td>
			<td></td>
		</tr>
		<tr>
			<td>Dextran (35 -45 kDa)</td>
			<td>Sigma-Aldrich</td>
			<td>D1662-10G</td>
			<td></td>
		</tr>
		<tr>
			<td>Absolute Ethanol</td>
			<td>Sigma-Aldrich</td>
			<td>32205-1L-D</td>
			<td></td>
		</tr>
		<tr>
			<td>BsiHKAI</td>
			<td>NEB</td>
			<td>R0570L</td>
			<td></td>
		</tr>
		<tr>
			<td>SphI-HF</td>
			<td>NEB</td>
			<td>R3182L</td>
			<td></td>
		</tr>
		<tr>
			<td>Amplitaq Gold Taq kit</td>
			<td>Thermo Fisher Scientific</td>
			<td>4331816</td>
			<td>Use for first nest PCR</td>
		</tr>
		<tr>
			<td>Silicon sealing Mats for 96-Well PCR Plates</td>
			<td>Biorad</td>
			<td>2239442</td>
			<td></td>
		</tr>
		<tr>
			<td>DNAZap PCR DNA Degradation Solution</td>
			<td>Thermo Fisher Scientific</td>
			<td>AM9890</td>
			<td></td>
		</tr>
		<tr>
			<td>96-well PCR plates</td>
			<td>Sigma Aldrich</td>
			<td>CLS6509 SIGMA</td>
			<td></td>
		</tr>
		<tr>
			<td>96-pin replicator</td>
			<td>Thermo Fisher Scientific</td>
			<td>250520</td>
			<td></td>
		</tr>
		<tr>
			<td>GoTaq Flexi PCR kit</td>
			<td>Promega</td>
			<td>M8295</td>
			<td>Use for second nest PCR, use green buffer for easy loading of agarose gel</td>
		</tr>
		<tr>
			<td>Biozym LE Agarose</td>
			<td>Biozym</td>
			<td>840004</td>
			<td></td>
		</tr>
		<tr>
			<td>QIAEX II Gel extraction kit</td>
			<td>QIAGEN</td>
			<td>20051</td>
			<td></td>
		</tr>
	</tbody>
</table>

detection of low copy number integrated viral dna formed by in vitro hepatitis b infection

Hepatitis B Virus (HBV) is a common blood-borne pathogen causing liver cancer and liver cirrhosis resulting from chronic infection. The virus generally replicates through an episomal DNA intermediate; however, integration of HBV DNA fragments into the host genome has been observed, even though this form is not necessary for viral replication. The exact purpose, timing, and mechanism(s) by which HBV DNA integration occurs is not yet clear, but recent data show that it occurs very early after infection. Here, the in vitro generation and detection of HBV DNA integrations are described in detail. Our protocol specifically amplifies single copies of virus-cell DNA integrations and allows both absolute quantification and single-base pair resolution of the junction sequence. This technique has been applied to various HBV-susceptible cell types (including primary human hepatocytes), to various HBV mutants, and in conjunction with various drug exposures. We foresee this technique becoming a key assay to determine the underlying molecular mechanisms of this clinically relevant phenomenon.

