These studies were funded by US Public Health Services grants P01AI057005, R01AI047734, R01AI111806 and the Functional Profiling and Computational Biology Core of the University of Washington&#8217;s Center for AIDS Research (P30 AI027757).

<ol>
	<li>Domingo, E., Holland, J. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA+virus+mutations+and+fitness+for+survival.">RNA virus mutations and fitness for survival.</a> Annu Rev Microbiol. 51, 151-178 (1997).</li><li>Domingo, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mechanisms+of+viral+emergence.">Mechanisms of viral emergence.</a> Veterinary research. 41 (6), 38 (2010).</li><li>Martinez-Picado, J., Martinez, M. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=HIV-1+reverse+transcriptase+inhibitor+resistance+mutations+and+fitness:+a+view+from+the+clinic+and+ex+vivo.">HIV-1 reverse transcriptase inhibitor resistance mutations and fitness: a view from the clinic and ex vivo.</a> Virus Res. 134 (1-2), 104-123 (2008).</li><li>Troyer, R. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Variable+fitness+impact+of+HIV-1+escape+mutations+to+cytotoxic+T+lymphocyte+(CTL)+response.">Variable fitness impact of HIV-1 escape mutations to cytotoxic T lymphocyte (CTL) response.</a> PLoS Pathog. 5 (4), e1000365 (2009).</li><li>Rolland, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Amino-acid+co-variation+in+HIV-1+Gag+subtype+C:+HLA-mediated+selection+pressure+and+compensatory+dynamics.">Amino-acid co-variation in HIV-1 Gag subtype C: HLA-mediated selection pressure and compensatory dynamics.</a> PLoS One. 5 (9), e12463 (2010).</li><li>Abraha, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=CCR5-+and+CXCR4-tropic+subtype+C+human+immunodeficiency+virus+type+1+isolates+have+a+lower+level+of+pathogenic+fitness+than+other+dominant+group+M+subtypes:+implications+for+the+epidemic.">CCR5- and CXCR4-tropic subtype C human immunodeficiency virus type 1 isolates have a lower level of pathogenic fitness than other dominant group M subtypes: implications for the epidemic.</a> J Virol. 83 (11), 5592-5605 (2009).</li><li>Quinones-Mateu, M. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+dual+infection/competition+assay+shows+a+correlation+between+ex+vivo+human+immunodeficiency+virus+type+1+fitness+and+disease+progression.">A dual infection/competition assay shows a correlation between ex vivo human immunodeficiency virus type 1 fitness and disease progression.</a> J Virol. 74 (19), 9222-9233 (2000).</li><li>Ball, S. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparing+the+ex+vivo+fitness+of+CCR5-tropic+human+immunodeficiency+virus+type+1+isolates+of+subtypes.">Comparing the ex vivo fitness of CCR5-tropic human immunodeficiency virus type 1 isolates of subtypes.</a> B and C. J Virol. 77 (2), 1021-1038 (2003).</li><li>Lanxon-Cookson, E. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Factors+affecting+relative+fitness+measurements+in+pairwise+competition+assays+of+human+immunodeficiency+viruses.">Factors affecting relative fitness measurements in pairwise competition assays of human immunodeficiency viruses.</a> J Virol Methods. 194 (1-2), 7-13 (2013).</li><li>Garcia-Lerma, J. G., MacInnes, H., Bennett, D., Weinstock, H., Heneine, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transmitted+human+immunodeficiency+virus+type+1+carrying+the+D67N+or+K219Q/E+mutation+evolves+rapidly+to+zidovudine+resistance+in+vitro+and+shows+a+high+replicative+fitness+in+the+presence+of+zidovudine.">Transmitted human immunodeficiency virus type 1 carrying the D67N or K219Q/E mutation evolves rapidly to zidovudine resistance in vitro and shows a high replicative fitness in the presence of zidovudine.</a> J Virol. 78 (14), 7545-7552 (2004).</li><li>Sharma, P. L., Crumpacker, C. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Attenuated+replication+of+human+immunodeficiency+virus+type+1+with+a+didanosine-selected+reverse+transcriptase+mutation.">Attenuated replication of human immunodeficiency virus type 1 with a didanosine-selected reverse transcriptase mutation.</a> J Virol. 71 (11), 8846-8851 (1997).</li><li>Martinez-Picado, J., Savara, A. V., Sutton, L., D'Aquila, R. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Replicative+fitness+of+protease+inhibitor-resistant+mutants+of+human+immunodeficiency+virus+type+1.">Replicative fitness of protease inhibitor-resistant mutants of human immunodeficiency virus type 1.</a> J Virol. 73 (5), 3744-3752 (1999).</li><li>Wang, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+HIV-1+reverse+transcriptase+mutants+G190S+and+G190A,+which+confer+resistance+to+non-nucleoside+reverse+transcriptase+inhibitors,+demonstrate+reductions+in+RNase+H+activity+and+DNA+synthesis+from+tRNA(Lys,+3)+that+correlate+with+reductions+in+replication+efficiency.">The HIV-1 reverse transcriptase mutants G190S and G190A, which confer resistance to non-nucleoside reverse transcriptase inhibitors, demonstrate reductions in RNase H activity and DNA synthesis from tRNA(Lys, 3) that correlate with reductions in replication efficiency.</a> Virology. 348 (2), 462-474 (2006).</li><li>Song, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Impact+of+immune+escape+mutations+on+HIV-1+fitness+in+the+context+of+the+cognate+transmitted/founder+genome.">Impact of immune escape mutations on HIV-1 fitness in the context of the cognate transmitted/founder genome.</a> Retrovirology. 9 (89), (2012).</li><li>Ali, A., Yang, O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+novel+small+reporter+gene+and+HIV-1+fitness+assay.">A novel small reporter gene and HIV-1 fitness assay.</a> Journal of Virological Methods. 133 (1), 41-47 (2006).</li><li>Maarseveen, N. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+novel+real-time+PCR+assay+to+determine+relative+replication+capacity+for+HIV-1+protease+variants+and/or+reverse+transcriptase+variants.">A novel real-time PCR assay to determine relative replication capacity for HIV-1 protease variants and/or reverse transcriptase variants.</a> J Virol Methods. 133 (2), 185-194 (2006).</li><li>Liu, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evolution+of+human+immunodeficiency+virus+type+1+cytotoxic+T-lymphocyte+epitopes:+fitness-balanced+escape.">Evolution of human immunodeficiency virus type 1 cytotoxic T-lymphocyte epitopes: fitness-balanced escape.</a> J Virol. 81 (22), 12179-12188 (2007).</li><li>Anastassopoulou, C. G., Ketas, T. J., Klasse, P. J., Moore, J. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Resistance+to+CCR5+inhibitors+caused+by+sequence+changes+in+the+fusion+peptide+of+HIV-1+gp41.">Resistance to CCR5 inhibitors caused by sequence changes in the fusion peptide of HIV-1 gp41.</a> Proc Natl Acad Sci U S A. 106 (13), 5318-5323 (2009).</li><li>Abraha, A., Troyer, R. M., Quinones-Mateu, M. E., Arts, E. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Methods+to+determine+HIV-1+ex+vivo+fitness.">Methods to determine HIV-1 ex vivo fitness.</a> Methods Mol Biol. 304, 355-368 (2005).</li><li>Liu, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+sensitive+real-time+PCR+based+assay+to+estimate+the+impact+of+amino+acid+substitutions+on+the+competitive+replication+fitness+of+human+immunodeficiency+virus+type+1+in+cell+culture.">A sensitive real-time PCR based assay to estimate the impact of amino acid substitutions on the competitive replication fitness of human immunodeficiency virus type 1 in cell culture.</a> J Virol Methods. 189 (1), 157-166 (2013).</li><li>Brumme, Z. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reduced+replication+capacity+of+NL4-3+recombinant+viruses+encoding+reverse+transcriptase-integrase+sequences+from+HIV-1+elite+controllers.">Reduced replication capacity of NL4-3 recombinant viruses encoding reverse transcriptase-integrase sequences from HIV-1 elite controllers.</a> J Acquir Immune Defic Syndr. 56 (2), 100-108 (2011).</li><li>Nomura, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Significant+reductions+in+Gag-protease-mediated+HIV-1+replication+capacity+during+the+course+of+the+epidemic+in.">Significant reductions in Gag-protease-mediated HIV-1 replication capacity during the course of the epidemic in.</a> Japan. J Virol. 87 (3), 1465-1476 (2013).</li><li>Rolland, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=HIV-1+conserved-element+vaccines:+relationship+between+sequence+conservation+and+replicative+capacity.">HIV-1 conserved-element vaccines: relationship between sequence conservation and replicative capacity.</a> J Virol. 87 (10), 5461-5467 (2013).</li><li>Martinez-Picado, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fitness+cost+of+escape+mutations+in+p24+Gag+in+association+with+control+of+human+immunodeficiency+virus+type+1.">Fitness cost of escape mutations in p24 Gag in association with control of human immunodeficiency virus type 1.</a> J Virol. 80 (7), 3617-3623 (2006).</li><li>Brockman, M. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Escape+and+Compensation+from+Early+HLA-B57-Mediated+Cytotoxic+T-Lymphocyte+Pressure+on+Human+Immunodeficiency+Virus+Type+1+Gag+Alter+Capsid+Interactions+with+Cyclophilin+A.">Escape and Compensation from Early HLA-B57-Mediated Cytotoxic T-Lymphocyte Pressure on Human Immunodeficiency Virus Type 1 Gag Alter Capsid Interactions with Cyclophilin A.</a> J Virol. 81 (22), 12608-12618 (2007).</li><li>Miura, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=HLA-associated+alterations+in+replication+capacity+of+chimeric+NL4-3+viruses+carrying+gag-protease+from+elite+controllers+of+human+immunodeficiency+virus+type+1.">HLA-associated alterations in replication capacity of chimeric NL4-3 viruses carrying gag-protease from elite controllers of human immunodeficiency virus type 1.</a> J Virol. 83 (1), 140-149 (2009).</li><li>Lee, P. Y., Costumbrado, J., Hsu, C. Y., Kim, Y. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Agarose+gel+electrophoresis+for+the+separation+of+DNA+fragments.">Agarose gel electrophoresis for the separation of DNA fragments.</a> Journal of visualized experiments : JoVE. 62 (Apr 20), (2012).</li><li>McClure, J., van't Wout, A. B., Tran, T., Mittler, J. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Granulocyte-monocyte+colony-stimulating+factor+upregulates+HIV-1+replication+in+monocyte-derived+macrophages+cultured+at+low+density.">Granulocyte-monocyte colony-stimulating factor upregulates HIV-1 replication in monocyte-derived macrophages cultured at low density.</a> J Acquir Immune Defic Syndr. 44 (3), 254-261 (2007).</li><li>Reed, L. J., Muench, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+simple+method+of+estimatingfifty+percent+endpoints.">A simple method of estimatingfifty percent endpoints.</a> Am J Hyg. 27 (3), 493-497 (1938).</li><li>Nickle, D. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Consensus+and+ancestral+state+HIV+vaccines.">Consensus and ancestral state HIV vaccines.</a> Science. 299 (5612), 1515-1518 (2003).</li><li>Rolland, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reconstruction+and+function+of+ancestral+center-of-tree+human+immunodeficiency+virus+type+1+proteins.">Reconstruction and function of ancestral center-of-tree human immunodeficiency virus type 1 proteins.</a> J Virol. 81 (16), 8507-8514 (2007).</li><li>Bryksin, A. V., Matsumura, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Overlap+extension+PCR+cloning:+a+simple+and+reliable+way+to+create+recombinant+plasmids.">Overlap extension PCR cloning: a simple and reliable way to create recombinant plasmids.</a> Biotechniques. 48 (6), 463-465 (2010).</li><li>Spira, A. I., Ho, D. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effect+of+different+donor+cells+on+human+immunodeficiency+virus+type+1+replication+and+selection+in+vitro.">Effect of different donor cells on human immunodeficiency virus type 1 replication and selection in vitro.</a> J. Virol. 69 (1), 422-429 (1995).</li><li>Manocheewa, S., Swain, J. V., Lanxon-Cookson, E., Rolland, M., Mullins, J. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fitness+costs+of+mutations+at+the+HIV-1+capsid+hexamerization+interface.">Fitness costs of mutations at the HIV-1 capsid hexamerization interface.</a> PLoS One. 8 (6), e66065 (2013).</li><li>Zakeri, H., Amparo, G., Chen, S. M., Spurgeon, S., Kwok, P. Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Peak+height+pattern+in+dichloro-rhodamine+and+energy+transfer+dye+terminator+sequencing.">Peak height pattern in dichloro-rhodamine and energy transfer dye terminator sequencing.</a> Biotechniques. 25 (3), 406-410 (1998).</li><li>Lalonde, M. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sensitive+oligonucleotide+ligation+assay+for+low-level+detection+of+nevirapine+resistance+mutations+in+human+immunodeficiency+virus+type+1+quasispecies.">Sensitive oligonucleotide ligation assay for low-level detection of nevirapine resistance mutations in human immunodeficiency virus type 1 quasispecies.</a> J Clin Microbiol. 45 (8), 2604-2615 (2007).</li></ol>

