The emerging novel avian leukosis virus with mutations in the pol gene shows competitive replication advantages both in vivo and in vitro

Abstract

The avian leukosis virus subgroup K (ALV-K), a novel subgroup in Chinese indigenous chicken breeds, has been difficult to isolate in the past due to its poor replication ability. However, according to the latest monitoring data, the replication ability and isolation rate of ALV-K have clearly increased, and new strains with mutations in the pol gene have also been found. To determine the effects of such mutations on the biological characteristics of ALV-K, a pair of infectious clones were constructed and rescued. The first virus was an ALV-K Chinese isolate with mutations in its pol gene, named rSDAUAK-11. The second virus was a recuperative rSDAUAK-11 from which mutations in the pol gene were recovered according to the corresponding region of the ALV-K prototype virus JS11C1, named rRSDAUAK-11. In addition, two quantitative real-time polymerase chain reaction assays were developed to specifically detect these virus strains. Using such methods, we observed a marked improvement of the reverse transcriptase activity, replication ability and vertical transmission ability of rSDAUAK-11, which also revealed a formidable competitive advantage in mixed infection with rRSDAUAK-11 and corresponded to the differences between the wild strains SDAUAK-11 and JS11C1. Accordingly, our findings not only show that mutations in the pol gene are an important molecular mechanism contributing to corresponding changes in the biological characteristics of the newest ALV-K but also emphasize the potential future eradication of ALV.

Fig. 1. Genetic sequence comparison of the pol gene of SDAUAK-11 and reference ALV strains.

a Nucleotide sequence comparison. b Amino acid sequence comparison. Boxes indicate the genetic difference between the SDAUAK-11 and reference strains

Fig. 2. Effects of the mutations in the pol gene on reverse transcriptase activity and replication ability both in vitro and in vivo.

a The results of the reverse transcriptase activity (RT) assays performed with equivalent virus particle amounts (five million copies) isolated from the cell culture supernatants of DF-1 cells infected or transfected with SDAUAK-11 (wild strain), JS11C1 (wild strain), rSDAUAK-11 and rRSDAUAK-11 are shown. b Virus titers for these viruses in DF-1 cell culture supernatant at 48, 72, and 96 HPI and viral titers harvested at different intervals were calculated and expressed as TCID₅₀ per milliliter using Reed-Muench methods. c Viral loads for these viruses at 48, 72 and 96 HPI were determined by the presence of ALV in DF-1 cells (10⁶ cells) treated with different virus strains (five million copies) using QRT-PCR methods, and ALV viral load levels were normalized to beta-actin. d Proviral loads (PVLs) for those viruses at 2, 3, and 4 HPI were determined by the presence of ALV-cDNA in DF-1 cells (10⁶ cells) treated with different virus strains (five million copies) using QRT-PCR, and ALV PVL levels were normalized to HMG14b. e Viral loads for these viruses at 48, 72 and 96 HPI were determined by the presence of ALV in the blood of SPF chicks treated with different virus strains (five million copies) using QRT-PCR, and the viral RNA concentration (log₁₀) was normalized per 1 µg of total RNA. f PVLs for those viruses at 48, 72 and 96 HPI were determined by the presence of ALV-cDNA in the leukomonocytes of SPF chicks treated with different virus strains (five million copies) using QRT-PCR methods, and ALV proviral load levels were normalized to HMG14b. g Viral loads for these viruses at 48, 72 and 96 HPI were determined by the presence of ALV in the liver, kidney and spleen of SPF chicks treated with different virus strains (five million copies) using QRT-PCR, and ALV viral load levels were normalized to beta-actin. h PVLs for these viruses at 48, 72 and 96 HPI were determined by the presence of ALV-cDNA in the liver, kidney and spleen of SPF chicks treated with different virus strains (five million copies) using QRT-PCR methods, and ALV PVL levels were normalized to HMG14b. The standard deviations from independent experiments are shown. P value (*P < 0.05, **P < 0.01) determined by Duncan’s multiple-range test is shown

Fig. 3. Effects of mutations in the pol gene on the competition advantage both in vitro and in vivo

a Viral load proportion (VLP) for rSDAUAK-11, rRSDAUAK-11, SDAUAK-11 (wild strain), and JS11C1 (wild strain) in DF-1 cells (10⁶ cells) treated simultaneously with these viruses (five million copies and five million copies) or culture supernatant at 48, 72 and 96 HPI, and the VLP of each sample harvested at different intervals was calculated as VLP (JS11C1) = VL (JS11C1)/[VL (SDAUAK-11) + VL (JS11C1)]. Primers rR-F and rR-R were used to quantify the viral load of JS11C1, and primers r-F and r-R were used to quantify the total viral load of SDAUAK-11 and JS11C1. The same methods were used to analyze the rescued viruses and subsequent tests. b VLP for ALVs in DF-1 cells treated simultaneously with two wild/rescued ALVs at 48, 72, and 96 HPI. c PVL proportion for ALVs in DF-1 cells treated simultaneously with two wild/rescued ALVs at 48, 72, and 96 HPI. d VLP for ALVs in the blood of SPF chicks treated simultaneously with two wild/rescued ALVs. € PVL for ALVs in leukomonocytes of SPF chicks treated simultaneously with two wild/rescued ALVs. f VLP for ALVs in liver, kidney and spleen of SPF chicks treated simultaneously with two wild/rescued ALVs. g PVL proportion for ALVs in liver, kidney and spleen of SPF chicks treated simultaneously with two wild/rescued ALVs. The standard deviations from independent experiments are shown. P value (*P < 0.05, **P < 0.01) determined by Duncan’s multiple-range test is shown

Fig. 4. Schematic diagrams showing the construction of p-rSDAUAK-11 and p-rRSDAUAK-11.

F1/R1, F2/R2, and F3/R3 were primers used for amplification of the whole genome of SDAUAK-11. Xba I and Mlu I were restriction enzyme sequences located in the genome itself, while Eag I, BamH I, and Xho I were incorporated into the amplicons. With the exception of Mlu I, the other four restriction enzymes can be found in pBlueScript II KS. Amplicons I, II, and III were inserted into pBlueScript II KS in order using restriction enzyme digestion. Amplicon I was first inserted into pBlueScript II KS via BamH I and Xho I; amplicon II was then inserted via Eag I and Xba I; and finally, amplicon III was inserted into the genome itself via Xba I and Mlu I