A schematic representation of the invPCR technique is shown in Figure 1. An example agarose gel electrophoresis of a successful invPCR is shown in Figure 2 before and after the PCR product isolation. Figure 3 shows the BLAST analysis output from step 5.1 in the cases of (i) amplification of virus-cell DNA junction and (ii) amplification of an HBV DNA replicative intermediate.
Expected results from positive controls: Huh7-NTCP cells infected with heparin-purified HBV stocks as described above (Figure 1) can serve as a positive control. In this instance, single PCR products should be achieved by the second or third 1:3 dilution of each sample (corresponding to ~104 cell equivalents per dilution, Figure 2). At these dilutions, approximately 50% of products will represent true virus-cell DNA junctions, while the other half represents amplification of HBV DNA intermediates (Figure 3).
In previous studies13, we have found few instances of repeated virus-cell junctions, suggesting no cellular genomic sites of preferential HBV DNA integration. We also find that &#62;80% of virus-cell junctions occur between nucleotides 1732 and 1832 (according to the nucleotide numbering of HBV genotype D, GenBank Accession #U95551.1), where the latter represents the right-hand terminus of the HBV dslDNA form. Sequences of true virus-cell junctions found through our method in in vitro experiments are publicly available on GenBank (Accession numbers MH057851 to MH058006).
Expected results from negative controls: Either uninfected Huh7-NTCP cells or inoculated Huh7-NTCP cells pre-treated with Myrcludex B can act as negative controls. InvPCR analysis of DNA extracted from these cells should produce no PCR products. Running these negative-control samples on the same PCR plate as positive samples allows for testing of cross-contamination during the nested-PCR process. The most stringent test for cross-contamination is the running of a negative-control sample in wells A-D and the positive sample in wells E-H on a 96-well plate. In this case, the most concentrated dilution of the positive sample is run in a row directly adjacent to the least concentrated dilution of the negative sample. If amplification products are observed in negative-control samples, institute the measures suggested in the discussion to minimize cross-contamination events.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/58202/58202fig1.jpg" /> 
Figure 1: Schematic figure of the invPCR process to detect HBV DNA integrations. After HBV infection, only a minority of Huh7-NTCP cells contain HBV dslDNA (red) integrated into the host cell genome (red), depicted in the top section. Total DNA is then extracted from the cells (step 1), inverted (step 2), and amplified by nested PCR (step 3). Shown are the relative positions of the restriction enzyme sites (NcoI and BsiHKAI) in the excised virus-cell DNA junction. The figure is adapted from a previous publication13. <a href="https://www.jove.com/files/ftp_upload/58202/58202fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/58202/58202fig2.jpg" /> 
Figure 2: Agarose gel electrophoresis and subsequent gel extraction of a successful invPCR. &#34;M&#34; represents DNA marker ladder. Each row of 12 represents technical replicates at a single dilution on the PCR plate. Two inverted DNA samples can be run per PCR plate/agarose gel. The PCR products for each dilution should titrate out in a ~1:3 ratio. Extraction of the products from the two least concentrated dilutions where single bands can be easily isolated is generally sufficient, as HBV DNA integration rate is determined by end-point titration. <a href="https://www.jove.com/files/ftp_upload/58202/58202fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/58202/58202fig3.jpg" /> 
Figure 3: BLAST analysis of invPCR product sequences. As long tracts of sequence are generated from Sanger sequencing, the source of DNA sequences is generally unambiguous. Strong alignment to HBV and cellular genomes is observed in different areas of the FASTA sequence file generated from Sanger sequencing in the top panel, suggesting a true virus-cell DNA junction. In the bottom panel, the sequence aligns only to fragments of the HBV genome, suggesting a product generated by the amplification of a rearranged HBV DNA genome. <a href="https://www.jove.com/files/ftp_upload/58202/58202fig3large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about Detection of Low Copy Number Integrated Viral DNA Formed by In Vitro Hepatitis B Infection at JoVE.com

Detection of Low Copy Number Integrated Viral DNA Formed by In Vitro Hepatitis B Infection

We describe here the in vitro generation of HBV DNA via a Hepatitis B virus infection system and the highly sensitive detection of its (1&#8211;2 copies) integration using inverse nested PCR.

Detection of Low Copy Number Integrated Viral DNA Formed by In Vitro Hepatitis B Infection

Hepatitis B Virus (HBV) is a common blood-borne pathogen causing liver cancer and liver cirrhosis resulting from chronic infection. The virus generally ...

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Immunology and Infection

18.2K Views.  Heidelberg University Hospital. We describe here the in vitro generation of HBV DNA via a Hepatitis B virus infection system and the highly sensitive detection of its (1–2 copies) integration using inverse nested PCR.