Gli autori dichiarano di non avere interessi finanziari in competizione. Le opinioni qui espresse sono quelle degli autori e non devono essere interpretati come ufficiale o che rappresentano il punto di vista del Dipartimento della Difesa statunitense e il Dipartimento dell&#39;Esercito.

I protocolli presentati consisteva di due parti principali: costruzione di ricombinanti HIV-1 cloni molecolari e saggi di competizione crescita. Per distinguere due virus in coltura cellulare infettata doppiamente, è importante che i cloni molecolari concorrenti contengono tag di sequenza, che può essere rilevata da un RT-qPCR assay primer sonda o da Sanger sequenziamento. Questo protocollo fa uso di tag VIFA e VifB, che occupano la stessa regione del virus HIV-1 NL4-3 vif e codificano la stessa sequenza aminoacidica ma differiscono da sei mutazioni sinonimi. Queste mutazioni non hanno mostrato di influenzare virale replica fisica 20. Il metodo di clonazione PCR-based utilizzati in questo protocollo offre una maggiore flessibilità nella selezione dei siti clonazione, rispetto alla clonazione basata sito di restrizione. Tuttavia, l&#39;efficienza di clonazione PCR diminuisce all&#39;aumentare della dimensione dell&#39;inserto aumenta. Il limite di corrente della dimensione inserto è ~ 5 kb 34. Per clonazione PCR-based e sito diretto mutagenesis, l&#39;uso di una DNA polimerasi ad alta fedeltà è fondamentale per ridurre la probabilità di mutazioni supplementari. È anche raccomandato l&#39;uso di un numero minimo di cicli di PCR necessari a produrre adeguate quantità di prodotti. Nella nostra esperienza, non abbiamo rilevato alcun mutazioni in più dopo la clonazione e sito-passi mutagenesi basate sulla PCR qui descritti. Tuttavia i prodotti di PCR devono essere sequenziati per verificare eventuali mutazioni indesiderate. Idealmente, l&#39;intera regione codificante HIV dovrebbe essere resequenced. Almeno tre punti di tempo di campionamento dovrebbero essere esaminate entro la fase di crescita esponenziale 9. La cinetica di crescita virale devono prima essere stabilite mediante campionamento giornaliero di determinare il periodo della cultura e tempo di campionamento punti appropriati per il concorso di crescita. Un fattore che influenza la cinetica di crescita virale è la molteplicità di infezione (MOI). Questo protocollo utilizza un MOI totale di 0,005 per entrambi monoinfezione e la concorrenza la crescita, come è stato dimostrato per produrre più rorisultati busto di basso MOI 9. Tuttavia, MOI inferiore possono essere utilizzati per ottenere una fase di crescita esponenziale più se necessario, ma a scapito della consistenza risultato. Questo protocollo suggerisce un rapporto infezione iniziale di 50:50, supponendo che le differenze di idoneità dei virus sono generalmente sconosciuti anticipo. Tuttavia, l&#39;uso di tali rapporti ineguali sono appropriati quando ci sono dati preliminari suggeriscono differenze significative nella cinetica di replicazione virale. In questi casi, un rapporto di infezione di 70:30 è raccomandato per consentire il rilevamento di una grande differenza di fitness dove il virus meno allenati è posto in eccesso 9. Il protocollo per la determinazione della TCID 50, cinetica di crescita virale, e per l&#39;esecuzione di saggi di crescita della concorrenza sono stati ottimizzati utilizzando HIV-1 sottotipo B, NL4-3 COTB-p24 e PBMC da un singolo donatore il cui sangue periferico hanno dimostrato sensibilità coerente per HIV 1 infezione in vitro. Il periodo di colturae punti di tempo di campionamento presentate in questo protocollo sono suscettibili di essere adatto per studiare HIV-1 gruppo M virus in PBMC umani. Utilizzando PBMC da una singola fonte è altamente raccomandato per ottenere risultati coerenti come la replicazione virale può variare in diverse cellule del donatore 35. Sebbene meno desiderabile, PBMC raccolti da donatori multipli possono essere utilizzati come una sostituzione a condizione che la stessa piscina è utilizzata in tutti gli esperimenti. Un&#39;altra alternativa è l&#39;uso di linee cellulari. Il protocollo presentato qui è stato utilizzato con successo con la linea di cellule T CEMx174 23,36. Tuttavia, è importante che il numero di cellule seminate sono ri-ottimizzati per raggiungere la crescita delle cellule coerente. Cinetica di crescita virale devono essere ripristinati, in quanto può variare in diverse linee cellulari, per determinare i punti di tempo appropriati campionamento nei passaggi concorrenza crescita. Due metodi differenti per determinare il rapporto virale per calcolare fitness sono inclusi nel ProtoColo. Il primo utilizza RT-qPCR per misurare virale numero di copie di cDNA in ogni punto di campionamento. Viral idoneità replica stata quindi calcolata dal rapporto virale, basata sul numero di copia cDNA. In alternativa, il rapporto virale può essere determinato in base al rapporto tra l&#39;altezza di picco cromatogramma nei siti tag VifAB. I due metodi hanno fornito risultati comparabili (Figura 4). Il metodo altezza del picco cromatogramma può essere applicato ad altri ceppi HIV-1 senza un tag sequenza ingegnerizzato. Per RT-qPCR, l&#39;uso di primer o sonde per distinguere varianti virali deve prima essere attentamente valutato (vedi 20). Tuttavia, RT-qPCR conferendo una maggiore sensibilità per campioni con una piccola quantità di RNA virale, come quelli del primo punto temporale all&#39;interno della fase di crescita esponenziale. La misura diretta della cDNA virale permette anche la rilevazione di problemi tecnici che possono sorgere dalle operazioni di estrazione di RNA e sintesi del DNA. Utilizzo di cloni molecolari con sequence tags fornisce una soluzione conveniente to metodi RT-qPCR, come sono necessari solo due coppie di primer e sonde per studiare più virus. Questa strategia evita anche il problema della variazione di picco altezza in sequenza cromatogrammi causa di basi adiacenti 37, come sequenziamento viene eseguito nello stesso sito attraverso tutti i virus in studio. I prodotti di PCR prodotti per RT-qPCR e sequenziamento Sanger può anche essere utilizzato con altri metodi per determinare il rapporto virale, come massa sequenziamento del singolo clone 12,13, HTA 4,7,17,19 o saggio oligonucleotide legatura (OLA) 38 .

