Sindbis control virus

Abstract

Disclosed are compositions and methods related to replication deficient Sindbis viruses that are able to function as controls for nucleic acid diagnostic assays (e.g., nucleic acid sequencing based assays and/or nucleic acid amplification based assays).

1 . A replication deficient recombinant Sindbis virus comprising a RNA genome comprising:
 an open reading frame (ORF) encoding functional Sindbis non-structural proteins; and   a heterologous RNA sequence.   
     
     
         2 . The replication deficient recombinant Sindbis virus of  claim 1 , wherein the ORF encoding functional Sindbis non-structural proteins is located 5′ of the heterologous RNA sequence. 
     
     
         3 . The replication deficient recombinant Sindbis virus of  claim 1 , wherein the ORF encoding Sindbis non-structural proteins has a nucleotide sequence that is at least 90% identical to nucleotides 1-7648 of SEQ ID NO: 1. 
     
     
         4 . (canceled) 
     
     
         5 . The replication deficient recombinant Sindbis virus of  claim 1 , wherein the RNA genome lacks a sequence encoding a functional version of one or more of the Sindbis structural proteins. 
     
     
         6 .- 9 . (canceled) 
     
     
         10 . The replication deficient recombinant Sindbis virus of  claim 1 , wherein the heterologous RNA sequence comprises a non-Sindbis RNA virus sequence or a retrovirus sequence. 
     
     
         11 .- 16 . (canceled) 
     
     
         17 . The replication deficient recombinant Sindbis virus of  claim 10 , wherein the heterologous RNA sequence comprises a non-Sindbis RNA virus sequence. 
     
     
         18 . The replication deficient recombinant Sindbis virus of  claim 17 , wherein the non-Sindbis RNA virus sequence is an Ebolavirus sequence, an influenza virus sequence, a SARS virus sequence, a hepatitis C virus sequence, a West Nile virus sequence, a Zika virus sequence, a poliovirus sequence, or a measles virus sequence. 
     
     
         19 . The replication deficient recombinant Sindbis virus of  claim 18 , wherein the non-Sindbis RNA virus sequence is an Ebolavirus sequence. 
     
     
         20 .- 26 . (canceled) 
     
     
         27 . The replication deficient recombinant Sindbis virus of  claim 10 , wherein the heterologous RNA sequence comprises a retrovirus sequence. 
     
     
         28 . The replication deficient recombinant Sindbis virus of  claim 27 , wherein the retrovirus sequence is an HIV-1 sequence, an HIV-2 sequence, an HTLV-1 sequence, or an HTLV-II sequence. 
     
     
         29 . The replication deficient recombinant Sindbis virus of  claim 28 , wherein the retrovirus sequence is an HIV-1 sequence. 
     
     
         30 .- 65 . (canceled) 
     
     
         66 . A composition, comprising a replication deficient Sindbis virus of  claim 1 . 
     
     
         67 . The composition of  claim 66 , wherein the replication deficient Sindbis virus comprising a RNA genome comprising a sequence that is at least 90% identical to SEQ ID NO: 11; and a replication deficient Sindbis virus comprising a RNA genome comprising a sequence that is at least 90% identical to SEQ ID NO: 13. 
     
     
         68 . (canceled) 
     
     
         69 . The composition of  claim 66 , wherein the replication deficient Sindbis virus comprising a RNA genome comprising a sequence that is at least 90% identical to SEQ ID NO: 12; and a replication deficient Sindbis virus comprising a RNA genome comprising a sequence that is at least 90% identical to SEQ ID NO: 14. 
     
     
         70 . (canceled) 
     
     
         71 . The composition of  claim 66 , wherein the replication deficient Sindbis virus comprising a RNA genome comprising a sequence that is at least 90% identical to either nucleotides 1-3446 of SEQ ID NO: 15, nucleotides 3294-5575 of SEQ ID NO: 15, nucleotides 5425-7722 of SEQ ID NO: 15, or nucleotides 7542-10272 of SEQ ID NO: 15. 
     
     
         72 .- 77 . (canceled) 
     
     
         78 . A nucleic acid molecule encoding the RNA genome of the replication deficient Sindbis virus of  claim 1 . 
     
     
         79 . The nucleic acid molecule of  claim 78 , wherein the nucleic acid molecule is an RNA molecule. 
     
     
         80 .- 82 . (canceled) 
     
     
         83 . A method of making a replication deficient Sindbis virus comprising:
 (a) transfecting a cell with the RNA molecule of  claim 79  encoding the RNA genome of the replication deficient Sindbis virus and a helper RNA molecule encoding functional Sindbis structural proteins;   (b) culturing the transfected cell of step (a) under conditions such that the cell produces a replication deficient Sindbis virus comprising the mRNA genome; and   (c) collecting the replication deficient Sindbis virus.   
     
     
         84 . (canceled) 
     
     
         85 . A method of testing a diagnostic assay, comprising performing the diagnostic assay on a composition of  claim 66 .