Video: Detection of Low Copy Number Integrated Viral DNA Formed by In Vitro Hepatitis B Infection

Preparation of Viral DNA from Nucleocapsids

Viruses are obligate cellular parasites, and thus the study of their DNA requires isolating viral material away from host cell contaminants and DNA. Several downstream applications require large quantities of pure viral DNA, which is provided by this protocol. These applications include viral genome sequencing, where the removal of host DNA is crucial to optimize data output for viral sequences, and the production of new viral recombinant strains, where co-transfection of purified plasmid and linear viral DNA facilitates recombination.1,2,3 
This procedure utilizes a combination of extractions and density-based centrifugation to isolate purified linear herpesvirus nucleocapsid DNA from infected cells.4,5 The initial purification steps aim to isolate purified viral capsids, which contain and protect the viral DNA during the extractions and centrifugation steps that remove cellular proteins and DNA. Lysis of nucleocapsids then releases viral DNA, and two final phenol-chloroform steps remove remaining proteins. The final DNA captured from solution is highly concentrated and pure, with an average OD260/280 of 1.90. Depending on the quantity of infected cells used, yields of viral DNA range from 150-800 &mu;g or more. The purity of this DNA makes it stable during long-term storage at 4C. This DNA is thus ideally suited for high-throughput sequencing, high fidelity PCR reactions, and transfections. 
Prior to beginning the protocol, it is important to know the average number of cells per dish (e.g. an average of 8 x 106 PK-15 cells in a confluent 15 cm dish), and the titer of the viral stock to be used (e.g. 1 x 108 plaque-forming units per ml). These are necessary to calculate the appropriate multiplicity of infection (MOI) for the protocol.6 For instance, to infect one 15 cm dish of PK-15 cells with the above viral stock, at an MOI of 5, you would use 400 &mu;l of viral stock and dilute it with 3.6 ml of medium (total inoculation volume of 4 ml for one 15 cm plate).
Multiple viral DNA preparations can be prepared at the same time. The number of simultaneous preparations is limited only by the number of tubes held by the ultracentrifuge rotor (one per virus; see step 3.9 below). Here we describe the procedure as though being done for one virus.

We describe the process of isolating high purity herpesvirus nucleocapsid DNA from infected cells. The final DNA captured from solution is of high concentration and purity, making it ideally suited for high-throughput sequencing, high fidelity PCR reactions, and transfections to produce new viral recombinants.

Viruses are obligate cellular parasites, and thus the study of their DNA requires isolating viral material away from host cell contaminants and DNA. ...

Establishment of an In vitro System to Study Intracellular Behavior of Candida glabrata in Human THP-1 Macrophages

A cell culture model system, if a close mimic of host environmental conditions, can serve as an inexpensive, reproducible and easily manipulatable alternative to animal model systems for the study of a specific step of microbial pathogen infection. A human monocytic cell line THP-1 which, upon phorbol ester treatment, is differentiated into macrophages, has previously been used to study virulence strategies of many intracellular pathogens including Mycobacterium tuberculosis. Here, we discuss a protocol to enact an in vitro cell culture model system using THP-1 macrophages to delineate the interaction of an opportunistic human yeast pathogen Candida glabrata with host phagocytic cells. This model system is simple, fast, amenable to high-throughput mutant screens, and requires no sophisticated equipment. A typical THP-1 macrophage infection experiment takes approximately 24 hr with an additional 24-48 hr to allow recovered intracellular yeast to grow on rich medium for colony forming unit-based viability analysis. Like other in vitro model systems, a possible limitation of this approach is difficulty in extrapolating the results obtained to a highly complex immune cell circuitry existing in the human host. However, despite this, the current protocol is very useful to elucidate the strategies that a fungal pathogen may employ to evade/counteract antimicrobial response and survive, adapt, and proliferate in the nutrient-poor environment of host immune cells.

Establishment of an In vitro System to Study Intracellular Behavior of Candida glabrata in Human THP-1 Macrophages

The current article outlines a protocol to establish an in vitro cell culture model system to study the interaction of a facultative intracellular human fungal pathogen Candida glabrata with human macrophages which will be a useful tool to advance our knowledge of fungal virulence mechanisms.

A cell culture model system, if a close mimic of host environmental conditions, can serve as an inexpensive, reproducible and easily manipulatable ...