Viral idoneità replica è definita come la capacità di un virus per produrre progenie infettiva in un dato ambiente 1 ed è un fattore importante che contribuisce a determinare la prevalenza di una variante del virus a livello della popolazione nel tempo 2. Come studi in vivo di fitness non sono realizzabili con virus umani patogeni, come l&#39;HIV-1, vari in vitro e ex vivo replica dosaggi di fitness sono stati sviluppati per studiare gli effetti sul benessere derivanti dalla resistenza ai farmaci e le mutazioni di fuga del sistema immunitario, epistasi e l&#39;evoluzione delle popolazioni virali 3-6. Tra i diversi dosaggi di fitness, analisi della concorrenza crescita sono riconosciuti a produrre misure più sensibili e validi di differenze di fitness, come due o più varianti virali competono per la stessa popolazione di cellule sotto precisamente le stesse condizioni ambientali, come avviene in vivo 1,7,8. Prima di avviare esperimenti di competizione di crescita, molti variables necessario determinare, compreso l&#39;uso di diverse molteplicità di infezione (MOI), rapporto input virale, e tempi di campionamento per l&#39;analisi. Abbiamo studiato gli effetti di questi parametri sulla cinetica di crescita virale e sul risultato di esperimenti di competizione, e abbiamo individuato i fattori chiave necessari per le misure di resistenza del virus HIV-1 di fitness in coltura cellulare 9. In aggiunta alle variabili saggio, ci sono una varietà di metodi per la quantificazione varianti virali in esperimenti di competizione crescita. Bulk 10,11 o sequenziamento clonale 12,13 è stata utilizzata per determinare il rapporto dei virus concorrenti basati sulle frequenze nucleotidiche del sito (s) di interesse. Idoneità relativa è derivato da cambiamenti in questo rapporto nel tempo. Questo metodo è conveniente come servizi di sequenziamento del DNA sono ampiamente disponibili. Il metodo (PASS) allele-specifica sequenziamento parallelo permette il sequenziamento in più siti e l&#39;individuazione di ricombinanti 14 </sup&gt;, Ma richiede anche reagenti appositamente sviluppati e sistemi di rilevazione. Essenzialmente, questi metodi sono stati sviluppati per studiare ceppi virali con un piccolo numero di differenze nucleotidiche in una regione di interesse. Altri metodi usano un piccolo gene reporter 15 o sinonimi mutazioni 4,16-18 come tag per distinguere i virus concorrenti di sequenziamento, le analisi di monitoraggio eteroduplex (HTA) 4,7,17,19 o invertire in tempo reale reazione di trascrizione-quantitativo a catena della polimerasi (RT-qPCR) 15,16,18,20, ognuno dei quali può essere reso applicabile a studiare ceppi competere indipendentemente similarità di sequenza. Un passo ulteriore è necessario per introdurre modifiche in genomi virali e il saggio RT-qPCR richiede anche reagenti e strumentazioni specifiche. Abbiamo scoperto che il sequenziamento di massa rese Sanger risultati comparabili 9. A seguito di concorso crescita, virale idoneità replica viene presentata come il fitness parente, o un rapporto di idoneità tra two varianti virali. L&#39;idoneità relativa di un virus può essere definita come la percentuale finale di una variante virale viene normalizzato mediante la sua proporzione iniziale in inoculo o come la differenza netta tasso di crescita tra i due virus concorrenti. Abbiamo scoperto che il secondo metodo, utilizzando punti di dati longitudinali solo all&#39;interno della fase di crescita esponenziale, ha prodotto i risultati più robusti 9,20. In vitro fitness sono utilizzati principalmente per studiare cloni biologici 6-8 e cloni molecolari infettivi di HIV-1. Quest&#39;ultimo, essendo suscettibili di manipolazione genetica, sono spesso impiegati per studiare l&#39;effetto sulla forma fisica di particolari mutazioni o sequenze specifiche di interesse 3-5,21,22. I seguenti protocolli descrivono un flusso di lavoro dal punto di costruire nuovo full-length HIV-1 cloni molecolari infettivi usando HIV-1 vettori contenenti un tag sequenza, introducendo mutazioni di interesse, rendendo stock virali e stabilendo cinetica di crescita virale, Di eseguire il test concorso crescita e calcolando fitness relativa (Figura 1). Utilizzando i nostri procedure ottimizzate, abbiamo creato tre ricombinanti HIV-1 mutanti e determinato la loro idoneità replica. Il clone molecolare ricombinante è stato costruito sostituendo il gag-p24 regione HIV-1 gene di pNL4-3, un plasmide contenente un integrale genoma infettiva del virus HIV-1 ceppo NL4-3 laboratorio, con un COTB sintetico (Centro-Of Albero, sottotipo B) sequenza gag-p24 23 per creare il ceppo prototipo. Modifiche amminoacidi singoli (T186M, T242N e I256V) sono stati poi introdotti per creare tre cloni mutanti. Ogni mutante era gareggiato contro il virus prototipo per osservare l&#39;impatto idoneità di ogni mutazione nel data background genetico. I tre mutanti dimostrato una diversi livelli di replicazione fsitness da lieve a significativamente inferiore al virus prototipo. La mutazione T242N è stato precedentemente segnalato per avere è d moderatass costano 24-26, simile al risultato mostrato in questo studio. Il costo idoneità delle altre due mutazioni non era stato riportato in precedenza.

<table border="0" cellpadding="0" cellspacing="0" width="1172">
	<tbody>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">Name of Material/ Equipment</td>
			<td style="width:484px;">Company</td>
			<td style="width:137px;">Catalog Number</td>
			<td style="width:196px;">Comments/Description</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Construction of recombinant clones</td>
			<td style="width:484px;"></td>
			<td style="width:137px;"></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">Chimeric primer/Mutagenic/Sequencing primers</td>
			<td style="width:484px;">IDT</td>
			<td style="width:137px;">N/A</td>
			<td>Custom DNA oligos</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">pNL4-3VifA and pNL4-3VifB plasmid</td>
			<td style="width:484px;">N/A</td>
			<td style="width:137px;">N/A</td>
			<td>Please contact Dr. James I Mullins (jmullins@uw.edu)</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">High-Fidelity DNA polymerase</td>
			<td style="width:484px;">Thermo Scientific</td>
			<td>F-549S</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">High-fidelity buffer</td>
			<td style="width:484px;">Thermo Scientific</td>
			<td>F-549S</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">dNTP</td>
			<td style="width:484px;">Bioline</td>
			<td style="width:137px;">Bio-39026</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Thermal cycler</td>
			<td style="width:484px;">Life Technologies</td>
			<td style="width:137px;">N/A</td>
			<td>Applied Biosystems&#174; GeneAmp&#174; PCR System 9700</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">DNA loading dye</td>
			<td style="width:484px;">Thermo Scientific</td>
			<td style="width:137px;">R0631</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">1kb Plus DNA ladder</td>
			<td style="width:484px;">Invitrogen</td>
			<td style="width:137px;">10787-018</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">QIAquick PCR Purification Kit</td>
			<td style="width:484px;">Qiagen</td>
			<td style="width:137px;">28104</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">QIAquick gel extraction kit</td>
			<td style="width:484px;">Qiagen</td>
			<td style="width:137px;">28704</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">DpnI enzyme</td>
			<td style="width:484px;">New England Biolabs</td>
			<td>R0176S</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">TOP10 chemically competent Escherichia coli</td>
			<td style="width:484px;">Invitrogen</td>
			<td>C4040-10</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">Luria Broth base powder</td>
			<td style="width:484px;">Invitrogen</td>
			<td style="width:137px;">12795-084</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">Carbenicillin</td>
			<td style="width:484px;">Research Products International</td>
			<td style="width:137px;">C46000-25.0</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">QIAprep Spin Miniprep kit&#160;</td>
			<td style="width:484px;">Qiagen</td>
			<td style="width:137px;">27104</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">EndoFree Plasmid Maxi Kit</td>
			<td style="width:484px;">Qiagen</td>
			<td style="width:137px;">12362</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Transfection</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">X-tremeGENE 9 DNA transfection reagent</td>
			<td style="width:484px;">Roche</td>
			<td>6365787001</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">HEK 293T-17</td>
			<td style="width:484px;">ATCC</td>
			<td style="width:137px;">CRL-11268</td>
			<td>http://www.atcc.org/</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">0.22um filter top tube</td>
			<td style="width:484px;">VWR International</td>
			<td>89220-716&#160;</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Cell culture</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Dulbecco&#39;s Modified Eagle Medium (DMEM)</td>
			<td style="width:484px;">Life Technologies</td>
			<td>10566016</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Iscove&#8242;s Modified Dulbecco&#8242;s Medium (IMDM)</td>
			<td style="width:484px;">Life Technologies</td>
			<td>31980-030</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">RPMI-1640 media</td>
			<td style="width:484px;">Life Technologies</td>
			<td>61870-036</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">Phytohemagglutinin (PHA)</td>
			<td style="width:484px;">Thermo Scientific</td>
			<td>R30852801</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">Human Interleukin-2</td>
			<td style="width:484px;">Roche</td>
			<td>11147528001</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">Fetal bovine serum</td>
			<td style="width:484px;">JR Scientific</td>
			<td style="width:137px;">43640</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">Penicillin and Streptomycin</td>
			<td style="width:484px;">Corning Cellgro</td>
			<td>30-001-CI</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">6 well plate</td>
			<td style="width:484px;">VWR Scientific</td>
			<td style="width:137px;">73520-906</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">48 well plate</td>
			<td style="width:484px;">VWR Scientific</td>
			<td style="width:137px;">62407-338</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">96 well flat-bottomed plate</td>
			<td style="width:484px;">ISC Bioexpress</td>
			<td style="width:137px;">T-3015-4</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">96 well round-bottomed plate</td>
			<td style="width:484px;">BD Falcon</td>
			<td style="width:137px;">353077</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">1.5 ml Microcentrifuge Tube</td>
			<td style="width:484px;">Mt. Baker Bio</td>
			<td style="width:137px;">MBD-1500</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">1.5 mL tubes w/ O-ring</td>
			<td style="width:484px;">VWR Scientific</td>
			<td style="width:137px;">89004-290</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:355px;">50 mL conical tube</td>
			<td style="width:484px;">ISC Bioexpress</td>
			<td>C-3317-6</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">ELISA</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">Triton-X 100</td>
			<td style="width:484px;">Sigma-Aldrich</td>
			<td>X100</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">Phosphate buffer saline (PBS)</td>
			<td style="width:484px;">Invitrogen</td>
			<td style="width:137px;">14190-250</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">Fetal bovine serum (FBS)</td>
			<td style="width:484px;">Sigma-Aldrich</td>
			<td>F0392</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">glycerol</td>
			<td style="width:484px;">Sigma-Aldrich</td>
			<td style="width:137px;">G5516</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">Tween 20</td>
			<td style="width:484px;">Sigma-Aldrich</td>
			<td>P1379</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">Bovine Serum Albumin (BSA)</td>
			<td style="width:484px;">Sigma-Aldrich</td>
			<td>A2153</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Rabbit anti-HIV-1 SF2 p24 antiserum</td>
			<td style="width:484px;">NIH AIDS Reagent Program</td>
			<td style="width:137px;">4250</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Goat anti-rabbit HRP</td>
			<td style="width:484px;">KPL</td>
			<td style="width:137px;">474-1516</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">TMB Microwell Peroxidase Substrate</td>
			<td style="width:484px;">KPL</td>
			<td style="width:137px;">52-00-01</td>
			<td></td>
		</tr>
		<tr height="26">
			<td height="26" style="height:26px;">H2SO4</td>
			<td>Fisher Scientific</td>
			<td>A300-500</td>
			<td>Causes severe burns by all exposure routes. Use personal protective equipment. Use only under a chemical fume hood. Wash off immediately with plenty of water for at least 15 minutes.</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">HIV p24 standard</td>
			<td style="width:484px;">AIDS and Cancer Virus program (NCI-Frederick)</td>
			<td style="width:137px;">N/A</td>
			<td>For order details please contact Julian Bess, Jr. (bessjw@mail.nih.gov); http://ncifrederick.cancer.gov/Programs/Science/Acvp/bio/Bess.aspx</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">Microplate reader</td>
			<td style="width:484px;">Molecular Devices</td>
			<td style="width:137px;">N/A</td>
			<td>VMax Kinetic ELISA Microplate Reader</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">RNA isolation cDNA synthesis</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">QIAxtractor</td>
			<td style="width:484px;">Qiagen</td>
			<td style="width:137px;">N/A</td>
			<td>http://www.qiagen.com/products/catalog/automated-solutions/sample-prep/qiaxtractor</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">QIAamp Viral RNA Mini Kit</td>
			<td style="width:484px;">Qiagen</td>
			<td style="width:137px;">52906</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">dNTP</td>
			<td style="width:484px;">Bioline</td>
			<td style="width:137px;">Bio-39026</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">SuperscriptIII</td>
			<td style="width:484px;">Invitrogen</td>
			<td>18080-085</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">First-strand buffer&#160;</td>
			<td style="width:484px;">Invitrogen</td>
			<td>18080-085</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Dithiothreitol (DTT)</td>
			<td style="width:484px;">Invitrogen</td>
			<td>18080-085</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">Rnase inhibitor</td>
			<td style="width:484px;">Roche</td>
			<td>3335402001</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">RnaseH</td>
			<td style="width:484px;">Invitrogen</td>
			<td>18021-071</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">qPCR</td>
			<td style="width:484px;"></td>
			<td style="width:137px;"></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">Real-time qPCR machine</td>
			<td style="width:484px;">Life Technologies</td>
			<td style="width:137px;">N/A</td>
			<td>Applied Biosystems 7300 Real-Time PCR&#160;</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">TaqMan&#174; Gene Expression Master Mix</td>
			<td style="width:484px;">Life Technologies</td>
			<td>4369016</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">Forward, reverse primer</td>
			<td style="width:484px;">IDT</td>
			<td style="width:137px;">N/A</td>
			<td>Custom order</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">Probe</td>
			<td style="width:484px;">Life Technologies</td>
			<td style="width:137px;">N/A</td>
			<td>Custom order</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">optical 96 well reaction plate</td>
			<td style="width:484px;">Life Technologies</td>
			<td style="width:137px;">I19N3Q216</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">PCR+sequencing</td>
			<td style="width:484px;"></td>
			<td style="width:137px;"></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">Taq DNA polymerase (Biolase)</td>
			<td style="width:484px;">Bioline</td>
			<td style="width:137px;">Bio-21043</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">NH4 buffer&#160;</td>
			<td style="width:484px;">Bioline</td>
			<td style="width:137px;">Bio-21043</td>
			<td></td>
		</tr>
		<tr height="26">
			<td height="26" style="height:26px;">MgCl2</td>
			<td style="width:484px;">Bioline</td>
			<td style="width:137px;">Bio-21043</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">Sequencing primer</td>
			<td style="width:484px;">IDT</td>
			<td style="width:137px;">N/A</td>
			<td>Custom order</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:355px;">QIAxcel</td>
			<td style="width:484px;">Qiagen</td>
			<td style="width:137px;"></td>
			<td>http://www.qiagen.com/products/catalog/automated-solutions/detection-and-analysis/qiaxcel-advanced-system</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">DNA sequencing service provider</td>
			<td>http://www.htseq.org/</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;"></td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;"></td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">GRC web tool</td>
			<td>http://indra.mullins.microbiol.washington.edu/grc/</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">ChromatQuan web tool</td>
			<td>http://indra.mullins.microbiol.washington.edu/cgi-bin/chromatquant.cgi</td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