Detection of True IgE-expressing Mouse B Lineage Cells

B lymphocyte immunoglobulin heavy chain (IgH) class switch recombination (CSR) is a process wherein initially expressed IgM switches to other IgH isotypes, such as IgA, IgE and IgG. Measurement of IgH CSR in vitro is a key method for the study of a number of biologic processes ranging from DNA recombination and repair to aspects of molecular and cellular immunology. In vitro CSR assay involves the flow cytometric measurement surface Ig expression on activated B cells. While measurement of IgA and IgG subclasses is straightforward, measurement of IgE by this method is problematic due to soluble IgE binding to Fc&#949;RII/CD23 expressed on the surface of activated B cells. Here we describe a unique procedure for accurate measurement of IgE-producing mouse B cells that have undergone CSR in culture. The method is based on trypsin-mediated cleavage of IgE-CD23 complexes on cell surfaces, allowing for detection of IgE-producing B lineage cells by cytoplasmic staining. This procedure offers a convenient solution for flow cytometric analysis of CSR to IgE.

In vitro analysis of class switch recombination in mice is challenging due to cytophilic IgE molecules bound to Fc receptors on the surface of B cells. We describe a method for IgE detection using trypsin-mediated cleavage of surface-bound IgE prior to fixation and permeabilization for cytoplasmic fluorescence staining.

B lymphocyte immunoglobulin heavy chain (IgH) class switch recombination (CSR) is a process wherein initially expressed IgM switches to other IgH ...

The Development of Lyophilized Loop-mediated Isothermal Amplification Reagents for the Detection of Coxiella burnetii

Coxiella burnetii, the agent causing Q fever, is an obligate intracellular bacterium. PCR based diagnostic assays have been developed for detecting C. burnetii DNA in cell cultures and clinical samples. PCR requires specialized equipment and extensive end user training, and therefore, it is not suitable for routine work especially in a resource-constrained area. We have developed a loop-mediated isothermal amplification (LAMP) assay to detect the presence of C. burnetii in patient samples. This method is performed at a single temperature around 60 &#176;C in a water bath or heating block. The sensitivity of this LAMP assay is very similar to PCR with a detection limit of about 25 copies per reaction. This report describes the preparation of the reaction using lyophilized reagents and visualization of results using hydroxynaphthol blue (HNB) or a UV lamp with fluorescent intercalating dye in the reaction. The LAMP reagents were lyophilized and stored at room temperature (RT) for one month without loss of detection sensitivity. This LAMP assay is particularly robust because the reaction mixture preparation does not involve complex steps. This method is ideal for use in resource-limited settings where Q fever is endemic.

The Development of Lyophilized Loop-mediated Isothermal Amplification Reagents for the Detection of Coxiella burnetii

We described here a simple loop-mediated isothermal amplification (LAMP) method using lyophilized reagents for the detection of C. burnetii in patient samples.

Coxiella burnetii, the agent causing Q fever, is an obligate intracellular bacterium. PCR based diagnostic assays have been developed for detecting C. ...

Measuring Influenza Neuraminidase Inhibition Antibody Titers by Enzyme-linked Lectin Assay

Antibodies to neuraminidase (NA), the second most abundant surface protein on influenza virus, contribute toward protection against influenza. Traditional methods to measure NA inhibiting (NI) antibody titers are not practical for routine serology. This protocol describes the enzyme-linked lectin assay (ELLA), a practical alternative method to measure NI titers that is performed in 96 well plates coated with a large glycoprotein substrate, fetuin. NA cleaves terminal sialic acids from fetuin, exposing the penultimate sugar, galactose. Peanut agglutinin (PNA) is a lectin with specificity for galactose and therefore the extent of desialylation can be quantified using a PNA-horseradish peroxidase conjugate, followed by addition of a chromogenic peroxidase substrate. The optical density that is measured is proportional to NA activity. To measure NI antibody titers, serial dilutions of sera are incubated at 37 &#176;C O/N on fetuin-coated plates with a fixed amount of NA. The reciprocal of the highest serum dilution that results in &#8805;50% inhibition of NA activity is designated as the NI antibody titer. The ELLA provides a practical format for routine evaluation of human antibody responses following influenza infection or vaccination.

We describe the enzyme-linked lectin assay (ELLA) for measuring influenza neuraminidase (NA)-inhibition antibody titers in sera. The assay uses peanut agglutinin to quantify galactose residues that become accessible when NA removes sialic acid from fetuin-coated, 96-well plates.

Antibodies to neuraminidase (NA), the second most abundant surface protein on influenza virus, contribute toward protection against influenza. Traditional ...