pairwise growth competition assay for determining the replication fitness of human immunodeficiency viruses

In vitro fitness assays are essential tools for determining viral replication fitness for viruses such as HIV-1. Various measurements have been used to extrapolate viral replication fitness, ranging from the number of viral particles per infectious unit, growth rate in cell culture, and relative fitness derived from multiple-cycle growth competition assays. Growth competition assays provide a particularly sensitive measurement of fitness since the viruses are competing for cellular targets under identical growth conditions. There are several experimental factors to consider when conducting growth competition assays, including the multiplicity of infection (MOI), sampling times, and viral detection and fitness calculation methods. Each factor can affect the end result and hence must be considered carefully during the experimental design. The protocol presented here includes steps from constructing a new recombinant HIV-1 clone to performing growth competition assays and analyzing the experimental results. This protocol utilizes experimental parameter values previously shown to yield consistent and robust results. Alternatives are discussed, as some parameters need to be adjusted according to the cell type and viruses being studied. The protocol contains two alternative viral detection methods to provide flexibility as the availability of instruments, reagents and expertise varies between laboratories.

Per studiare l&#39;impatto idoneità dei cambiamenti di aminoacidi singoli in HIV-1 Gag-p24, abbiamo usato oligonucleotide mutagenesi diretta a introdurre mutazioni in un plasmide pNL4-3 contenente il virus HIV-1 COTB-p24 gene 23,32,33. Scorte virali sono stati generati da trasfezione di cellule 293T e raccolte dopo 48 ore. Abbiamo stimato la dose del 50% coltura tissutale infettiva (TCID 50) di ciascun titolo virale con il metodo Reed-Muench 31. Il TCID50 del prototipo e virus mutanti variavano da 10 aprile - 10 MAGGIO UI / ml (Figura 3A). La cinetica di crescita del virus ricombinanti sono stati stabiliti in PBMC da un singolo donatore ad una MOI di 0,005. RT-qPCR è stato utilizzato per misurare il numero di copie virali cDNA al giorno per sei giorni. Tutti i virus mutanti e prototipi crescevano esponenzialmente tra il giorno 2 e il giorno 4, a seguito della quale la crescita virale rallentato, come indicato da una diminuita pendenza della crescita virale numero di copie di RNA (&lt;strong&gt; Figura 3B). La diminuzione cDNA numero di copie tra giorno 0 (corrispondente al inoculo) e il giorno 2 è dovuta all&#39;assorbimento di virus di cellule e la rimozione di virioni non legati dal giorno 1 di lavaggio (passo 5.1.6). Nella fase di crescita esponenziale, tutti tre mutanti avevano un tasso di crescita più lenta (g) che il virus prototipo (Figura 3C). Tutti e tre i mutanti sono stati gareggiato contro il virus prototipo nei test concorrenza crescita a un totale di 0.005 MOI. Cinetica di crescita virale in culture doppiamente infette erano simili a quelle di monoinfezione; la fase di crescita esponenziale virale era tra i giorni 2 e 4, e la crescita virale ha raggiunto un plateau intorno al giorno 5 (Figura 4A). Le differenze di crescita virale sono stati derivati ​​dalla variazione del rapporto virale nel tempo. Il rapporto virale è stato calcolato sulla base di cDNA numero di copie di riferimento e dei virus mutanti mediante RT-qPCR, e confrontando altezzein sequenza cromatogrammi in siti nucleotide distinguendo i due virus (Figura 4B). Le differenze di tasso di crescita determinati utilizzando la copia di RNA virale metodi numerici picco di altezza e hanno dato risultati simili (Figura 4C). Tutti e tre i mutanti avevano idoneità replica inferiore rispetto ai virus prototipo con il I256V mutante avere l&#39;idoneità più basso (Figura 4C). <img alt="Figura 1" src="/files/ftp_upload/52610/52610fig1.jpg" /> Figura 1: Diagramma di flusso dei protocolli presentati in questo documento il virus protocolli Preparazione preoccupazione costruzione di HIV-1 cloni ricombinanti e la generazione di titoli virali.. I protocolli Assays fitness sono per stabilire cinetica di crescita virale e la determinazione fitness virale relativa. Le linee tratteggiate rappresentano flussi alternativi per i protocolli. Ad esempio, una mutazione può essere introdotto direttamente nella HIV-1 NL4-3clone molecolare senza generare un clone ricombinante. <img alt="Figura 2" src="/files/ftp_upload/52610/52610fig2.jpg" /> Figura 2:. Costruzione di HIV-1 NL4-3 COTB Gag-p24 cloni molecolari ricombinanti con estensione sovrapposizione PCR (A) Progettare i primer chimerici. Il 5 &#39;metà dei primer contengono la sequenza vettoriale NL4-3 e il 3&#39; metà contengono le estremità della sequenza dell&#39;inserto. (B) primer chimerici sono usati per amplificare il frammento dell&#39;inserto, COTB Gag-p24. (C) I frammenti inserti sono utilizzati come primers per una seconda PCR per generare un nuovo plasmide ricombinante. <img alt="Figura 3" src="/files/ftp_upload/52610/52610fig3.jpg" /> Figura 3:. Caratteristiche di crescita virale in PBMC (A) Accedi 10 TCID 50 </sub&gt; delle scorte virali. (B) cinetica di crescita virale in monoinfections iniziato con un MOI = 0,005. (C) i tassi di crescita virale in sei giorni, compreso la fase esponenziale di crescita (2-4 giorni) derivato da pannello (B). I valori riportati rappresentano la media di tre repliche da un esperimento. Le barre di errore rappresentano 95% intervalli di confidenza. <img alt="Figura 4" src="/files/ftp_upload/52610/52610fig4.jpg" /> Figura 4: crescita virale e relativa idoneità determinazioni (A) la crescita virale in colture PBMC doppiamente infette.. (B) Rapporti di T242N e prototipo virus determinati con RT-qPCR o il metodo di sequenziamento picco altezza. (C) differenze nette virali tasso di crescita (d) tra il mutante ei virus prototipo in culture doppiamente infette, come illustrato in (A). d valori sono stati calcolati fROM i dati riportati in rapporto virale (B). I valori riportati rappresentano la media di tre repliche da un esperimento. Le barre di errore rappresentano 95% intervalli di confidenza.

Watch this Scientific Journal Video about Pairwise Growth Competition Assay for Determining the Replication Fitness of Human Immunodeficiency Viruses at JoVE.com

Pairwise Growth Competition Assay for Determining the Replication Fitness of Human Immunodeficiency Viruses

Growth competition between nearly isogenic viruses provides a sensitive measurement for determining relative replication fitness. The protocols described here include the construction of recombinant HIV-1 clones, virus propagation and growth competition and analysis methods optimized to yield sensitive and consistent results.

Pairwise crescita Concorso test per la determinazione della Fitness replica del virus dell&#39;immunodeficienza umana

In vitro fitness assays are essential tools for determining viral replication fitness for viruses such as HIV-1. Various measurements have been used to ...

pairwise-growth-competition-assay-for-determining-replication-fitness

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JoVE Journal

Immunology and Infection

11.0K Views.  University of Washington. Growth competition between nearly isogenic viruses provides a sensitive measurement for determining relative replication fitness. The protocols described here include the construction of recombinant HIV-1 clones, virus propagation and growth competition and analysis methods optimized to yield sensitive and consistent results.

Video: Pairwise Growth Competition Assay for Determining the Replication Fitness of Human Immunodeficiency Viruses

Determining the Reactivity and Titre of Serum using a Haemagglutination Assay

Haemagglutination is a specific form of agglutination and is used when antibodies bind to red blood cells, which act as a particulate antigen. Red blood cells are particularly useful targets as they are readily available and agglutination is observable using the naked eye. This technique is commonly used to determine the titre of an antibody (Ab), for blood grouping and viral quantification. In this video, the steps involved in preparing and performing a haemagglutination assay is demonstrated using antibodies specific to blood group A-antigens added to red blood cells (Revercells). The antiserum is serially diluted in a 96 well U-bottom microtitre tray, to which is added a suspension of Revercells. The samples are mixed and then incubated at 37&deg;C for 60 minutes. After this time, the samples can then be easily scored for  ve, +ve and intermediate (-/+) haemagglutination reactions. This approach allows for the reactivity and titre of a serum sample to be assessed using a rapid and simple technique. The video will cover the theory behind the assay, how the results are read and interpreted, how the titre is determined, how the assay can be modified and any issues associated with the use of this technique.

Haemagglutination is a form of agglutination where antibodies bind to red blood cells. Red blood cells are both readily available and the results are readily observable using the naked eye. This video demonstrates the steps involved in a haemagglutination assay, interpreting the results and determining the titre.

Determinazione della reattività e Titolo di siero usando un test dell&#39;emoagglutinazione

Haemagglutination is a specific form of agglutination and is used when antibodies bind to red blood cells, which act as a particulate antigen. Red blood ...

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Immunologia e infezioni

Cost-effective Method for Microbial Source Tracking Using Specific Human and Animal Viruses

Microbial contamination of the environment represents a significant health risk. Classical bacterial fecal indicators have shown to have significant limitations, viruses are more resistant to many inactivation processes and standard fecal indicators do not inform on the source of contamination. The development of cost-effective methods for the concentration of viruses from water and molecular assays facilitates the applicability of viruses as indicators of fecal contamination and as microbial source tracking (MST) tools. Adenoviruses and polyomaviruses are DNA viruses infecting specific vertebrate species including humans and are persistently excreted in feces and/or urine in all geographical areas studied. In previous studies, we suggested the quantification of human adenoviruses (HAdV) and JC polyomaviruses (JCPyV) by quantitative PCR (qPCR) as an index of human fecal contamination. Recently, we have developed qPCR assays for the specific quantification of porcine adenoviruses (PAdV) and bovine polyomaviruses (BPyV) as animal fecal markers of contamination with sensitivities of 1-10 genome copies per test tube. In this study, we present the procedure to be followed to identify the source of contamination in water samples using these tools. As example of representative results, analysis of viruses in ground water presenting high levels of nitrates is shown.
Detection of viruses in low or moderately polluted waters requires the concentration of the viruses from at least several liters of water into a much smaller volume, a procedure that usually includes two concentration steps in series. This somewhat cumbersome procedure and the variability observed in viral recoveries significantly hamper the simultaneous processing of a large number of water samples.
In order to eliminate the bottleneck caused by the two-step procedures we have applied a one-step protocol developed in previous studies and applicable to a diversity of water matrices. The procedure includes: acidification of ten-liter water samples, flocculation by skimmed milk, gravity sedimentation of the flocculated materials, collection of the precipitate and centrifugation, resuspension of the precipitate in 10 ml phosphate buffer. The viral concentrate is used for the extraction of viral nucleic acids and the specific adenoviruses and polyomaviruses of interest are quantified by qPCR. High number of samples may be simultaneously analyzed using this low-cost concentration method.
The procedure has been applied to the analysis of bathing waters, seawater and river water and in this study, we present results analyzing groundwater samples. This high-throughput quantitative method is reliable, straightforward, and cost-effective.

The study describes a cost-effective method for the identification of the source of fecal/urine contamination or contamination by nitrates in water using qPCR for the specific quantification of human/porcine/bovine DNA viruses, adenoviruses and polyomaviruses, proposed as MST tools.

Costo-efficace metodo per il rilevamento di origine microbica Utilizzando specifici virus umani e animali

Microbial contamination of the environment represents a significant health risk. Classical bacterial fecal indicators have shown to have significant ...

Determining Optimal Cytotoxic Activity of Human Her2neu Specific CD8 T cells by Comparing the Cr51 Release Assay to the xCELLigence System

Cytotoxic CD8 T cells constitute a subgroup of T cells that are capable of inducing the death of infected or malignant host cells1. These cells express a specialized receptor, called the T cell receptor (TCR), which can recognize a specific antigenic peptide bound to HLA class I molecules2. Engagement of infected cells or tumor cells through their HLA class I molecule results in production of lytic molecules such as granzymes and perforin resulting in target cell death. While it is useful to determine frequencies of antigen-specific CD8 T cells using assays such as the ELIspot or flow cytometry, it is also helpful to ascertain the strength of CD8 T cell responses using cytotoxicity assays3. The most recognizable assay for assessing cytotoxic function is the Chromium Release Assay (CRA), which is considered a standard assay 4. The CRA has several limitations, including exposure of cells to gamma radiation, lack of reproducibility, and a requirement for large numbers of cells. Over the past decade, there has been interest in adopting new strategies to overcome these limitations. Newer approaches include those that measure caspase 
release 4, BLT esterase activity 5 and surface expression of CD107 6. The impedance-based assay, using the Roche xCelligence system, was examined in the present paper for its potential as an alternative to the CRA. Impedance or opposition to an electric current occurs when adherent tumor cells bind to electrode plates. Tumor cells detach following killing and electrical impedance is reduced which can be measured by the xCelligence system. The ability to adapt the impedance-based approach to assess cell-mediated killing rests on the observation that T cells do not adhere tightly to most surfaces and do not appear to have much impact on impedance thus diminishing any concern of direct interference of the T cells with the measurement. Results show that the impedance-based assay can detect changes in the levels of antigen-specific cytotoxic CD8 T cells with increased sensitivity relative to the standard CRA. Based on these results, impedance-based approaches may be good alternatives to CRAs or other approaches that aim to measure cytotoxic CD8 T cell functionality.

The chromium release assay, a common assay for detecting cytotoxic T cell activity, has several limitations. Using antigen-specific CD8 T cells and the human breast cancer tumor line, SKBR3, in the present article, an impedance-based approach was examined for the capability of detecting cell killing.

Determinazione ottimale attività citotossica di specifiche cellule T umane Her2neu CD8 confrontando il Cr51 saggio di rilascio al Sistema xCELLigence

Cytotoxic CD8 T cells constitute a subgroup of T  cells that are capable of inducing the death of infected or malignant host  cells1. These cells express ...