High-throughput Detection of Respiratory Pathogens in Animal Specimens by Nanoscale PCR

Nanoliter scale real-time PCR uses spatial multiplexing to allow multiple assays to be run in parallel on a single plate without the typical drawbacks of combining reactions together. We designed and evaluated a panel based on this principle to rapidly identify the presence of common disease agents in dogs and horses with acute respiratory illness. This manuscript describes a nanoscale diagnostic PCR workflow for sample preparation, amplification, and analysis of target pathogen sequences, focusing on procedures that are different from microliter scale reactions. In the respiratory panel presented, 18 assays were each set up in triplicate, accommodating up to 48 samples per plate. A universal extraction and pre-amplification workflow was optimized for high-throughput sample preparation to accommodate multiple matrices and DNA and RNA based pathogens. Representative data are presented for one RNA target (influenza A matrix) and one DNA target (equine herpesvirus 1). The ability to quickly and accurately test for a comprehensive, syndrome-based group of pathogens is a valuable tool for improving efficiency and ergonomics of diagnostic testing and for acute respiratory disease diagnosis and management.

High-throughput testing of DNA and RNA based pathogens by nanoscale PCR is described using a syndromic canine and equine respiratory PCR panel.

Nanoliter scale real-time PCR uses spatial multiplexing to allow multiple assays to be run in parallel on a single plate without the typical drawbacks of ...

Development of a Hepatitis B Virus Reporter System to Monitor the Early Stages of the Replication Cycle

Currently, it is possible to construct recombinant forms of various viruses, such as human immunodeficiency virus 1 (HIV-1) and hepatitis C virus (HCV), that carry foreign genes such as a reporter or marker protein in their genomes. These recombinant viruses usually faithfully mimic the life cycle of the original virus in infected cells and exhibit the same host range dependence. The development of a recombinant virus enables the efficient screening of inhibitors and the identification of specific host factors. However, to date the construction of recombinant hepatitis B virus (HBV) has been difficult because of various experimental limitations. The main limitation is the compact genome size of HBV, and a fairly strict genome size that does not exceed 1.3 genome sizes, that must be packaged into virions. Thus, the size of a foreign gene to be inserted should be smaller than 0.4 kb if no deletion of the genome DNA is to be performed. Therefore, to overcome this size limitation, the deletion of some HBV DNA is required. Here, we report the construction of recombinant HBV encoding a reporter gene to monitor the early stage of the HBV replication cycle by replacing part of the HBV core-coding region with the reporter gene by deleting part of the HBV pol coding region. Detection of recombinant HBV infection, monitored by the reporter activity, was highly sensitive and less expensive than detection using the currently available conventional methods to evaluate HBV infection. This system will be useful for a number of applications including high-throughput screening for the identification of anti-HBV inhibitors, host factors and virus-susceptible cells.

Here we describe a newly developed hepatitis B virus (HBV) reporter system to monitor the early stages of the HBV life cycle. This simplified in vitro system will aid in the screening of anti-HBV agents using a high-throughput strategy.

Currently, it is possible to construct recombinant forms of various viruses, such as human immunodeficiency virus 1 (HIV-1) and hepatitis C virus (HCV), ...

Swab Sampling Method for the Detection of Human Norovirus on Surfaces

Human noroviruses are a leading cause of epidemic and sporadic gastroenteritis worldwide. Because most infections are either spread directly via the person-to-person route or indirectly through environmental surfaces or food, contaminated fomites and inanimate surfaces are important vehicles for the spread of the virus during norovirus outbreaks.
We developed and evaluated a protocol using macrofoam swabs for the detection and typing of human noroviruses from hard surfaces. Compared with fiber-tipped swabs or antistatic wipes, macrofoam swabs allow virus recovery (range 1.2-33.6%) from toilet seat surfaces of up to 700 cm2. The protocol includes steps for the extraction of the virus from the swabs and further concentration of the viral RNA using spin columns. In total, 127 (58.5%) of 217 swab samples that had been collected from surfaces in cruise ships and long-term care facilities where norovirus gastroenteritis had been reported tested positive for GII norovirus by RT-qPCR. Of these 29 (22.8%) could be successfully genotyped. In conclusion, detection of norovirus on environmental surfaces using the protocol we developed may assist in determining the level of environmental contamination during outbreaks as well as detection of virus when clinical samples are not available; it may also facilitate monitoring of effectiveness of remediation strategies.