Determining Soil-transmitted Helminth Infection Status and Physical Fitness of School-aged Children

Soil-transmitted helminth (STH) infections are common. Indeed, more than 1 billion people are affected, mainly in the developing world where poverty prevails and hygiene behavior, water supply, and sanitation are often deficient1,2. Ascaris lumbricoides, Trichuris trichiura, and the two hookworm species, Ancylostoma duodenale and Necator americanus, are the most prevalent STHs3. The estimated global burden due to hookworm disease, ascariasis, and trichuriasis is 22.1, 10.5, and 6.4 million disability-adjusted life years (DALYs), respectively4. Furthermore, an estimated 30-100 million people are infected with Strongyloides stercoralis, the most neglected STH species of global significance which arguably also causes a considerable public health impact5,6. Multiple-species infections (i.e., different STHs harbored in a single individual) are common, and infections have been linked to lowered productivity and thus economic outlook of developing countries1,3.
For the diagnosis of common STHs, the World Health Organization (WHO) recommends the Kato-Katz technique7,8, which is a relatively straightforward method for determining the prevalence and intensity of such infections. It facilitates the detection of parasite eggs that infected subjects pass in their feces.
With regard to the diagnosis of S.stercoralis, there is currently no simple and accurate tool available. The Baermann technique is the most widely employed method for its diagnosis. The principle behind the Baermann technique is that active S.stercoralis larvae migrate out of an illuminated fresh fecal sample as the larvae are phototactic9. It requires less sophisticated laboratory materials and is less time consuming than culture and immunological methods5.
Morbidities associated with STH infections range from acute but common symptoms, such as abdominal pain, diarrhea, and pruritus, to chronic symptoms, such as anemia, under- and malnutrition, and cognitive impairment10. Since the symptoms are generally unspecific and subtle, they often go unnoticed, are considered a normal condition by affected individuals, or are treated as symptoms of other diseases that might be more common in a given setting. Hence, it is conceivable that the true burden of STH infections is underestimated by assessment tools relying on self-declared signs and symptoms as is usually the case in population-based surveys.
In the late 1980s and early 1990s, Stephenson and colleagues highlighted the possibility of STH infections lowering the physical fitness of boys aged 6-12 years11,12. This line of scientific inquiry gained new momentum recently13,14,15. The 20-meter (m) shuttle run test was developed and validated by L&eacute;ger et al.16 and is used worldwide to measure the aerobic fitness of children17. The test is easy to standardize and can be performed wherever a 20-m long and flat running course and an audio source are available, making its use attractive in resource-constrained settings13. To facilitate and standardize attempts at assessing whether STH infections have an effect on the physical fitness of school-aged children, we present methodologies that diagnose STH infections or measure physical fitness that are simple to execute and yet, provide accurate and reproducible outcomes. This will help to generate new evidence regarding the health impact of STH infections.

Chronic infection with soil-transmitted helminths (STHs) causes malabsorption, stunting, and wasting in the growing child. Hence, it is plausible that these infections also reduce the physical fitness of children. Here, we visualize two techniques for the diagnosis of STHs and the 20-meter shuttle run test for assessing children's physical fitness.

Determinazione del suolo-infezione trasmessa elminti Stato e la forma fisica dei bambini in età scolare

Soil-transmitted helminth (STH) infections are common. Indeed, more than 1 billion people are affected, mainly in the developing world where poverty ...

A Visual Assay to Monitor T6SS-mediated Bacterial Competition

Type VI secretion systems (T6SSs) are molecular nanomachines allowing Gram-negative bacteria to transport and inject proteins into a wide variety of target cells1,2. The T6SS is composed of 13 core components and displays structural similarities with the tail-tube of bacteriophages3. The phage uses a tube and a puncturing device to penetrate the cell envelope of target bacteria and inject DNA. It is proposed that the T6SS is an inverted bacteriophage device creating a specific path in the bacterial cell envelope to drive effectors and toxins to the surface. The process could be taken further and the T6SS device could perforate other cells with which the bacterium is in contact, thus injecting the effectors into these targets. The tail tube and puncturing device parts of the T6SS are made with Hcp and VgrG proteins, respectively4,5.
The versatility of the T6SS has been demonstrated through studies using various bacterial pathogens. The Vibrio cholerae T6SS can remodel the cytoskeleton of eukaryotic host cells by injecting an "evolved" VgrG carrying a C-terminal actin cross-linking domain6,7. Another striking example was recently documented using Pseudomonas aeruginosa which is able to target and kill bacteria in a T6SS-dependent manner, therefore promoting the establishment of bacteria in specific microbial niches and competitive environment8,9,10.
In the latter case, three T6SS-secreted proteins, namely Tse1, Tse2 and Tse3 have been identified as the toxins injected in the target bacteria (Figure 1). The donor cell is protected from the deleterious effect of these effectors via an anti-toxin mechanism, mediated by the Tsi1, Tsi2 and Tsi3 immunity proteins8,9,10. This antimicrobial activity can be monitored when T6SS-proficient bacteria are co-cultivated on solid surfaces in competition with other bacterial species or with T6SS-inactive bacteria of the same species8,11,12,13.
The data available emphasized a numerical approach to the bacterial competition assay, including time-consuming CFU counting that depends greatly on antibiotic makers. In the case of antibiotic resistant strains like P. aeruginosa, these methods can be inappropriate. Moreover, with the identification of about 200 different T6SS loci in more than 100 bacterial genomes14, a convenient screening tool is highly desirable. We developed an assay that is easy to use and requires standard laboratory material and reagents. The method offers a rapid and qualitative technique to monitor the T6SS-dependent bactericidal/bacteriostasis activity by using a reporter strain as a prey (in this case Escherichia coli DH5&alpha;) allowing a-complementation of the lacZ gene. Overall, this method is graphic and allows rapid identification of T6SS-related phenotypes on agar plates. This experimental protocol may be adapted to other strains or bacterial species taking into account specific conditions such as growth media, temperature or time of contact.

We describe a qualitative assay to monitor bacterial competition mediated by the Pseudomonas aeruginosa type VI secretion system (T6SS). The assay relies on the survival/killing of Escherichia coli target cells carrying a lacZ-reporter. This technique is adjustable to assess the bactericidal/bacteriostasis activity of T6SS-proficient microorganisms.

Un test per il monitoraggio visivo T6SS-mediata Concorso batterica

Type VI secretion systems (T6SSs) are molecular  nanomachines allowing Gram-negative bacteria to transport and inject proteins  into a wide variety of ...

Establishing a Liquid-covered Culture of Polarized Human Airway Epithelial Calu-3 Cells to Study Host Cell Response to Respiratory Pathogens In vitro

The apical and basolateral surfaces of airway epithelial cells demonstrate directional responses to pathogen exposure in vivo. Thus, ideal in vitro models for examining cellular responses to respiratory pathogens polarize, forming apical and basolateral surfaces. One such model is differentiated normal human bronchial epithelial cells (NHBE). However, this system requires lung tissue samples, expertise isolating and culturing epithelial cells from tissue, and time to generate an air-liquid interface culture.
Calu-3 cells, derived from a human bronchial adenocarcinoma, are an alternative model for examining the response of proximal airway epithelial cells to respiratory insult1, pharmacological compounds2-6, and bacterial7-9 and viral pathogens, including influenza virus, rhinovirus and severe acute respiratory syndrome - associated coronavirus10-14. Recently, we demonstrated that Calu-3 cells are susceptible to respiratory syncytial virus (RSV) infection in a manner consistent with NHBE15,16 . Here, we detail the establishment of a polarized, liquid-covered culture (LCC) of Calu-3 cells, focusing on the technical details of growing and culturing Calu-3 cells, maintaining cells that have been cultured into LCC, and we present the method for performing respiratory virus infection of polarized Calu-3 cells.
To consistently obtain polarized Calu-3 LCC, Calu-3 cells must be carefully subcultured before culturing in Transwell inserts. Calu-3 monolayer cultures should remain below 90% confluence, should be subcultured fewer than 10 times from frozen stock, and should regularly be supplied with fresh medium. Once cultured in Transwells, Calu-3 LCC must be handled with care. Irregular media changes and mechanical or physical disruption of the cell layers or plates negatively impact polarization for several hours or days. Polarization is monitored by evaluating trans-epithelial electrical resistance (TEER) and is verified by evaluating the passive equilibration of sodium fluorescein between the apical and basolateral compartments17,18 . Once TEER plateaus at or above 1,000 &Omega;&times;cm2, Calu-3 LCC are ready to use to examine cellular responses to respiratory pathogens.

Establishing a Liquid-covered Culture of Polarized Human Airway Epithelial Calu-3 Cells to Study Host Cell Response to Respiratory Pathogens In vitro

The findings and conclusions in this report are those of the authors and do not necessarily represent the views of the Centers for Disease Control and Prevention.