A macrofoam based sampling methodology was developed and evaluated for the detection and quantification of norovirus on environmental hard surfaces.

Human noroviruses are a leading cause of epidemic and sporadic gastroenteritis worldwide. Because most infections are either spread directly via the ...

Purification of Viral DNA for the Identification of Associated Viral and Cellular Proteins

The goal of this protocol is to isolate herpes simplex virus type 1 (HSV-1) DNA from infected cells for the identification of associated viral and cellular proteins by mass spectrometry. Although proteins that interact with viral genomes play major roles in determining the outcome of infection, a comprehensive analysis of viral genome associated proteins was not previously feasible. Here we demonstrate a method that enables the direct purification of HSV-1 genomes from infected cells. Replicating viral DNA is selectively labeled with modified nucleotides that contain an alkyne functional group. Labeled DNA is then specifically and irreversibly tagged via the covalent attachment of biotin azide via a copper(I)-catalyzed azide-alkyne cycloaddition or click reaction. Biotin-tagged DNA is purified on streptavidin-coated beads and associated proteins are eluted and identified by mass spectrometry. This method enables the selective targeting and isolation of HSV-1 replication forks or whole genomes from complex biological environments. Furthermore, adaptation of this approach will allow for the investigation of various aspects of herpesviral infection, as well as the examination of the genomes of other DNA viruses.

The goal of this protocol is to specifically tag and selectively isolate viral DNA from infected cells for the characterization of viral genome associated proteins.

The goal of this protocol is to isolate herpes simplex virus type 1 (HSV-1) DNA from infected cells for the identification of associated viral and ...

"Liver-on-a-Chip" Cultures of Primary Hepatocytes and Kupffer Cells for Hepatitis B Virus Infection

Despite the exceptional infectivity of the hepatitis B virus (HBV) in vivo, where only three viral genomes can result in a chronicity of experimentally infected chimpanzees, most in vitro models require several hundreds to thousands of viral genomes per cell in order to initiate a transient infection. Additionally, static 2D cultures of primary human hepatocytes (PHH) allow only short-term studies due to their rapid dedifferentiation. Here, we describe 3D liver-on-a-chip cultures of PHH, either in monocultures or in cocultures with other nonparenchymal liver-resident cells. These offer a significant improvement to studying long-term HBV infections with physiological host cell responses. In addition to facilitating drug efficacy studies, toxicological analysis, and investigations into pathogenesis, these microfluidic culture systems enable the evaluation of curative therapies for HBV infection aimed at eliminating covalently closed, circular (ccc)DNA. This presented method describes the set-up of PHH monocultures and PHH/Kupffer cell co-cultures, their infection with purified HBV, and the analysis of host responses. This method is particularly applicable to the evaluation of long-term effects of HBV infection, treatment combinations, and pathogenesis.

The goal of this protocol is to provide a step-by-step guide to perform 3-D &#34;liver-on-a-chip&#34; infection experiments with the hepatitis B virus.

Despite the exceptional infectivity of the hepatitis B virus (HBV) in vivo, where only three viral genomes can result in a chronicity of experimentally ...

Detection of Low Copy Number Integrated Viral DNA Formed by In Vitro Hepatitis B Infection

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Chapters in this video

Preparation of Viral DNA from Nucleocapsids

Establishment of an In vitro System to Study Intracellular Behavior of Candida glabrata in Human THP-1 Macrophages

Detection of True IgE-expressing Mouse B Lineage Cells

The Development of Lyophilized Loop-mediated Isothermal Amplification Reagents for the Detection of Coxiella burnetii

Measuring Influenza Neuraminidase Inhibition Antibody Titers by Enzyme-linked Lectin Assay

High-throughput Detection of Respiratory Pathogens in Animal Specimens by Nanoscale PCR

Development of a Hepatitis B Virus Reporter System to Monitor the Early Stages of the Replication Cycle

Swab Sampling Method for the Detection of Human Norovirus on Surfaces

Purification of Viral DNA for the Identification of Associated Viral and Cellular Proteins

"Liver-on-a-Chip" Cultures of Primary Hepatocytes and Kupffer Cells for Hepatitis B Virus Infection