Creazione di un liquido coperto Cultura polarizzata Airway epiteliali umane Calu-3 celle per studio cellulare risposta dell&#39;ospite agli agenti patogeni delle vie respiratorie<em&gt; In vitro</em

The  apical and basolateral surfaces of airway epithelial cells demonstrate  directional responses to pathogen exposure in  vivo. Thus, ideal in vitro ...

A Restriction Enzyme Based Cloning Method to Assess the In vitro Replication Capacity of HIV-1 Subtype C Gag-MJ4 Chimeric Viruses

The protective effect of many HLA class I alleles on HIV-1 pathogenesis and disease progression is, in part, attributed to their ability to target conserved portions of the HIV-1 genome that escape with difficulty. Sequence changes attributed to cellular immune pressure arise across the genome during infection, and if found within conserved regions of the genome such as Gag, can affect the ability of the virus to replicate in vitro. Transmission of HLA-linked polymorphisms in Gag to HLA-mismatched recipients has been associated with reduced set point viral loads. We hypothesized this may be due to a reduced replication capacity of the virus. Here we present a novel method for assessing the in vitro replication of HIV-1 as influenced by the gag gene isolated from acute time points from subtype C infected Zambians. This method uses restriction enzyme based cloning to insert the gag gene into a common subtype C HIV-1 proviral backbone, MJ4. This makes it more appropriate to the study of subtype C sequences than previous recombination based methods that have assessed the in vitro replication of chronically derived gag-pro sequences. Nevertheless, the protocol could be readily modified for studies of viruses from other subtypes. Moreover, this protocol details a robust and reproducible method for assessing the replication capacity of the Gag-MJ4 chimeric viruses on a CEM-based T cell line. This method was utilized for the study of Gag-MJ4 chimeric viruses derived from 149 subtype C acutely infected Zambians, and has allowed for the identification of residues in Gag that affect replication. More importantly, the implementation of this technique has facilitated a deeper understanding of how viral replication defines parameters of early HIV-1 pathogenesis such as set point viral load and longitudinal CD4+ T cell decline.

A Restriction Enzyme Based Cloning Method to Assess the In vitro Replication Capacity of HIV-1 Subtype C Gag-MJ4 Chimeric Viruses

HIV-1 pathogenesis is defined by both viral characteristics and host genetic factors. Here we describe a robust method that allows for reproducible measurements to assess the impact of the gag gene sequence variation on the in vitro replication capacity of the virus.

Un enzima di restrizione metodo basato clonazione per valutare l&#39;<em&gt; In vitro</em&gt; Replica Capacità di HIV-1 Sottotipo C Gag-MJ4 chimerici virus

The protective effect of many HLA class I alleles on HIV-1 pathogenesis and disease progression is, in part, attributed to their ability to target ...

Intranasal Administration of Recombinant Influenza Vaccines in Chimeric Mouse Models to Study Mucosal Immunity

Vaccines are one of the greatest achievements of mankind, and have saved millions of lives over the last century. Paradoxically, little is known about the physiological mechanisms that mediate immune responses to vaccines perhaps due to the overall success of vaccination, which has reduced interest into the molecular and physiological mechanisms of vaccine immunity. However, several important human pathogens including influenza virus still pose a challenge for vaccination, and may benefit from immune-based strategies. 
Although influenza reverse genetics has been successfully applied to the generation of live-attenuated influenza vaccines (LAIVs), the addition of molecular tools in vaccine preparations such as tracer components to follow up the kinetics of vaccination in vivo, has not been addressed. In addition, the recent generation of mouse models that allow specific depletion of leukocytes during kinetic studies has opened a window of opportunity to understand the basic immune mechanisms underlying vaccine-elicited protection. Here, we describe how the combination of reverse genetics and chimeric mouse models may help to provide new insights into how vaccines work at physiological and molecular levels, using as example a recombinant, cold-adapted, live-attenuated influenza vaccine (LAIV). We utilized laboratory-generated LAIVs harboring cell tracers as well as competitive bone marrow chimeras (BMCs) to determine the early kinetics of vaccine immunity and the main physiological mechanisms responsible for the initiation of vaccine-specific adaptive immunity. In addition, we show how this technique may facilitate gene function studies in single animals during immune responses to vaccines. We propose that this technique can be applied to improve current prophylactic strategies against pathogens for which urgent medical countermeasures are needed, for example influenza, HIV, Plasmodium, and hemorrhagic fever viruses such as Ebola virus.

There is an overall lack of knowledge about how vaccines work. Here we propose the combined use of reverse genetics and bone marrow chimeric mice to gain insight into the early host immune responses to vaccines with a special focus on dendritic cells and T cell immunity.

Intranasale somministrazione di ricombinante Influenza vaccini nei modelli chimerico topo per studiare immunità delle mucose

Vaccines are one of the greatest achievements of mankind, and have saved millions of lives over the last century. Paradoxically, little is known about the ...

Fluorescence-based Neuraminidase Inhibition Assay to Assess the Susceptibility of Influenza Viruses to The Neuraminidase Inhibitor Class of Antivirals

The neuraminidase (NA) inhibitors are the only class of antivirals approved for the treatment and prophylaxis of influenza that are effective against currently circulating strains. In addition to their use in treating seasonal influenza, the NA inhibitors have been stockpiled by a number of countries for use in the event of a pandemic. It is therefore important to monitor the susceptibility of circulating influenza viruses to this class of antivirals. There are different types of assays that can be used to assess the susceptibility of influenza viruses to the NA inhibitors, but the enzyme inhibition assays using either a fluorescent substrate or a chemiluminescent substrate are the most widely used and recommended. This protocol describes the use of a fluorescence-based assay to assess influenza virus susceptibility to NA inhibitors. The assay is based on the NA enzyme cleaving the 2&#8242;-(4-Methylumbelliferyl)-&#945;-D-N-acetylneuraminic acid (MUNANA) substrate to release the fluorescent product 4-methylumbelliferone (4-MU). Therefore, the inhibitory effect of an NA inhibitor on the influenza virus NA is determined based on the concentration of the NA inhibitor that is required to reduce 50% of the NA activity, given as an IC50 value.

We describe the use of a phenotypic fluorescence-based neuraminidase inhibition assay to assess the susceptibility of influenza A and B viruses to the neuraminidase inhibitor class of antivirals.

Basato sulla fluorescenza neuraminidasi Inibizione Assay per valutare la suscettibilità dei virus influenzali di neuraminidasi Inhibitor classe di antivirali

The neuraminidase (NA) inhibitors are the only class of antivirals approved for the treatment and prophylaxis of influenza that are effective against ...

Ex Vivo Infection of Human Lymphoid Tissue and Female Genital Mucosa with Human Immunodeficiency Virus 1 and Histoculture

Histocultures allow studying intercellular interactions within human tissues, and they can be employed to model host-pathogen interactions under controlled laboratory conditions. Ex vivo infection of human tissues with human immunodeficiency virus (HIV), among other viruses, has been successfully used to investigate early disease pathogenesis, as well as a platform to test the efficacy and toxicity of antiviral drugs. In the present protocol, we explain how to process and infect with HIV-1 tissue explants from human tonsils and cervical mucosae, and maintain them in culture on top of gelatin sponges at the liquid-air interface for about two weeks. This non-polarized culture setting maximizes access to nutrients in culture medium and oxygen, although progressive loss of tissue integrity and functional architectures remains its main limitation. This method allows monitoring HIV-1 replication and pathogenesis using several techniques, including immunoassays, qPCR, and flow cytometry. Of importance, the physiologic variability between tissue donors, as well as between explants from different areas of the same specimen, may significantly affect experimental results. To ensure result reproducibility, it is critical to use an adequate number of explants, technical replicates, and donor-matched control conditions to normalize the results of the experimental treatments when compiling data from multiple experiments (i.e., conducted using tissue from different donors) for statistical analysis.

Ex Vivo Infection of Human Lymphoid Tissue and Female Genital Mucosa with Human Immunodeficiency Virus 1 and Histoculture

Infection of human tissues with human immunodeficiency virus (HIV) ex vivo provides a valuable 3D model of virus pathogenesis. Here, we describe a protocol to process and infect tissue specimens from human tonsils and female genital mucosae with HIV-1 and maintain them in culture at the liquid-air interface.